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import os.path as op
from sfepy.base.base import *
from sfepy.base.conf import transform_variables, transform_fields
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def do_interpolation(m2, m1, data, field_name):
"""Interpolate data from m1 to m2. """
from sfepy.fem import Domain, Field, Variables
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = Domain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field('f', nm.float64, f[0], d1.regions[f[1]], approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = Domain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field('f', nm.float64, f[0], d2.regions[f[1]], approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.fem import Mesh, Domain, Field, Variables
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = Domain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field('scalar_tp', nm.float64, (1,1), omega1, approx_order=1)
ff1 = {field1.name : field1}
d2 = Domain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field('scalar_si', nm.float64, (1,1), omega2, approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf( | transform_variables(variables1) | sfepy.base.conf.transform_variables |
import os.path as op
from sfepy.base.base import *
from sfepy.base.conf import transform_variables, transform_fields
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def do_interpolation(m2, m1, data, field_name):
"""Interpolate data from m1 to m2. """
from sfepy.fem import Domain, Field, Variables
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = Domain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field('f', nm.float64, f[0], d1.regions[f[1]], approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = Domain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field('f', nm.float64, f[0], d2.regions[f[1]], approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.fem import Mesh, Domain, Field, Variables
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = Domain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field('scalar_tp', nm.float64, (1,1), omega1, approx_order=1)
ff1 = {field1.name : field1}
d2 = Domain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field('scalar_si', nm.float64, (1,1), omega2, approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf( | transform_variables(variables2) | sfepy.base.conf.transform_variables |
import os.path as op
from sfepy.base.base import *
from sfepy.base.conf import transform_variables, transform_fields
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def do_interpolation(m2, m1, data, field_name):
"""Interpolate data from m1 to m2. """
from sfepy.fem import Domain, Field, Variables
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = Domain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field('f', nm.float64, f[0], d1.regions[f[1]], approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = Domain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field('f', nm.float64, f[0], d2.regions[f[1]], approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = | make_axis_rotation_matrix([0, 1, 0], angle) | sfepy.linalg.make_axis_rotation_matrix |
#!/usr/bin/env python
def configuration(parent_package='', top_path=None):
import os.path as op
from numpy.distutils.misc_util import Configuration
from sfepy import Config
site_config = | Config() | sfepy.Config |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = | Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp') | sfepy.discrete.fem.Mesh.from_file |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = | FEDomain('domain', mesh) | sfepy.discrete.fem.FEDomain |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = | Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1) | sfepy.discrete.fem.Field.from_args |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = | FieldVariable('u', 'unknown', field) | sfepy.discrete.FieldVariable |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = | FieldVariable('v', 'test', field, primary_var_name='u') | sfepy.discrete.FieldVariable |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = | Integral('i', order=1) | sfepy.discrete.Integral |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = | Equation('balance', t1) | sfepy.discrete.Equation |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = | Equations([eq]) | sfepy.discrete.Equations |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = | ScipyDirect({}) | sfepy.solvers.ls.ScipyDirect |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = | IndexedStruct() | sfepy.base.base.IndexedStruct |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = | Newton({}, lin_solver=ls, status=nls_status) | sfepy.solvers.nls.Newton |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)
pb = | Problem('elasticity', equations=eqs) | sfepy.discrete.Problem |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)
pb = Problem('elasticity', equations=eqs)
pb.save_regions_as_groups('regions')
pb.set_bcs(ebcs=Conditions([Fixed, Displaced]))
pb.set_solver(nls)
status = | IndexedStruct() | sfepy.base.base.IndexedStruct |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)
pb = Problem('elasticity', equations=eqs)
pb.save_regions_as_groups('regions')
pb.set_bcs(ebcs=Conditions([Fixed, Displaced]))
pb.set_solver(nls)
status = IndexedStruct()
#####
state = pb.solve(status=status, save_results=True, post_process_hook=post_process)
out = state.create_output_dict()
out = post_process(out, pb, state, extend=True)
pb.save_state('postprocess.vtk', out=out)
prb = | Probe(out,pb.domain.mesh) | sfepy.postprocess.probes_vtk.Probe |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D= | stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3) | sfepy.mechanics.matcoefs.stiffness_from_youngpoisson |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 25 09:19:35 2020
@author: dhulls
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import numpy as nm
import sys
sys.path.append('.')
from sfepy.base.base import IndexedStruct, Struct
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.probes_vtk import ProbeFromFile, Probe
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.matcoefs import stiffness_for_transIso
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
import numpy as np
def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2
return val
helps = {
'show' : 'show the results figure',
}
def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
ev = problem.evaluate
stress = ev('ev_cauchy_stress.%d.Omega(m.D, u)' % (2), mode='el_avg',
copy_materials=False, verbose=False)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
return out
from sfepy import data_dir
parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.inp')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
Bottom = domain.create_region('Bottom', 'vertices in (z < -0.049)', 'facet')
Top = domain.create_region('Top', 'vertices in (z > 0.049)', 'facet')
field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', D=stiffness_from_youngpoisson(dim=3, young=2, poisson=0.3))
# m = Material('m', D=stiffness_for_transIso(dim=3, Ex=2.5, Ez=2, vxy=0.25, vxz=0.3, Gxz=1.75))
integral = Integral('i', order=1)
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
Fixed = EssentialBC('Fixed', Bottom, {'u.all' : 0.0})
Displaced = EssentialBC('Displaced', Top, {'u.1' : 0.01, 'u.[0,2]' : 0.0})
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)
pb = Problem('elasticity', equations=eqs)
pb.save_regions_as_groups('regions')
pb.set_bcs(ebcs= | Conditions([Fixed, Displaced]) | sfepy.discrete.conditions.Conditions |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = | Function('get_refine', _get_refine) | sfepy.discrete.Function |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = | Function('get_coarse', _get_coarse) | sfepy.discrete.Function |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = | Functions([get_refine, get_coarse]) | sfepy.discrete.Functions |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = Functions([get_refine, get_coarse])
region0 = domain.create_region('coarse', 'cells by get_coarse',
functions=functions, add_to_regions=False,
allow_empty=True)
region1 = domain.create_region('refine', 'cells by get_refine',
functions=functions, add_to_regions=False)
cmesh = domain.mesh.cmesh
dim = cmesh.dim
if dim == 2:
oe = 0
facets = nm.intersect1d(region0.facets, region1.facets)
cmesh.setup_connectivity(dim - 1, dim)
cells, offs = cmesh.get_incident(dim, facets, dim - 1,
ret_offsets=True)
assert_((nm.diff(offs) == 2).all())
ii = cmesh.get_local_ids(facets, dim - 1, cells, offs, dim)
ii = ii.reshape((-1, 2))
cells = cells.reshape((-1, 2))
ii = nm.where(refine_flag[cells], ii[:, :1], ii[:, 1:])
cells = nm.where(refine_flag[cells], cells[:, :1], cells[:, 1:])
facets = nm.c_[facets, ii]
cells = nm.c_[cells, nm.zeros_like(cells[:, 1])]
else: # if dim == 3:
gel = domain.geom_els['3_8']
epf = gel.get_edges_per_face()
cmesh.setup_connectivity(dim, dim)
fc, coffs = cmesh.get_incident(dim, region1.cells, dim,
ret_offsets=True)
cc = nm.repeat(region1.cells, nm.diff(coffs))
aux = nm.c_[cc, fc]
"""
nnn[:, 0] cells to refine, nnn[:, 1] non-refined neighbours, nnn[:, 2]
neighbour kind : 0 face, 1 edge.
"""
nn = aux[refine_flag[fc] == 0]
cf = nn[:, 0].copy().astype(nm.uint32)
cc = nn[:, 1].copy().astype(nm.uint32)
vc, vco = cmesh.get_incident(0, cc, dim, ret_offsets=True)
vf, vfo = cmesh.get_incident(0, cf, dim, ret_offsets=True)
vc = vc.reshape((-1, 8))
vf = vf.reshape((-1, 8))
nnn = []
oe = 0
ov = nn.shape[0]
for ii in range(vc.shape[0]):
aux = set(vc[ii]).intersection(vf[ii])
nc = len(aux)
if nc == 1:
nnn.append((0, 0, 2))
ov -= 1
elif nc == 4:
nnn.append((nn[ii, 0], nn[ii, 1], 0))
oe += 1
else:
nnn.append((nn[ii, 0], nn[ii, 1], 1))
nnn = nm.array(nnn)
if nnn.shape[0] == 0:
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 4), dtype=nm.uint32)
return facets, cells, 0, region0, region1
# Sort by neighbour kind, skip vertex-only neighbours.
ii = nm.argsort(nnn[:, 2])
nnn = nnn[ii][:ov]
cf = cf[ii][:ov]
cc = cc[ii][:ov]
ec, eco = cmesh.get_incident(1, cc, dim, ret_offsets=True)
ef, efo = cmesh.get_incident(1, cf, dim, ret_offsets=True)
ec = ec.reshape((-1, 12))
ef = ef.reshape((-1, 12))
fc, fco = cmesh.get_incident(2, cc, dim, ret_offsets=True)
ff, ffo = cmesh.get_incident(2, cf, dim, ret_offsets=True)
fc = fc.reshape((-1, 6))
ff = ff.reshape((-1, 6))
emask = nm.zeros((domain.shape.n_el, 12), dtype=nm.bool)
ffs = []
for ii in range(oe):
facet = nm.intersect1d(fc[ii], ff[ii])[0]
i1 = nm.where(ff[ii] == facet)[0][0]
i0 = nm.where(fc[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
emask[nnn[ii, 0], epf[i1]] = True
for ii in range(oe, nnn.shape[0]):
facet = nm.intersect1d(ec[ii], ef[ii])[0]
i1 = nm.where(ef[ii] == facet)[0][0]
i0 = nm.where(ec[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
ffs = nm.array(ffs)
ie = nm.where(nnn[:, 2] == 1)[0]
ennn = nnn[ie]
effs = ffs[ie]
omit = ie[emask[ennn[:, 0], effs[:, 1]]]
valid = nm.ones(nnn.shape[0], dtype=nm.bool)
valid[omit] = False
cells = nnn[valid]
facets = ffs[valid]
return facets, cells, oe, region0, region1
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = | Mesh.from_region(region1, mesh0) | sfepy.discrete.fem.Mesh.from_region |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = Functions([get_refine, get_coarse])
region0 = domain.create_region('coarse', 'cells by get_coarse',
functions=functions, add_to_regions=False,
allow_empty=True)
region1 = domain.create_region('refine', 'cells by get_refine',
functions=functions, add_to_regions=False)
cmesh = domain.mesh.cmesh
dim = cmesh.dim
if dim == 2:
oe = 0
facets = nm.intersect1d(region0.facets, region1.facets)
cmesh.setup_connectivity(dim - 1, dim)
cells, offs = cmesh.get_incident(dim, facets, dim - 1,
ret_offsets=True)
assert_((nm.diff(offs) == 2).all())
ii = cmesh.get_local_ids(facets, dim - 1, cells, offs, dim)
ii = ii.reshape((-1, 2))
cells = cells.reshape((-1, 2))
ii = nm.where(refine_flag[cells], ii[:, :1], ii[:, 1:])
cells = nm.where(refine_flag[cells], cells[:, :1], cells[:, 1:])
facets = nm.c_[facets, ii]
cells = nm.c_[cells, nm.zeros_like(cells[:, 1])]
else: # if dim == 3:
gel = domain.geom_els['3_8']
epf = gel.get_edges_per_face()
cmesh.setup_connectivity(dim, dim)
fc, coffs = cmesh.get_incident(dim, region1.cells, dim,
ret_offsets=True)
cc = nm.repeat(region1.cells, nm.diff(coffs))
aux = nm.c_[cc, fc]
"""
nnn[:, 0] cells to refine, nnn[:, 1] non-refined neighbours, nnn[:, 2]
neighbour kind : 0 face, 1 edge.
"""
nn = aux[refine_flag[fc] == 0]
cf = nn[:, 0].copy().astype(nm.uint32)
cc = nn[:, 1].copy().astype(nm.uint32)
vc, vco = cmesh.get_incident(0, cc, dim, ret_offsets=True)
vf, vfo = cmesh.get_incident(0, cf, dim, ret_offsets=True)
vc = vc.reshape((-1, 8))
vf = vf.reshape((-1, 8))
nnn = []
oe = 0
ov = nn.shape[0]
for ii in range(vc.shape[0]):
aux = set(vc[ii]).intersection(vf[ii])
nc = len(aux)
if nc == 1:
nnn.append((0, 0, 2))
ov -= 1
elif nc == 4:
nnn.append((nn[ii, 0], nn[ii, 1], 0))
oe += 1
else:
nnn.append((nn[ii, 0], nn[ii, 1], 1))
nnn = nm.array(nnn)
if nnn.shape[0] == 0:
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 4), dtype=nm.uint32)
return facets, cells, 0, region0, region1
# Sort by neighbour kind, skip vertex-only neighbours.
ii = nm.argsort(nnn[:, 2])
nnn = nnn[ii][:ov]
cf = cf[ii][:ov]
cc = cc[ii][:ov]
ec, eco = cmesh.get_incident(1, cc, dim, ret_offsets=True)
ef, efo = cmesh.get_incident(1, cf, dim, ret_offsets=True)
ec = ec.reshape((-1, 12))
ef = ef.reshape((-1, 12))
fc, fco = cmesh.get_incident(2, cc, dim, ret_offsets=True)
ff, ffo = cmesh.get_incident(2, cf, dim, ret_offsets=True)
fc = fc.reshape((-1, 6))
ff = ff.reshape((-1, 6))
emask = nm.zeros((domain.shape.n_el, 12), dtype=nm.bool)
ffs = []
for ii in range(oe):
facet = nm.intersect1d(fc[ii], ff[ii])[0]
i1 = nm.where(ff[ii] == facet)[0][0]
i0 = nm.where(fc[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
emask[nnn[ii, 0], epf[i1]] = True
for ii in range(oe, nnn.shape[0]):
facet = nm.intersect1d(ec[ii], ef[ii])[0]
i1 = nm.where(ef[ii] == facet)[0][0]
i0 = nm.where(ec[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
ffs = nm.array(ffs)
ie = nm.where(nnn[:, 2] == 1)[0]
ennn = nnn[ie]
effs = ffs[ie]
omit = ie[emask[ennn[:, 0], effs[:, 1]]]
valid = nm.ones(nnn.shape[0], dtype=nm.bool)
valid[omit] = False
cells = nnn[valid]
facets = ffs[valid]
return facets, cells, oe, region0, region1
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = | FEDomain('d', mesh1) | sfepy.discrete.fem.FEDomain |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = Functions([get_refine, get_coarse])
region0 = domain.create_region('coarse', 'cells by get_coarse',
functions=functions, add_to_regions=False,
allow_empty=True)
region1 = domain.create_region('refine', 'cells by get_refine',
functions=functions, add_to_regions=False)
cmesh = domain.mesh.cmesh
dim = cmesh.dim
if dim == 2:
oe = 0
facets = nm.intersect1d(region0.facets, region1.facets)
cmesh.setup_connectivity(dim - 1, dim)
cells, offs = cmesh.get_incident(dim, facets, dim - 1,
ret_offsets=True)
assert_((nm.diff(offs) == 2).all())
ii = cmesh.get_local_ids(facets, dim - 1, cells, offs, dim)
ii = ii.reshape((-1, 2))
cells = cells.reshape((-1, 2))
ii = nm.where(refine_flag[cells], ii[:, :1], ii[:, 1:])
cells = nm.where(refine_flag[cells], cells[:, :1], cells[:, 1:])
facets = nm.c_[facets, ii]
cells = nm.c_[cells, nm.zeros_like(cells[:, 1])]
else: # if dim == 3:
gel = domain.geom_els['3_8']
epf = gel.get_edges_per_face()
cmesh.setup_connectivity(dim, dim)
fc, coffs = cmesh.get_incident(dim, region1.cells, dim,
ret_offsets=True)
cc = nm.repeat(region1.cells, nm.diff(coffs))
aux = nm.c_[cc, fc]
"""
nnn[:, 0] cells to refine, nnn[:, 1] non-refined neighbours, nnn[:, 2]
neighbour kind : 0 face, 1 edge.
"""
nn = aux[refine_flag[fc] == 0]
cf = nn[:, 0].copy().astype(nm.uint32)
cc = nn[:, 1].copy().astype(nm.uint32)
vc, vco = cmesh.get_incident(0, cc, dim, ret_offsets=True)
vf, vfo = cmesh.get_incident(0, cf, dim, ret_offsets=True)
vc = vc.reshape((-1, 8))
vf = vf.reshape((-1, 8))
nnn = []
oe = 0
ov = nn.shape[0]
for ii in range(vc.shape[0]):
aux = set(vc[ii]).intersection(vf[ii])
nc = len(aux)
if nc == 1:
nnn.append((0, 0, 2))
ov -= 1
elif nc == 4:
nnn.append((nn[ii, 0], nn[ii, 1], 0))
oe += 1
else:
nnn.append((nn[ii, 0], nn[ii, 1], 1))
nnn = nm.array(nnn)
if nnn.shape[0] == 0:
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 4), dtype=nm.uint32)
return facets, cells, 0, region0, region1
# Sort by neighbour kind, skip vertex-only neighbours.
ii = nm.argsort(nnn[:, 2])
nnn = nnn[ii][:ov]
cf = cf[ii][:ov]
cc = cc[ii][:ov]
ec, eco = cmesh.get_incident(1, cc, dim, ret_offsets=True)
ef, efo = cmesh.get_incident(1, cf, dim, ret_offsets=True)
ec = ec.reshape((-1, 12))
ef = ef.reshape((-1, 12))
fc, fco = cmesh.get_incident(2, cc, dim, ret_offsets=True)
ff, ffo = cmesh.get_incident(2, cf, dim, ret_offsets=True)
fc = fc.reshape((-1, 6))
ff = ff.reshape((-1, 6))
emask = nm.zeros((domain.shape.n_el, 12), dtype=nm.bool)
ffs = []
for ii in range(oe):
facet = nm.intersect1d(fc[ii], ff[ii])[0]
i1 = nm.where(ff[ii] == facet)[0][0]
i0 = nm.where(fc[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
emask[nnn[ii, 0], epf[i1]] = True
for ii in range(oe, nnn.shape[0]):
facet = nm.intersect1d(ec[ii], ef[ii])[0]
i1 = nm.where(ef[ii] == facet)[0][0]
i0 = nm.where(ec[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
ffs = nm.array(ffs)
ie = nm.where(nnn[:, 2] == 1)[0]
ennn = nnn[ie]
effs = ffs[ie]
omit = ie[emask[ennn[:, 0], effs[:, 1]]]
valid = nm.ones(nnn.shape[0], dtype=nm.bool)
valid[omit] = False
cells = nnn[valid]
facets = ffs[valid]
return facets, cells, oe, region0, region1
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = FEDomain('d', mesh1)
domain1r = domain1.refine()
mesh1r = domain1r.mesh
n_cell = region1.shape.n_cell
n_sub = 4 if mesh0.cmesh.tdim == 2 else 8
sub_cells = nm.empty((n_cell, n_sub + 1), dtype=nm.uint32)
sub_cells[:, 0] = region1.cells
sub_cells[:, 1] = region1.cells
aux = nm.arange((n_sub - 1) * n_cell, dtype=nm.uint32)
sub_cells[:, 2:] = mesh0.n_el + aux.reshape((n_cell, -1))
coors0, vgs0, conns0, mat_ids0, descs0 = mesh0._get_io_data()
coors, vgs, _conns, _mat_ids, descs = mesh1r._get_io_data()
# Preserve vertex groups of non-refined cells.
vgs[:len(vgs0)] = vgs0
def _interleave_refined(c0, c1):
if c1.ndim == 1:
c0 = c0[:, None]
c1 = c1[:, None]
n_row, n_col = c1.shape
n_new = region0.shape.n_cell + n_row
out = nm.empty((n_new, n_col), dtype=c0.dtype)
out[region0.cells] = c0[region0.cells]
out[region1.cells] = c1[::n_sub]
aux = c1.reshape((-1, n_col * n_sub))
out[mesh0.n_el:] = aux[:, n_col:].reshape((-1, n_col))
return out
conn = _interleave_refined(conns0[0], _conns[0])
mat_id = _interleave_refined(mat_ids0[0], _mat_ids[0]).squeeze()
mesh = | Mesh.from_data('a', coors, vgs, [conn], [mat_id], descs) | sfepy.discrete.fem.Mesh.from_data |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = Functions([get_refine, get_coarse])
region0 = domain.create_region('coarse', 'cells by get_coarse',
functions=functions, add_to_regions=False,
allow_empty=True)
region1 = domain.create_region('refine', 'cells by get_refine',
functions=functions, add_to_regions=False)
cmesh = domain.mesh.cmesh
dim = cmesh.dim
if dim == 2:
oe = 0
facets = nm.intersect1d(region0.facets, region1.facets)
cmesh.setup_connectivity(dim - 1, dim)
cells, offs = cmesh.get_incident(dim, facets, dim - 1,
ret_offsets=True)
assert_((nm.diff(offs) == 2).all())
ii = cmesh.get_local_ids(facets, dim - 1, cells, offs, dim)
ii = ii.reshape((-1, 2))
cells = cells.reshape((-1, 2))
ii = nm.where(refine_flag[cells], ii[:, :1], ii[:, 1:])
cells = nm.where(refine_flag[cells], cells[:, :1], cells[:, 1:])
facets = nm.c_[facets, ii]
cells = nm.c_[cells, nm.zeros_like(cells[:, 1])]
else: # if dim == 3:
gel = domain.geom_els['3_8']
epf = gel.get_edges_per_face()
cmesh.setup_connectivity(dim, dim)
fc, coffs = cmesh.get_incident(dim, region1.cells, dim,
ret_offsets=True)
cc = nm.repeat(region1.cells, nm.diff(coffs))
aux = nm.c_[cc, fc]
"""
nnn[:, 0] cells to refine, nnn[:, 1] non-refined neighbours, nnn[:, 2]
neighbour kind : 0 face, 1 edge.
"""
nn = aux[refine_flag[fc] == 0]
cf = nn[:, 0].copy().astype(nm.uint32)
cc = nn[:, 1].copy().astype(nm.uint32)
vc, vco = cmesh.get_incident(0, cc, dim, ret_offsets=True)
vf, vfo = cmesh.get_incident(0, cf, dim, ret_offsets=True)
vc = vc.reshape((-1, 8))
vf = vf.reshape((-1, 8))
nnn = []
oe = 0
ov = nn.shape[0]
for ii in range(vc.shape[0]):
aux = set(vc[ii]).intersection(vf[ii])
nc = len(aux)
if nc == 1:
nnn.append((0, 0, 2))
ov -= 1
elif nc == 4:
nnn.append((nn[ii, 0], nn[ii, 1], 0))
oe += 1
else:
nnn.append((nn[ii, 0], nn[ii, 1], 1))
nnn = nm.array(nnn)
if nnn.shape[0] == 0:
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 4), dtype=nm.uint32)
return facets, cells, 0, region0, region1
# Sort by neighbour kind, skip vertex-only neighbours.
ii = nm.argsort(nnn[:, 2])
nnn = nnn[ii][:ov]
cf = cf[ii][:ov]
cc = cc[ii][:ov]
ec, eco = cmesh.get_incident(1, cc, dim, ret_offsets=True)
ef, efo = cmesh.get_incident(1, cf, dim, ret_offsets=True)
ec = ec.reshape((-1, 12))
ef = ef.reshape((-1, 12))
fc, fco = cmesh.get_incident(2, cc, dim, ret_offsets=True)
ff, ffo = cmesh.get_incident(2, cf, dim, ret_offsets=True)
fc = fc.reshape((-1, 6))
ff = ff.reshape((-1, 6))
emask = nm.zeros((domain.shape.n_el, 12), dtype=nm.bool)
ffs = []
for ii in range(oe):
facet = nm.intersect1d(fc[ii], ff[ii])[0]
i1 = nm.where(ff[ii] == facet)[0][0]
i0 = nm.where(fc[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
emask[nnn[ii, 0], epf[i1]] = True
for ii in range(oe, nnn.shape[0]):
facet = nm.intersect1d(ec[ii], ef[ii])[0]
i1 = nm.where(ef[ii] == facet)[0][0]
i0 = nm.where(ec[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
ffs = nm.array(ffs)
ie = nm.where(nnn[:, 2] == 1)[0]
ennn = nnn[ie]
effs = ffs[ie]
omit = ie[emask[ennn[:, 0], effs[:, 1]]]
valid = nm.ones(nnn.shape[0], dtype=nm.bool)
valid[omit] = False
cells = nnn[valid]
facets = ffs[valid]
return facets, cells, oe, region0, region1
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = FEDomain('d', mesh1)
domain1r = domain1.refine()
mesh1r = domain1r.mesh
n_cell = region1.shape.n_cell
n_sub = 4 if mesh0.cmesh.tdim == 2 else 8
sub_cells = nm.empty((n_cell, n_sub + 1), dtype=nm.uint32)
sub_cells[:, 0] = region1.cells
sub_cells[:, 1] = region1.cells
aux = nm.arange((n_sub - 1) * n_cell, dtype=nm.uint32)
sub_cells[:, 2:] = mesh0.n_el + aux.reshape((n_cell, -1))
coors0, vgs0, conns0, mat_ids0, descs0 = mesh0._get_io_data()
coors, vgs, _conns, _mat_ids, descs = mesh1r._get_io_data()
# Preserve vertex groups of non-refined cells.
vgs[:len(vgs0)] = vgs0
def _interleave_refined(c0, c1):
if c1.ndim == 1:
c0 = c0[:, None]
c1 = c1[:, None]
n_row, n_col = c1.shape
n_new = region0.shape.n_cell + n_row
out = nm.empty((n_new, n_col), dtype=c0.dtype)
out[region0.cells] = c0[region0.cells]
out[region1.cells] = c1[::n_sub]
aux = c1.reshape((-1, n_col * n_sub))
out[mesh0.n_el:] = aux[:, n_col:].reshape((-1, n_col))
return out
conn = _interleave_refined(conns0[0], _conns[0])
mat_id = _interleave_refined(mat_ids0[0], _mat_ids[0]).squeeze()
mesh = Mesh.from_data('a', coors, vgs, [conn], [mat_id], descs)
domain = | FEDomain('d', mesh) | sfepy.discrete.fem.FEDomain |
"""
Functions for a mesh refinement with hanging nodes.
Notes
-----
Using LCBCs with hanging nodes is not supported.
"""
from __future__ import absolute_import
from six.moves import range, zip
import numpy as nm
from sfepy.base.base import assert_
from sfepy.discrete import Functions, Function
from sfepy.discrete.fem import Mesh, FEDomain
# Rows = facets of reference cell, columns = [sub_cell_i, local facet_i]
refine_edges_2_4 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]]])
refine_faces_3_8 = nm.array([[[0, 0], [1, 0], [2, 0], [3, 0]],
[[0, 1], [3, 2], [4, 2], [7, 1]],
[[0, 2], [1, 1], [4, 1], [5, 2]],
[[4, 0], [5, 0], [6, 0], [7, 0]],
[[1, 2], [2, 1], [5, 1], [6, 2]],
[[2, 2], [3, 1], [6, 1], [7, 2]]])
refine_edges_3_8 = nm.array([[[0, 0], [1, 3]],
[[1, 0], [2, 3]],
[[2, 0], [3, 3]],
[[3, 0], [0, 3]],
[[4, 3], [5, 0]],
[[5, 3], [6, 0]],
[[6, 3], [7, 0]],
[[7, 3], [4, 0]],
[[0, 8], [4, 8]],
[[1, 8], [5, 8]],
[[2, 8], [6, 8]],
[[3, 8], [7, 8]]])
def find_level_interface(domain, refine_flag):
"""
Find facets of the coarse mesh that are on the coarse-refined cell
boundary.
ids w.r.t. current mesh:
- facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
- interface cells:
- cells[:, 0] - cells to refine
- cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes)
- cells[:, 2] - facet kind: 0 = face, 1 = edge
"""
if not refine_flag.any():
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 3), dtype=nm.uint32)
return facets, cells, 0, None, None
def _get_refine(coors, domain=None):
return nm.nonzero(refine_flag)[0]
def _get_coarse(coors, domain=None):
return nm.nonzero(1 - refine_flag)[0]
get_refine = Function('get_refine', _get_refine)
get_coarse = Function('get_coarse', _get_coarse)
functions = Functions([get_refine, get_coarse])
region0 = domain.create_region('coarse', 'cells by get_coarse',
functions=functions, add_to_regions=False,
allow_empty=True)
region1 = domain.create_region('refine', 'cells by get_refine',
functions=functions, add_to_regions=False)
cmesh = domain.mesh.cmesh
dim = cmesh.dim
if dim == 2:
oe = 0
facets = nm.intersect1d(region0.facets, region1.facets)
cmesh.setup_connectivity(dim - 1, dim)
cells, offs = cmesh.get_incident(dim, facets, dim - 1,
ret_offsets=True)
assert_((nm.diff(offs) == 2).all())
ii = cmesh.get_local_ids(facets, dim - 1, cells, offs, dim)
ii = ii.reshape((-1, 2))
cells = cells.reshape((-1, 2))
ii = nm.where(refine_flag[cells], ii[:, :1], ii[:, 1:])
cells = nm.where(refine_flag[cells], cells[:, :1], cells[:, 1:])
facets = nm.c_[facets, ii]
cells = nm.c_[cells, nm.zeros_like(cells[:, 1])]
else: # if dim == 3:
gel = domain.geom_els['3_8']
epf = gel.get_edges_per_face()
cmesh.setup_connectivity(dim, dim)
fc, coffs = cmesh.get_incident(dim, region1.cells, dim,
ret_offsets=True)
cc = nm.repeat(region1.cells, nm.diff(coffs))
aux = nm.c_[cc, fc]
"""
nnn[:, 0] cells to refine, nnn[:, 1] non-refined neighbours, nnn[:, 2]
neighbour kind : 0 face, 1 edge.
"""
nn = aux[refine_flag[fc] == 0]
cf = nn[:, 0].copy().astype(nm.uint32)
cc = nn[:, 1].copy().astype(nm.uint32)
vc, vco = cmesh.get_incident(0, cc, dim, ret_offsets=True)
vf, vfo = cmesh.get_incident(0, cf, dim, ret_offsets=True)
vc = vc.reshape((-1, 8))
vf = vf.reshape((-1, 8))
nnn = []
oe = 0
ov = nn.shape[0]
for ii in range(vc.shape[0]):
aux = set(vc[ii]).intersection(vf[ii])
nc = len(aux)
if nc == 1:
nnn.append((0, 0, 2))
ov -= 1
elif nc == 4:
nnn.append((nn[ii, 0], nn[ii, 1], 0))
oe += 1
else:
nnn.append((nn[ii, 0], nn[ii, 1], 1))
nnn = nm.array(nnn)
if nnn.shape[0] == 0:
facets = nm.zeros((0, 3), dtype=nm.uint32)
cells = nm.zeros((0, 4), dtype=nm.uint32)
return facets, cells, 0, region0, region1
# Sort by neighbour kind, skip vertex-only neighbours.
ii = nm.argsort(nnn[:, 2])
nnn = nnn[ii][:ov]
cf = cf[ii][:ov]
cc = cc[ii][:ov]
ec, eco = cmesh.get_incident(1, cc, dim, ret_offsets=True)
ef, efo = cmesh.get_incident(1, cf, dim, ret_offsets=True)
ec = ec.reshape((-1, 12))
ef = ef.reshape((-1, 12))
fc, fco = cmesh.get_incident(2, cc, dim, ret_offsets=True)
ff, ffo = cmesh.get_incident(2, cf, dim, ret_offsets=True)
fc = fc.reshape((-1, 6))
ff = ff.reshape((-1, 6))
emask = nm.zeros((domain.shape.n_el, 12), dtype=nm.bool)
ffs = []
for ii in range(oe):
facet = nm.intersect1d(fc[ii], ff[ii])[0]
i1 = nm.where(ff[ii] == facet)[0][0]
i0 = nm.where(fc[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
emask[nnn[ii, 0], epf[i1]] = True
for ii in range(oe, nnn.shape[0]):
facet = nm.intersect1d(ec[ii], ef[ii])[0]
i1 = nm.where(ef[ii] == facet)[0][0]
i0 = nm.where(ec[ii] == facet)[0][0]
ffs.append((facet, i1, i0))
ffs = nm.array(ffs)
ie = nm.where(nnn[:, 2] == 1)[0]
ennn = nnn[ie]
effs = ffs[ie]
omit = ie[emask[ennn[:, 0], effs[:, 1]]]
valid = nm.ones(nnn.shape[0], dtype=nm.bool)
valid[omit] = False
cells = nnn[valid]
facets = ffs[valid]
return facets, cells, oe, region0, region1
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = FEDomain('d', mesh1)
domain1r = domain1.refine()
mesh1r = domain1r.mesh
n_cell = region1.shape.n_cell
n_sub = 4 if mesh0.cmesh.tdim == 2 else 8
sub_cells = nm.empty((n_cell, n_sub + 1), dtype=nm.uint32)
sub_cells[:, 0] = region1.cells
sub_cells[:, 1] = region1.cells
aux = nm.arange((n_sub - 1) * n_cell, dtype=nm.uint32)
sub_cells[:, 2:] = mesh0.n_el + aux.reshape((n_cell, -1))
coors0, vgs0, conns0, mat_ids0, descs0 = mesh0._get_io_data()
coors, vgs, _conns, _mat_ids, descs = mesh1r._get_io_data()
# Preserve vertex groups of non-refined cells.
vgs[:len(vgs0)] = vgs0
def _interleave_refined(c0, c1):
if c1.ndim == 1:
c0 = c0[:, None]
c1 = c1[:, None]
n_row, n_col = c1.shape
n_new = region0.shape.n_cell + n_row
out = nm.empty((n_new, n_col), dtype=c0.dtype)
out[region0.cells] = c0[region0.cells]
out[region1.cells] = c1[::n_sub]
aux = c1.reshape((-1, n_col * n_sub))
out[mesh0.n_el:] = aux[:, n_col:].reshape((-1, n_col))
return out
conn = _interleave_refined(conns0[0], _conns[0])
mat_id = _interleave_refined(mat_ids0[0], _mat_ids[0]).squeeze()
mesh = Mesh.from_data('a', coors, vgs, [conn], [mat_id], descs)
domain = FEDomain('d', mesh)
return domain, sub_cells
def find_facet_substitutions(facets, cells, sub_cells, refine_facets):
"""
Find facet substitutions in connectivity.
sub = [coarse cell, coarse facet, fine1 cell, fine1 facet, fine2 cell,
fine2 facet]
"""
subs = []
for ii, fac in enumerate(facets):
fine = cells[ii, 0]
coarse = cells[ii, 1]
isub = nm.searchsorted(sub_cells[:, 0], fine)
refined = sub_cells[isub, 1:]
rf = refine_facets[fac[1]]
used = refined[rf[:, 0]]
fused = rf[:, 1]
master = [coarse, fac[2]]
slave = list(zip(used, fused))
sub = nm.r_[[master], slave].ravel()
subs.append(sub)
subs = nm.array(subs)
return subs
def refine(domain0, refine, subs=None, ret_sub_cells=False):
desc = domain0.mesh.descs[0]
| assert_(desc in ['2_4', '3_8']) | sfepy.base.base.assert_ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
| Container.__init__(self, objs=objs) | sfepy.base.base.Container.__init__ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
| Container.insert(self, ii, obj) | sfepy.base.base.Container.insert |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
| Container.append(self, obj) | sfepy.base.base.Container.append |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = | Struct.get(self, 'function', None) | sfepy.base.base.Struct.get |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = | get_default(step, self.arg_steps[name]) | sfepy.base.base.get_default |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = | get_default(integration, self.geometry_types[name]) | sfepy.base.base.get_default |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = | dim2sym(dim) | sfepy.mechanics.tensors.dim2sym |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = | create_adof_conns(conn_info, None) | sfepy.discrete.create_adof_conns |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
| terms.append(term) | sfepy.terms.extmods.terms.append |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = | Integrals() | sfepy.discrete.Integrals |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = | as_float_or_complex(other) | sfepy.base.base.as_float_or_complex |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', | Struct() | sfepy.base.base.Struct |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = | Struct.get(self, 'mode', None) | sfepy.base.base.Struct.get |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = | PhysicalQPs() | sfepy.discrete.common.mappings.PhysicalQPs |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = | get_physical_qps(self.region, self.integral) | sfepy.discrete.common.mappings.get_physical_qps |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
| output('allowed argument shapes for term "%s":' % term_str) | sfepy.base.base.output |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
| output(allowed_shapes) | sfepy.base.base.output |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
| output('actual argument shapes:') | sfepy.base.base.output |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
| output(actual_shapes) | sfepy.base.base.output |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
if status:
| terms.errclear() | sfepy.terms.extmods.terms.errclear |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
| terms.errclear() | sfepy.terms.extmods.terms.errclear |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
| terms.errclear() | sfepy.terms.extmods.terms.errclear |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
if status:
terms.errclear()
raise ValueError('term evaluation failed! (%s)' % self.name)
return status
def eval_real(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
out = nm.empty(shape, dtype=nm.float64)
if mode == 'eval':
status = self.call_function(out, fargs)
# Sum over elements but not over components.
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
status = self.call_function(out, fargs)
return out, status
def eval_complex(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
rout = nm.empty(shape, dtype=nm.float64)
fargsd = split_complex_args(fargs)
# Assuming linear forms. Then the matrix is the
# same both for real and imaginary part.
rstatus = self.call_function(rout, fargsd['r'])
if (diff_var is None) and len(fargsd) >= 2:
iout = nm.empty(shape, dtype=nm.float64)
istatus = self.call_function(iout, fargsd['i'])
if mode == 'eval' and len(fargsd) >= 4:
irout = nm.empty(shape, dtype=nm.float64)
irstatus = self.call_function(irout, fargsd['ir'])
riout = nm.empty(shape, dtype=nm.float64)
ristatus = self.call_function(riout, fargsd['ri'])
out = (rout - iout) + (riout + irout) * 1j
status = rstatus or istatus or ristatus or irstatus
else:
out = rout + 1j * iout
status = rstatus or istatus
else:
out, status = rout + 0j, rstatus
if mode == 'eval':
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
return out, status
def evaluate(self, mode='eval', diff_var=None,
standalone=True, ret_status=False, **kwargs):
"""
Evaluate the term.
Parameters
----------
mode : 'eval' (default), or 'weak'
The term evaluation mode.
Returns
-------
val : float or array
In 'eval' mode, the term returns a single value (the
integral, it does not need to be a scalar), while in 'weak'
mode it returns an array for each element.
status : int, optional
The flag indicating evaluation success (0) or failure
(nonzero). Only provided if `ret_status` is True.
iels : array of ints, optional
The local elements indices in 'weak' mode. Only provided in
non-'eval' modes.
"""
if standalone:
self.standalone_setup()
kwargs = kwargs.copy()
term_mode = kwargs.pop('term_mode', None)
if mode in ('eval', 'el_eval', 'el_avg', 'qp'):
args = self.get_args(**kwargs)
self.check_shapes(*args)
emode = 'eval' if mode == 'el_eval' else mode
_args = tuple(args) + (emode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
shape, dtype = self.get_eval_shape(*_args, **kwargs)
if dtype == nm.float64:
val, status = self.eval_real(shape, fargs, mode, term_mode,
**kwargs)
elif dtype == nm.complex128:
val, status = self.eval_complex(shape, fargs, mode, term_mode,
**kwargs)
else:
raise ValueError('unsupported term dtype! (%s)' % dtype)
val *= self.sign
out = (val,)
elif mode == 'weak':
varr = self.get_virtual_variable()
if varr is None:
raise ValueError('no virtual variable in weak mode! (in "%s")'
% self.get_str())
if diff_var is not None:
varc = self.get_variables(as_list=False)[diff_var]
args = self.get_args(**kwargs)
self.check_shapes(*args)
_args = tuple(args) + (mode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
n_elr, n_qpr, dim, n_enr, n_cr = self.get_data_shape(varr)
n_row = n_cr * n_enr
if diff_var is None:
shape = (n_elr, 1, n_row, 1)
else:
n_elc, n_qpc, dim, n_enc, n_cc = self.get_data_shape(varc)
n_col = n_cc * n_enc
shape = (n_elr, 1, n_row, n_col)
if varr.dtype == nm.float64:
vals, status = self.eval_real(shape, fargs, mode, term_mode,
diff_var, **kwargs)
elif varr.dtype == nm.complex128:
vals, status = self.eval_complex(shape, fargs, mode, term_mode,
diff_var, **kwargs)
else:
raise ValueError('unsupported term dtype! (%s)'
% varr.dtype)
if not isinstance(vals, tuple):
vals *= self.sign
iels = self.get_assembling_cells(vals.shape)
else:
vals = (self.sign * vals[0],) + vals[1:]
iels = None
out = (vals, iels)
if goptions['check_term_finiteness']:
assert_(nm.isfinite(out[0]).all(),
msg='"%s" term values not finite!' % self.get_str())
if ret_status:
out = out + (status,)
if len(out) == 1:
out = out[0]
return out
def assemble_to(self, asm_obj, val, iels, mode='vector', diff_var=None):
"""
Assemble the results of term evaluation.
For standard terms, assemble the values in `val` corresponding to
elements/cells `iels` into a vector or a CSR sparse matrix `asm_obj`,
depending on `mode`.
For terms with a dynamic connectivity (e.g. contact terms), in
`'matrix'` mode, return the extra COO sparse matrix instead. The extra
matrix has to be added to the global matrix by the caller. By default,
this is done in :func:`Equations.evaluate()
<sfepy.discrete.equations.Equations.evaluate()>`.
"""
import sfepy.discrete.common.extmods.assemble as asm
vvar = self.get_virtual_variable()
dc_type = self.get_dof_conn_type()
extra = None
if mode == 'vector':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_vector
else:
| assert_(asm_obj.dtype == nm.complex128) | sfepy.base.base.assert_ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
if status:
terms.errclear()
raise ValueError('term evaluation failed! (%s)' % self.name)
return status
def eval_real(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
out = nm.empty(shape, dtype=nm.float64)
if mode == 'eval':
status = self.call_function(out, fargs)
# Sum over elements but not over components.
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
status = self.call_function(out, fargs)
return out, status
def eval_complex(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
rout = nm.empty(shape, dtype=nm.float64)
fargsd = split_complex_args(fargs)
# Assuming linear forms. Then the matrix is the
# same both for real and imaginary part.
rstatus = self.call_function(rout, fargsd['r'])
if (diff_var is None) and len(fargsd) >= 2:
iout = nm.empty(shape, dtype=nm.float64)
istatus = self.call_function(iout, fargsd['i'])
if mode == 'eval' and len(fargsd) >= 4:
irout = nm.empty(shape, dtype=nm.float64)
irstatus = self.call_function(irout, fargsd['ir'])
riout = nm.empty(shape, dtype=nm.float64)
ristatus = self.call_function(riout, fargsd['ri'])
out = (rout - iout) + (riout + irout) * 1j
status = rstatus or istatus or ristatus or irstatus
else:
out = rout + 1j * iout
status = rstatus or istatus
else:
out, status = rout + 0j, rstatus
if mode == 'eval':
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
return out, status
def evaluate(self, mode='eval', diff_var=None,
standalone=True, ret_status=False, **kwargs):
"""
Evaluate the term.
Parameters
----------
mode : 'eval' (default), or 'weak'
The term evaluation mode.
Returns
-------
val : float or array
In 'eval' mode, the term returns a single value (the
integral, it does not need to be a scalar), while in 'weak'
mode it returns an array for each element.
status : int, optional
The flag indicating evaluation success (0) or failure
(nonzero). Only provided if `ret_status` is True.
iels : array of ints, optional
The local elements indices in 'weak' mode. Only provided in
non-'eval' modes.
"""
if standalone:
self.standalone_setup()
kwargs = kwargs.copy()
term_mode = kwargs.pop('term_mode', None)
if mode in ('eval', 'el_eval', 'el_avg', 'qp'):
args = self.get_args(**kwargs)
self.check_shapes(*args)
emode = 'eval' if mode == 'el_eval' else mode
_args = tuple(args) + (emode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
shape, dtype = self.get_eval_shape(*_args, **kwargs)
if dtype == nm.float64:
val, status = self.eval_real(shape, fargs, mode, term_mode,
**kwargs)
elif dtype == nm.complex128:
val, status = self.eval_complex(shape, fargs, mode, term_mode,
**kwargs)
else:
raise ValueError('unsupported term dtype! (%s)' % dtype)
val *= self.sign
out = (val,)
elif mode == 'weak':
varr = self.get_virtual_variable()
if varr is None:
raise ValueError('no virtual variable in weak mode! (in "%s")'
% self.get_str())
if diff_var is not None:
varc = self.get_variables(as_list=False)[diff_var]
args = self.get_args(**kwargs)
self.check_shapes(*args)
_args = tuple(args) + (mode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
n_elr, n_qpr, dim, n_enr, n_cr = self.get_data_shape(varr)
n_row = n_cr * n_enr
if diff_var is None:
shape = (n_elr, 1, n_row, 1)
else:
n_elc, n_qpc, dim, n_enc, n_cc = self.get_data_shape(varc)
n_col = n_cc * n_enc
shape = (n_elr, 1, n_row, n_col)
if varr.dtype == nm.float64:
vals, status = self.eval_real(shape, fargs, mode, term_mode,
diff_var, **kwargs)
elif varr.dtype == nm.complex128:
vals, status = self.eval_complex(shape, fargs, mode, term_mode,
diff_var, **kwargs)
else:
raise ValueError('unsupported term dtype! (%s)'
% varr.dtype)
if not isinstance(vals, tuple):
vals *= self.sign
iels = self.get_assembling_cells(vals.shape)
else:
vals = (self.sign * vals[0],) + vals[1:]
iels = None
out = (vals, iels)
if goptions['check_term_finiteness']:
assert_(nm.isfinite(out[0]).all(),
msg='"%s" term values not finite!' % self.get_str())
if ret_status:
out = out + (status,)
if len(out) == 1:
out = out[0]
return out
def assemble_to(self, asm_obj, val, iels, mode='vector', diff_var=None):
"""
Assemble the results of term evaluation.
For standard terms, assemble the values in `val` corresponding to
elements/cells `iels` into a vector or a CSR sparse matrix `asm_obj`,
depending on `mode`.
For terms with a dynamic connectivity (e.g. contact terms), in
`'matrix'` mode, return the extra COO sparse matrix instead. The extra
matrix has to be added to the global matrix by the caller. By default,
this is done in :func:`Equations.evaluate()
<sfepy.discrete.equations.Equations.evaluate()>`.
"""
import sfepy.discrete.common.extmods.assemble as asm
vvar = self.get_virtual_variable()
dc_type = self.get_dof_conn_type()
extra = None
if mode == 'vector':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_vector
else:
assert_(asm_obj.dtype == nm.complex128)
assemble = asm.assemble_vector_complex
for ii in range(len(val)):
if not(val[ii].dtype == nm.complex128):
val[ii] = nm.complex128(val[ii])
if not isinstance(val, tuple):
dc = vvar.get_dof_conn(dc_type)
| assert_(val.shape[2] == dc.shape[1]) | sfepy.base.base.assert_ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [ | Struct(terms=[self]) | sfepy.base.base.Struct |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
if status:
terms.errclear()
raise ValueError('term evaluation failed! (%s)' % self.name)
return status
def eval_real(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
out = nm.empty(shape, dtype=nm.float64)
if mode == 'eval':
status = self.call_function(out, fargs)
# Sum over elements but not over components.
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
status = self.call_function(out, fargs)
return out, status
def eval_complex(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
rout = nm.empty(shape, dtype=nm.float64)
fargsd = split_complex_args(fargs)
# Assuming linear forms. Then the matrix is the
# same both for real and imaginary part.
rstatus = self.call_function(rout, fargsd['r'])
if (diff_var is None) and len(fargsd) >= 2:
iout = nm.empty(shape, dtype=nm.float64)
istatus = self.call_function(iout, fargsd['i'])
if mode == 'eval' and len(fargsd) >= 4:
irout = nm.empty(shape, dtype=nm.float64)
irstatus = self.call_function(irout, fargsd['ir'])
riout = nm.empty(shape, dtype=nm.float64)
ristatus = self.call_function(riout, fargsd['ri'])
out = (rout - iout) + (riout + irout) * 1j
status = rstatus or istatus or ristatus or irstatus
else:
out = rout + 1j * iout
status = rstatus or istatus
else:
out, status = rout + 0j, rstatus
if mode == 'eval':
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
return out, status
def evaluate(self, mode='eval', diff_var=None,
standalone=True, ret_status=False, **kwargs):
"""
Evaluate the term.
Parameters
----------
mode : 'eval' (default), or 'weak'
The term evaluation mode.
Returns
-------
val : float or array
In 'eval' mode, the term returns a single value (the
integral, it does not need to be a scalar), while in 'weak'
mode it returns an array for each element.
status : int, optional
The flag indicating evaluation success (0) or failure
(nonzero). Only provided if `ret_status` is True.
iels : array of ints, optional
The local elements indices in 'weak' mode. Only provided in
non-'eval' modes.
"""
if standalone:
self.standalone_setup()
kwargs = kwargs.copy()
term_mode = kwargs.pop('term_mode', None)
if mode in ('eval', 'el_eval', 'el_avg', 'qp'):
args = self.get_args(**kwargs)
self.check_shapes(*args)
emode = 'eval' if mode == 'el_eval' else mode
_args = tuple(args) + (emode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
shape, dtype = self.get_eval_shape(*_args, **kwargs)
if dtype == nm.float64:
val, status = self.eval_real(shape, fargs, mode, term_mode,
**kwargs)
elif dtype == nm.complex128:
val, status = self.eval_complex(shape, fargs, mode, term_mode,
**kwargs)
else:
raise ValueError('unsupported term dtype! (%s)' % dtype)
val *= self.sign
out = (val,)
elif mode == 'weak':
varr = self.get_virtual_variable()
if varr is None:
raise ValueError('no virtual variable in weak mode! (in "%s")'
% self.get_str())
if diff_var is not None:
varc = self.get_variables(as_list=False)[diff_var]
args = self.get_args(**kwargs)
self.check_shapes(*args)
_args = tuple(args) + (mode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
n_elr, n_qpr, dim, n_enr, n_cr = self.get_data_shape(varr)
n_row = n_cr * n_enr
if diff_var is None:
shape = (n_elr, 1, n_row, 1)
else:
n_elc, n_qpc, dim, n_enc, n_cc = self.get_data_shape(varc)
n_col = n_cc * n_enc
shape = (n_elr, 1, n_row, n_col)
if varr.dtype == nm.float64:
vals, status = self.eval_real(shape, fargs, mode, term_mode,
diff_var, **kwargs)
elif varr.dtype == nm.complex128:
vals, status = self.eval_complex(shape, fargs, mode, term_mode,
diff_var, **kwargs)
else:
raise ValueError('unsupported term dtype! (%s)'
% varr.dtype)
if not isinstance(vals, tuple):
vals *= self.sign
iels = self.get_assembling_cells(vals.shape)
else:
vals = (self.sign * vals[0],) + vals[1:]
iels = None
out = (vals, iels)
if goptions['check_term_finiteness']:
assert_(nm.isfinite(out[0]).all(),
msg='"%s" term values not finite!' % self.get_str())
if ret_status:
out = out + (status,)
if len(out) == 1:
out = out[0]
return out
def assemble_to(self, asm_obj, val, iels, mode='vector', diff_var=None):
"""
Assemble the results of term evaluation.
For standard terms, assemble the values in `val` corresponding to
elements/cells `iels` into a vector or a CSR sparse matrix `asm_obj`,
depending on `mode`.
For terms with a dynamic connectivity (e.g. contact terms), in
`'matrix'` mode, return the extra COO sparse matrix instead. The extra
matrix has to be added to the global matrix by the caller. By default,
this is done in :func:`Equations.evaluate()
<sfepy.discrete.equations.Equations.evaluate()>`.
"""
import sfepy.discrete.common.extmods.assemble as asm
vvar = self.get_virtual_variable()
dc_type = self.get_dof_conn_type()
extra = None
if mode == 'vector':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_vector
else:
assert_(asm_obj.dtype == nm.complex128)
assemble = asm.assemble_vector_complex
for ii in range(len(val)):
if not(val[ii].dtype == nm.complex128):
val[ii] = nm.complex128(val[ii])
if not isinstance(val, tuple):
dc = vvar.get_dof_conn(dc_type)
assert_(val.shape[2] == dc.shape[1])
assemble(asm_obj, val, iels, 1.0, dc)
else:
vals, rows, var = val
if var.eq_map is not None:
eq = var.eq_map.eq
rows = eq[rows]
active = (rows >= 0)
vals, rows = vals[active], rows[active]
# Assumes no repeated indices in rows!
asm_obj[rows] += vals
elif mode == 'matrix':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_matrix
else:
| assert_(asm_obj.dtype == nm.complex128) | sfepy.base.base.assert_ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted(term_table.keys()))
raise ValueError(msg)
obj = constructor(name, arg_str, integral, region, **kwargs)
return obj
@staticmethod
def from_desc(constructor, desc, region, integrals=None):
from sfepy.discrete import Integrals
if integrals is None:
integrals = Integrals()
integral = integrals.get(desc.integral)
obj = constructor(desc.name, desc.args, integral, region)
obj.sign = desc.sign
return obj
def __init__(self, name, arg_str, integral, region, **kwargs):
self.name = name
self.arg_str = arg_str
self.region = region
self._kwargs = kwargs
self._integration = self.integration
self.sign = 1.0
self.set_integral(integral)
def __mul__(self, other):
try:
mul = as_float_or_complex(other)
except ValueError:
raise ValueError('cannot multiply Term with %s!' % other)
out = self.copy(name=self.name)
out.sign = mul * self.sign
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = Terms([self, other])
else:
out = NotImplemented
return out
def __sub__(self, other):
if isinstance(other, Term):
out = Terms([self, -1.0 * other])
else:
out = NotImplemented
return out
def __pos__(self):
return self
def __neg__(self):
out = -1.0 * self
return out
def get_str(self):
return ('%+.2e * %s.%d.%s(%s)'
% (self.sign, self.name, self.integral.order,
self.region.name, self.arg_str))
def set_integral(self, integral):
"""
Set the term integral.
"""
self.integral = integral
if self.integral is not None:
self.integral_name = self.integral.name
def setup(self):
self.function = Struct.get(self, 'function', None)
self.step = 0
self.dt = 1.0
self.is_quasistatic = False
self.has_region = True
self.setup_formal_args()
if self._kwargs:
self.setup_args(**self._kwargs)
else:
self.args = []
def setup_formal_args(self):
self.arg_names = []
self.arg_steps = {}
self.arg_derivatives = {}
self.arg_traces = {}
parser = create_arg_parser()
self.arg_desc = parser.parseString(self.arg_str)
for arg in self.arg_desc:
trace = False
derivative = None
if isinstance(arg[1], int):
name, step = arg
else:
kind = arg[0]
name, step = arg[1]
if kind == 'd':
derivative = arg[2]
elif kind == 'tr':
trace = True
match = _match_material_root(name)
if match:
name = (match.group(1), match.group(2))
self.arg_names.append(name)
self.arg_steps[name] = step
self.arg_derivatives[name] = derivative
self.arg_traces[name] = trace
def setup_args(self, **kwargs):
self._kwargs = kwargs
self.args = []
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
self.args.append(self._kwargs[arg_name])
else:
self.args.append((self._kwargs[arg_name[0]], arg_name[1]))
self.classify_args()
self.check_args()
def assign_args(self, variables, materials, user=None):
"""
Check term argument existence in variables, materials, user data
and assign the arguments to terms. Also check compatibility of
field and term regions.
"""
if user is None:
user = {}
user.setdefault('ts', Struct())
kwargs = {}
for arg_name in self.arg_names:
if isinstance(arg_name, basestr):
if arg_name in variables.names:
kwargs[arg_name] = variables[arg_name]
elif arg_name in user:
kwargs[arg_name] = user[arg_name]
else:
raise ValueError('argument %s not found!' % arg_name)
else:
arg_name = arg_name[0]
if arg_name in materials.names:
kwargs[arg_name] = materials[arg_name]
else:
raise ValueError('material argument %s not found!'
% arg_name)
self.setup_args(**kwargs)
def classify_args(self):
"""
Classify types of the term arguments and find matching call
signature.
A state variable can be in place of a parameter variable and
vice versa.
"""
self.names = Struct(name='arg_names',
material=[], variable=[], user=[],
state=[], virtual=[], parameter=[])
# Prepare for 'opt_material' - just prepend a None argument if needed.
if isinstance(self.arg_types[0], tuple):
arg_types = self.arg_types[0]
else:
arg_types = self.arg_types
if len(arg_types) == (len(self.args) + 1):
self.args.insert(0, (None, None))
self.arg_names.insert(0, (None, None))
if isinstance(self.arg_types[0], tuple):
assert_(len(self.modes) == len(self.arg_types))
# Find matching call signature using variable arguments - material
# and user arguments are ignored!
matched = []
for it, arg_types in enumerate(self.arg_types):
arg_kinds = get_arg_kinds(arg_types)
if self._check_variables(arg_kinds):
matched.append((it, arg_kinds))
if len(matched) == 1:
i_match, arg_kinds = matched[0]
arg_types = self.arg_types[i_match]
self.mode = self.modes[i_match]
elif len(matched) == 0:
msg = 'cannot match arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
msg = 'ambiguous arguments! (%s)' % self.arg_names
raise ValueError(msg)
else:
arg_types = self.arg_types
arg_kinds = get_arg_kinds(self.arg_types)
self.mode = Struct.get(self, 'mode', None)
if not self._check_variables(arg_kinds):
raise ValueError('cannot match variables! (%s)'
% self.arg_names)
# Set actual argument types.
self.ats = list(arg_types)
for ii, arg_kind in enumerate(arg_kinds):
name = self.arg_names[ii]
if arg_kind.endswith('variable'):
names = self.names.variable
if arg_kind == 'virtual_variable':
self.names.virtual.append(name)
elif arg_kind == 'state_variable':
self.names.state.append(name)
elif arg_kind == 'parameter_variable':
self.names.parameter.append(name)
elif arg_kind.endswith('material'):
names = self.names.material
else:
names = self.names.user
names.append(name)
self.n_virtual = len(self.names.virtual)
if self.n_virtual > 1:
raise ValueError('at most one virtual variable is allowed! (%d)'
% self.n_virtual)
self.set_arg_types()
self.setup_integration()
def _check_variables(self, arg_kinds):
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind.endswith('variable'):
var = self.args[ii]
check = {'virtual_variable' : var.is_virtual,
'state_variable' : var.is_state_or_parameter,
'parameter_variable' : var.is_state_or_parameter}
if not check[arg_kind]():
return False
else:
return True
def set_arg_types(self):
pass
def check_args(self):
"""
Common checking to all terms.
Check compatibility of field and term regions.
"""
vns = self.get_variable_names()
for name in vns:
field = self._kwargs[name].get_field()
if field is None:
continue
if not nm.all(in1d(self.region.vertices,
field.region.vertices)):
msg = ('%s: incompatible regions: (self, field %s)'
+ '(%s in %s)') %\
(self.name, field.name,
self.region.vertices, field.region.vertices)
raise ValueError(msg)
def get_variable_names(self):
return self.names.variable
def get_material_names(self):
out = []
for aux in self.names.material:
if aux[0] is not None:
out.append(aux[0])
return out
def get_user_names(self):
return self.names.user
def get_virtual_name(self):
if not self.names.virtual:
return None
var = self.get_virtual_variable()
return var.name
def get_state_names(self):
"""
If variables are given, return only true unknowns whose data are of
the current time step (0).
"""
variables = self.get_state_variables()
return [var.name for var in variables]
def get_parameter_names(self):
return copy(self.names.parameter)
def get_conn_key(self):
"""The key to be used in DOF connectivity information."""
key = (self.name,) + tuple(self.arg_names)
key += (self.integral_name, self.region.name)
return key
def get_conn_info(self):
vvar = self.get_virtual_variable()
svars = self.get_state_variables()
pvars = self.get_parameter_variables()
all_vars = self.get_variables()
dc_type = self.get_dof_conn_type()
tgs = self.get_geometry_types()
v_tg = None
if vvar is not None:
field = vvar.get_field()
if field is not None:
if vvar.name in tgs:
v_tg = tgs[vvar.name]
else:
v_tg = None
else:
# No virtual variable -> all unknowns are in fact known parameters.
pvars += svars
svars = []
region = self.get_region()
if region is not None:
is_any_trace = reduce(lambda x, y: x or y,
list(self.arg_traces.values()))
if is_any_trace:
region.setup_mirror_region()
vals = []
aux_pvars = []
for svar in svars:
# Allow only true state variables.
if not svar.is_state():
aux_pvars.append(svar)
continue
field = svar.get_field()
is_trace = self.arg_traces[svar.name]
if svar.name in tgs:
ps_tg = tgs[svar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=svar,
primary=svar,
has_virtual=True,
has_state=True,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
pvars += aux_pvars
for pvar in pvars:
field = pvar.get_field()
is_trace = self.arg_traces[pvar.name]
if pvar.name in tgs:
ps_tg = tgs[pvar.name]
else:
ps_tg = v_tg
val = ConnInfo(virtual=vvar,
state=None,
primary=pvar.get_primary(),
has_virtual=vvar is not None,
has_state=False,
is_trace=is_trace,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=ps_tg,
region=region,
all_vars=all_vars)
vals.append(val)
if vvar and (len(vals) == 0):
# No state, parameter variables, just the virtual one.
val = ConnInfo(virtual=vvar,
state=vvar.get_primary(),
primary=vvar.get_primary(),
has_virtual=True,
has_state=False,
is_trace=False,
dc_type=dc_type,
v_tg=v_tg,
ps_tg=v_tg,
region=region,
all_vars=all_vars)
vals.append(val)
return vals
def get_args_by_name(self, arg_names):
"""
Return arguments by name.
"""
out = []
for name in arg_names:
try:
ii = self.arg_names.index(name)
except ValueError:
raise ValueError('non-existing argument! (%s)' % name)
out.append(self.args[ii])
return out
def get_args(self, arg_types=None, **kwargs):
"""
Return arguments by type as specified in arg_types (or
self.ats). Arguments in **kwargs can override the ones assigned
at the term construction - this is useful for passing user data.
"""
ats = self.ats
if arg_types is None:
arg_types = ats
args = []
region_name, iorder = self.region.name, self.integral.order
for at in arg_types:
ii = ats.index(at)
arg_name = self.arg_names[ii]
if isinstance(arg_name, basestr):
if arg_name in kwargs:
args.append(kwargs[arg_name])
else:
args.append(self.args[ii])
else:
mat, par_name = self.args[ii]
if mat is not None:
mat_data = mat.get_data((region_name, iorder), par_name)
else:
mat_data = None
args.append(mat_data)
return args
def get_kwargs(self, keys, **kwargs):
"""Extract arguments from **kwargs listed in keys (default is
None)."""
return [kwargs.get(name) for name in keys]
def get_arg_name(self, arg_type, full=False, join=None):
"""
Get the name of the argument specified by `arg_type.`
Parameters
----------
arg_type : str
The argument type string.
full : bool
If True, return the full name. For example, if the name of a
variable argument is 'u' and its time derivative is
requested, the full name is 'du/dt'.
join : str, optional
Optionally, the material argument name tuple can be joined
to a single string using the `join` string.
Returns
-------
name : str
The argument name.
"""
try:
ii = self.ats.index(arg_type)
except ValueError:
return None
name = self.arg_names[ii]
if full:
# Include derivatives.
if self.arg_derivatives[name]:
name = 'd%s/%s' % (name, self.arg_derivatives[name])
if (join is not None) and isinstance(name, tuple):
name = join.join(name)
return name
def setup_integration(self):
self.has_geometry = True
self.geometry_types = {}
if isinstance(self.integration, basestr):
for var in self.get_variables():
self.geometry_types[var.name] = self.integration
else:
if self.mode is not None:
self.integration = self._integration[self.mode]
if self.integration is not None:
for arg_type, gtype in six.iteritems(self.integration):
var = self.get_args(arg_types=[arg_type])[0]
self.geometry_types[var.name] = gtype
gtypes = list(set(self.geometry_types.values()))
if 'surface_extra' in gtypes:
self.dof_conn_type = 'volume'
elif len(gtypes):
self.dof_conn_type = gtypes[0]
def get_region(self):
return self.region
def get_geometry_types(self):
"""
Returns
-------
out : dict
The required geometry types for each variable argument.
"""
return self.geometry_types
def get_dof_conn_type(self):
return Struct(name='dof_conn_info', type=self.dof_conn_type,
region_name=self.region.name)
def get_assembling_cells(self, shape=None):
"""
Return the assembling cell indices into a DOF connectivity.
"""
cells = nm.arange(shape[0], dtype=nm.int32)
return cells
def time_update(self, ts):
if ts is not None:
self.step = ts.step
self.dt = ts.dt
self.is_quasistatic = ts.is_quasistatic
if 'ts' in self._kwargs:
self._kwargs['ts'].update(ts)
def advance(self, ts):
"""
Advance to the next time step. Implemented in subclasses.
"""
def get_vector(self, variable):
"""Get the vector stored in `variable` according to self.arg_steps
and self.arg_derivatives. Supports only the backward difference w.r.t.
time."""
name = variable.name
return variable(step=self.arg_steps[name],
derivative=self.arg_derivatives[name])
def get_variables(self, as_list=True):
if as_list:
variables = self.get_args_by_name(self.names.variable)
else:
variables = {}
for var in self.get_args_by_name(self.names.variable):
variables[var.name] = var
return variables
def get_virtual_variable(self):
aux = self.get_args_by_name(self.names.virtual)
if len(aux) == 1:
var = aux[0]
else:
var = None
return var
def get_state_variables(self, unknown_only=False):
variables = self.get_args_by_name(self.names.state)
if unknown_only:
variables = [var for var in variables
if (var.kind == 'unknown') and
(self.arg_steps[var.name] == 0)]
return variables
def get_parameter_variables(self):
return self.get_args_by_name(self.names.parameter)
def get_materials(self, join=False):
materials = self.get_args_by_name(self.names.material)
for mat in materials:
if mat[0] is None:
materials.remove(mat)
if join:
materials = list(set(mat[0] for mat in materials))
return materials
def get_qp_key(self):
"""
Return a key identifying uniquely the term quadrature points.
"""
return (self.region.name, self.integral.order)
def get_physical_qps(self):
"""
Get physical quadrature points corresponding to the term region
and integral.
"""
from sfepy.discrete.common.mappings import get_physical_qps, PhysicalQPs
if self.integration == 'point':
phys_qps = PhysicalQPs()
else:
phys_qps = get_physical_qps(self.region, self.integral)
return phys_qps
def get_mapping(self, variable, get_saved=False, return_key=False):
"""
Get the reference mapping from a variable.
Notes
-----
This is a convenience wrapper of Field.get_mapping() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.field.get_mapping(region,
self.integral, integration,
get_saved=get_saved,
return_key=return_key)
return out
def get_data_shape(self, variable):
"""
Get data shape information from variable.
Notes
-----
This is a convenience wrapper of FieldVariable.get_data_shape() that
initializes the arguments using the term data.
"""
integration = self.geometry_types[variable.name]
is_trace = self.arg_traces[variable.name]
if is_trace:
region = self.region.get_mirror_region()
else:
region = self.region
out = variable.get_data_shape(self.integral, integration, region.name)
return out
def get(self, variable, quantity_name, bf=None, integration=None,
step=None, time_derivative=None):
"""
Get the named quantity related to the variable.
Notes
-----
This is a convenience wrapper of Variable.evaluate() that
initializes the arguments using the term data.
"""
name = variable.name
step = get_default(step, self.arg_steps[name])
time_derivative = get_default(time_derivative,
self.arg_derivatives[name])
integration = get_default(integration, self.geometry_types[name])
data = variable.evaluate(mode=quantity_name,
region=self.region, integral=self.integral,
integration=integration,
step=step, time_derivative=time_derivative,
is_trace=self.arg_traces[name], bf=bf)
return data
def check_shapes(self, *args, **kwargs):
"""
Check term argument shapes at run-time.
"""
from sfepy.base.base import output
from sfepy.mechanics.tensors import dim2sym
dim = self.region.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'D2':
return dim**2
elif sh == 'S':
return sym
elif sh == 'N': # General number.
return nm.inf
elif sh == 'str':
return 'str'
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return tuple((_parse_scalar_shape(ii.strip())
for ii in sh.split(',')))
else:
return (int(sh),)
arg_kinds = get_arg_kinds(self.ats)
arg_shapes_list = self.arg_shapes
if not isinstance(arg_shapes_list, list):
arg_shapes_list = [arg_shapes_list]
# Loop allowed shapes until a match is found, else error.
allowed_shapes = []
prev_shapes = {}
actual_shapes = {}
for _arg_shapes in arg_shapes_list:
# Unset shapes are taken from the previous iteration.
arg_shapes = copy(prev_shapes)
arg_shapes.update(_arg_shapes)
prev_shapes = arg_shapes
allowed_shapes.append(arg_shapes)
n_ok = 0
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind in ('user', 'ts'):
n_ok += 1
continue
arg = args[ii]
key = '%s:%s' % (self.ats[ii], self.arg_names[ii])
if self.mode is not None:
extended_ats = self.ats[ii] + ('/%s' % self.mode)
else:
extended_ats = self.ats[ii]
try:
sh = arg_shapes[self.ats[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
n_el, n_qp, _dim, n_en, n_c = self.get_data_shape(arg)
actual_shapes[key] = (n_c,)
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple)
else sh)
if nm.isinf(shape):
n_ok += 1
else:
n_ok += shape == n_c
elif arg_kind.endswith('material'):
if arg is None: # Switched-off opt_material.
n_ok += sh is None
continue
if sh is None:
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if sh == 'str':
n_ok += isinstance(arg, basestr)
continue
shape = _parse_tuple_shape(sh)
ls = len(shape)
aarg = nm.array(arg, ndmin=1)
actual_shapes[key] = aarg.shape
# Substiture general dimension 'N' with actual value.
iinfs = nm.where(nm.isinf(shape))[0]
if len(iinfs):
shape = list(shape)
for iinf in iinfs:
shape[iinf] = aarg.shape[-ls+iinf]
shape = tuple(shape)
if (ls > 1) or (shape[0] > 1):
# Array.
n_ok += shape == aarg.shape[-ls:]
actual_shapes[key] = aarg.shape[-ls:]
elif (ls == 1) and (shape[0] == 1):
# Scalar constant.
from numbers import Number
n_ok += isinstance(arg, Number)
else:
n_ok += 1
if n_ok == len(arg_kinds):
break
else:
term_str = self.get_str()
output('allowed argument shapes for term "%s":' % term_str)
output(allowed_shapes)
output('actual argument shapes:')
output(actual_shapes)
raise ValueError('wrong arguments shapes for "%s" term! (see above)'
% term_str)
def standalone_setup(self):
from sfepy.discrete import create_adof_conns, Variables
conn_info = {'aux' : self.get_conn_info()}
adcs = create_adof_conns(conn_info, None)
variables = Variables(self.get_variables())
variables.set_adof_conns(adcs)
materials = self.get_materials(join=True)
for mat in materials:
mat.time_update(None, [Struct(terms=[self])])
def call_get_fargs(self, args, kwargs):
try:
fargs = self.get_fargs(*args, **kwargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
return fargs
def call_function(self, out, fargs):
try:
status = self.function(out, *fargs)
except (RuntimeError, ValueError):
terms.errclear()
raise
if status:
terms.errclear()
raise ValueError('term evaluation failed! (%s)' % self.name)
return status
def eval_real(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
out = nm.empty(shape, dtype=nm.float64)
if mode == 'eval':
status = self.call_function(out, fargs)
# Sum over elements but not over components.
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
status = self.call_function(out, fargs)
return out, status
def eval_complex(self, shape, fargs, mode='eval', term_mode=None,
diff_var=None, **kwargs):
rout = nm.empty(shape, dtype=nm.float64)
fargsd = split_complex_args(fargs)
# Assuming linear forms. Then the matrix is the
# same both for real and imaginary part.
rstatus = self.call_function(rout, fargsd['r'])
if (diff_var is None) and len(fargsd) >= 2:
iout = nm.empty(shape, dtype=nm.float64)
istatus = self.call_function(iout, fargsd['i'])
if mode == 'eval' and len(fargsd) >= 4:
irout = nm.empty(shape, dtype=nm.float64)
irstatus = self.call_function(irout, fargsd['ir'])
riout = nm.empty(shape, dtype=nm.float64)
ristatus = self.call_function(riout, fargsd['ri'])
out = (rout - iout) + (riout + irout) * 1j
status = rstatus or istatus or ristatus or irstatus
else:
out = rout + 1j * iout
status = rstatus or istatus
else:
out, status = rout + 0j, rstatus
if mode == 'eval':
out1 = nm.sum(out, 0).squeeze()
return out1, status
else:
return out, status
def evaluate(self, mode='eval', diff_var=None,
standalone=True, ret_status=False, **kwargs):
"""
Evaluate the term.
Parameters
----------
mode : 'eval' (default), or 'weak'
The term evaluation mode.
Returns
-------
val : float or array
In 'eval' mode, the term returns a single value (the
integral, it does not need to be a scalar), while in 'weak'
mode it returns an array for each element.
status : int, optional
The flag indicating evaluation success (0) or failure
(nonzero). Only provided if `ret_status` is True.
iels : array of ints, optional
The local elements indices in 'weak' mode. Only provided in
non-'eval' modes.
"""
if standalone:
self.standalone_setup()
kwargs = kwargs.copy()
term_mode = kwargs.pop('term_mode', None)
if mode in ('eval', 'el_eval', 'el_avg', 'qp'):
args = self.get_args(**kwargs)
self.check_shapes(*args)
emode = 'eval' if mode == 'el_eval' else mode
_args = tuple(args) + (emode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
shape, dtype = self.get_eval_shape(*_args, **kwargs)
if dtype == nm.float64:
val, status = self.eval_real(shape, fargs, mode, term_mode,
**kwargs)
elif dtype == nm.complex128:
val, status = self.eval_complex(shape, fargs, mode, term_mode,
**kwargs)
else:
raise ValueError('unsupported term dtype! (%s)' % dtype)
val *= self.sign
out = (val,)
elif mode == 'weak':
varr = self.get_virtual_variable()
if varr is None:
raise ValueError('no virtual variable in weak mode! (in "%s")'
% self.get_str())
if diff_var is not None:
varc = self.get_variables(as_list=False)[diff_var]
args = self.get_args(**kwargs)
self.check_shapes(*args)
_args = tuple(args) + (mode, term_mode, diff_var)
fargs = self.call_get_fargs(_args, kwargs)
n_elr, n_qpr, dim, n_enr, n_cr = self.get_data_shape(varr)
n_row = n_cr * n_enr
if diff_var is None:
shape = (n_elr, 1, n_row, 1)
else:
n_elc, n_qpc, dim, n_enc, n_cc = self.get_data_shape(varc)
n_col = n_cc * n_enc
shape = (n_elr, 1, n_row, n_col)
if varr.dtype == nm.float64:
vals, status = self.eval_real(shape, fargs, mode, term_mode,
diff_var, **kwargs)
elif varr.dtype == nm.complex128:
vals, status = self.eval_complex(shape, fargs, mode, term_mode,
diff_var, **kwargs)
else:
raise ValueError('unsupported term dtype! (%s)'
% varr.dtype)
if not isinstance(vals, tuple):
vals *= self.sign
iels = self.get_assembling_cells(vals.shape)
else:
vals = (self.sign * vals[0],) + vals[1:]
iels = None
out = (vals, iels)
if goptions['check_term_finiteness']:
assert_(nm.isfinite(out[0]).all(),
msg='"%s" term values not finite!' % self.get_str())
if ret_status:
out = out + (status,)
if len(out) == 1:
out = out[0]
return out
def assemble_to(self, asm_obj, val, iels, mode='vector', diff_var=None):
"""
Assemble the results of term evaluation.
For standard terms, assemble the values in `val` corresponding to
elements/cells `iels` into a vector or a CSR sparse matrix `asm_obj`,
depending on `mode`.
For terms with a dynamic connectivity (e.g. contact terms), in
`'matrix'` mode, return the extra COO sparse matrix instead. The extra
matrix has to be added to the global matrix by the caller. By default,
this is done in :func:`Equations.evaluate()
<sfepy.discrete.equations.Equations.evaluate()>`.
"""
import sfepy.discrete.common.extmods.assemble as asm
vvar = self.get_virtual_variable()
dc_type = self.get_dof_conn_type()
extra = None
if mode == 'vector':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_vector
else:
assert_(asm_obj.dtype == nm.complex128)
assemble = asm.assemble_vector_complex
for ii in range(len(val)):
if not(val[ii].dtype == nm.complex128):
val[ii] = nm.complex128(val[ii])
if not isinstance(val, tuple):
dc = vvar.get_dof_conn(dc_type)
assert_(val.shape[2] == dc.shape[1])
assemble(asm_obj, val, iels, 1.0, dc)
else:
vals, rows, var = val
if var.eq_map is not None:
eq = var.eq_map.eq
rows = eq[rows]
active = (rows >= 0)
vals, rows = vals[active], rows[active]
# Assumes no repeated indices in rows!
asm_obj[rows] += vals
elif mode == 'matrix':
if asm_obj.dtype == nm.float64:
assemble = asm.assemble_matrix
else:
assert_(asm_obj.dtype == nm.complex128)
assemble = asm.assemble_matrix_complex
svar = diff_var
tmd = (asm_obj.data, asm_obj.indptr, asm_obj.indices)
if ((asm_obj.dtype == nm.complex128)
and (val.dtype == nm.float64)):
val = val.astype(nm.complex128)
sign = 1.0
if self.arg_derivatives[svar.name]:
if not self.is_quasistatic or (self.step > 0):
sign *= 1.0 / self.dt
else:
sign = 0.0
if not isinstance(val, tuple):
rdc = vvar.get_dof_conn(dc_type)
is_trace = self.arg_traces[svar.name]
cdc = svar.get_dof_conn(dc_type, is_trace=is_trace)
| assert_(val.shape[2:] == (rdc.shape[1], cdc.shape[1])) | sfepy.base.base.assert_ |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted(term_table.keys()))
raise ValueError(msg)
try:
region = regions[td.region]
except IndexError:
raise KeyError('region "%s" does not exist!' % td.region)
term = Term.from_desc(constructor, td, region, integrals=integrals)
terms.append(term)
return terms
def __init__(self, objs=None):
Container.__init__(self, objs=objs)
self.update_expression()
def insert(self, ii, obj):
Container.insert(self, ii, obj)
self.update_expression()
def append(self, obj):
Container.append(self, obj)
self.update_expression()
def update_expression(self):
self.expression = []
for term in self:
aux = [term.sign, term.name, term.arg_str,
term.integral_name, term.region.name]
self.expression.append(aux)
def __mul__(self, other):
out = Terms()
for name, term in self.iteritems():
out.append(term * other)
return out
def __rmul__(self, other):
return self * other
def __add__(self, other):
if isinstance(other, Term):
out = self.copy()
out.append(other)
elif isinstance(other, Terms):
out = Terms(self._objs + other._objs)
else:
raise ValueError('cannot add Terms with %s!' % other)
return out
def __radd__(self, other):
return self + other
def __sub__(self, other):
if isinstance(other, Term):
out = self + (-other)
elif isinstance(other, Terms):
out = self + (-other)
else:
raise ValueError('cannot subtract Terms with %s!' % other)
return out
def __rsub__(self, other):
return -self + other
def __pos__(self):
return self
def __neg__(self):
return -1.0 * self
def setup(self):
for term in self:
term.setup()
def assign_args(self, variables, materials, user=None):
"""
Assign all term arguments.
"""
for term in self:
term.assign_args(variables, materials, user)
def get_variable_names(self):
out = []
for term in self:
out.extend(term.get_variable_names())
return list(set(out))
def get_material_names(self):
out = []
for term in self:
out.extend(term.get_material_names())
return list(set(out))
def get_user_names(self):
out = []
for term in self:
out.extend(term.get_user_names())
return list(set(out))
class Term(Struct):
name = ''
arg_types = ()
arg_shapes = {}
integration = 'volume'
geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']
@staticmethod
def new(name, integral, region, **kwargs):
from sfepy.terms import term_table
arg_str = _match_args(name)
if arg_str is not None:
name, arg_str = arg_str.groups()
else:
raise ValueError('bad term syntax! (%s)' % name)
if name in term_table:
constructor = term_table[name]
else:
msg = "term '%s' is not in %s" % (name, sorted( | term_table.keys() | sfepy.terms.term_table.keys |
from __future__ import absolute_import
import re
from copy import copy
import numpy as nm
from sfepy.base.base import (as_float_or_complex, get_default, assert_,
Container, Struct, basestr, goptions)
from sfepy.base.compat import in1d
# Used for imports in term files.
from sfepy.terms.extmods import terms
import six
from six.moves import range
from functools import reduce
_match_args = re.compile('^([^\(\}]*)\((.*)\)$').match
_match_virtual = re.compile('^virtual$').match
_match_state = re.compile('^state(_[_a-zA-Z0-9]+)?$').match
_match_parameter = re.compile('^parameter(_[_a-zA-Z0-9]+)?$').match
_match_material = re.compile('^material(_[_a-zA-Z0-9]+)?$').match
_match_material_opt = re.compile('^opt_material(_[_a-zA-Z0-9]+)?$').match
_match_material_root = re.compile('(.+)\.(.*)').match
_match_ts = re.compile('^ts$').match
def get_arg_kinds(arg_types):
"""
Translate `arg_types` of a Term to a canonical form.
Parameters
----------
arg_types : tuple of strings
The term argument types, as given in the `arg_types` attribute.
Returns
-------
arg_kinds : list of strings
The argument kinds - one of 'virtual_variable', 'state_variable',
'parameter_variable', 'opt_material', 'ts', 'user'.
"""
arg_kinds = []
for ii, arg_type in enumerate(arg_types):
if _match_virtual(arg_type):
arg_kinds.append('virtual_variable')
elif _match_state(arg_type):
arg_kinds.append('state_variable')
elif _match_parameter(arg_type):
arg_kinds.append('parameter_variable')
elif _match_material(arg_type):
arg_kinds.append('material')
elif _match_material_opt(arg_type):
arg_kinds.append('opt_material')
if ii > 0:
msg = 'opt_material at position %d, must be at 0!' % ii
raise ValueError(msg)
elif _match_ts(arg_type):
arg_kinds.append('ts')
else:
arg_kinds.append('user')
return arg_kinds
def get_shape_kind(integration):
"""
Get data shape kind for given integration type.
"""
if integration == 'surface':
shape_kind = 'surface'
elif integration in ('volume', 'plate', 'surface_extra'):
shape_kind = 'volume'
elif integration == 'point':
shape_kind = 'point'
else:
raise NotImplementedError('unsupported term integration! (%s)'
% integration)
return shape_kind
def split_complex_args(args):
"""
Split complex arguments to real and imaginary parts.
Returns
-------
newargs : dictionary
Dictionary with lists corresponding to `args` such that each
argument of numpy.complex128 data type is split to its real and
imaginary part. The output depends on the number of complex
arguments in 'args':
- 0: list (key 'r') identical to input one
- 1: two lists with keys 'r', 'i' corresponding to real
and imaginary parts
- 2: output dictionary contains four lists:
- 'r' - real(arg1), real(arg2)
- 'i' - imag(arg1), imag(arg2)
- 'ri' - real(arg1), imag(arg2)
- 'ir' - imag(arg1), real(arg2)
"""
newargs = {}
cai = []
for ii, arg in enumerate(args):
if isinstance(arg, nm.ndarray) and (arg.dtype == nm.complex128):
cai.append(ii)
if len(cai) > 0:
newargs['r'] = list(args[:])
newargs['i'] = list(args[:])
arg1 = cai[0]
newargs['r'][arg1] = args[arg1].real.copy()
newargs['i'][arg1] = args[arg1].imag.copy()
if len(cai) == 2:
arg2 = cai[1]
newargs['r'][arg2] = args[arg2].real.copy()
newargs['i'][arg2] = args[arg2].imag.copy()
newargs['ri'] = list(args[:])
newargs['ir'] = list(args[:])
newargs['ri'][arg1] = newargs['r'][arg1]
newargs['ri'][arg2] = newargs['i'][arg2]
newargs['ir'][arg1] = newargs['i'][arg1]
newargs['ir'][arg2] = newargs['r'][arg2]
elif len(cai) > 2:
raise NotImplementedError('more than 2 complex arguments! (%d)'
% len(cai))
else:
newargs['r'] = args[:]
return newargs
def create_arg_parser():
from pyparsing import Literal, Word, delimitedList, Group, \
StringStart, StringEnd, Optional, nums, alphas, alphanums
inumber = Word("+-" + nums, nums)
history = Optional(Literal('[').suppress() + inumber
+ Literal(']').suppress(), default=0)("history")
history.setParseAction(lambda str, loc, toks: int(toks[0]))
variable = Group(Word(alphas, alphanums + '._') + history)
derivative = Group(Literal('d') + variable\
+ Literal('/').suppress() + Literal('dt'))
trace = Group(Literal('tr') + Literal('(').suppress() + variable \
+ Literal(')').suppress())
generalized_var = derivative | trace | variable
args = StringStart() + delimitedList(generalized_var) + StringEnd()
return args
class ConnInfo(Struct):
def get_region(self, can_trace=True):
if self.is_trace and can_trace:
return self.region.get_mirror_region()
else:
return self.region
def get_region_name(self, can_trace=True):
if self.is_trace and can_trace:
reg = self.region.get_mirror_region()
else:
reg = self.region
if reg is not None:
return reg.name
else:
return None
class Terms(Container):
@staticmethod
def from_desc(term_descs, regions, integrals=None):
"""
Create terms, assign each term its region.
"""
from sfepy.terms import term_table
terms = Terms()
for td in term_descs:
try:
constructor = term_table[td.name]
except:
msg = "term '%s' is not in %s" % (td.name,
sorted( | term_table.keys() | sfepy.terms.term_table.keys |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = | Mesh.from_file(mesh_path) | sfepy.discrete.fem.Mesh.from_file |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = | FEDomain('domain', mesh) | sfepy.discrete.fem.FEDomain |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = | Field.from_args('fu', np.float64, 'vector', omega, approx_order=2) | sfepy.discrete.fem.Field.from_args |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = | FieldVariable('u', 'unknown', field) | sfepy.discrete.FieldVariable |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = | FieldVariable('v', 'test', field, primary_var_name='u') | sfepy.discrete.FieldVariable |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))
f = | Material('f', val=[[0.02], [0.01]]) | sfepy.discrete.Material |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))
f = Material('f', val=[[0.02], [0.01]])
integral = | Integral('i', order=3) | sfepy.discrete.Integral |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))
f = Material('f', val=[[0.02], [0.01]])
integral = Integral('i', order=3)
# %%
from sfepy.terms import Term
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
t2 = Term.new('dw_volume_lvf(f.val, v)',
integral, omega, f=f, v=v)
eq = | Equation('balance', t1 + t2) | sfepy.discrete.Equation |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))
f = Material('f', val=[[0.02], [0.01]])
integral = Integral('i', order=3)
# %%
from sfepy.terms import Term
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
t2 = Term.new('dw_volume_lvf(f.val, v)',
integral, omega, f=f, v=v)
eq = Equation('balance', t1 + t2)
eqs = | Equations([eq]) | sfepy.discrete.Equations |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))
f = Material('f', val=[[0.02], [0.01]])
integral = Integral('i', order=3)
# %%
from sfepy.terms import Term
t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
t2 = Term.new('dw_volume_lvf(f.val, v)',
integral, omega, f=f, v=v)
eq = Equation('balance', t1 + t2)
eqs = Equations([eq])
#%%
pb = | Problem('elasticity', equations=eqs) | sfepy.discrete.Problem |
#%%
import numpy as np
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh_path = 'C:/Users/lzy71/miniconda3/envs/lego/lib/site-packages/sfepy/meshes/2d/rectangle_tri.mesh'
#%%
mesh = Mesh.from_file(mesh_path)
domain = FEDomain('domain', mesh)
min_x, max_x = domain.get_mesh_bounding_box()[:, 0]
eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
# %%
from sfepy.discrete import (
FieldVariable, Material, Integral, Function,
Equation, Equations, Problem
)
field = Field.from_args('fu', np.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
# %%
from sfepy.mechanics.matcoefs import stiffness_from_lame
m = Material('m', D= | stiffness_from_lame(dim=2, lam=1.0, mu=1.0) | sfepy.mechanics.matcoefs.stiffness_from_lame |
from __future__ import absolute_import
import numpy as nm
from sfepy.base.base import load_classes, Struct
from sfepy import get_paths
def transform_basis(transform, bf):
"""
Transform a basis `bf` using `transform` array of matrices.
"""
if bf.ndim == 3:
nbf = nm.einsum('cij,qdj->cqdi', transform, bf, order='C')
elif bf.ndim == 4:
if bf.shape[0] == 1:
nbf = nm.einsum('cij,qdj->cqdi', transform, bf[0], order='C')
else:
nbf = nm.einsum('cij,cqdj->cqdi', transform, bf, order='C')
# Note: the 2nd derivatives are not supported here.
# Workaround for NumPy 1.14.0 - order is ignored(?)
nbf = nm.ascontiguousarray(nbf)
return nbf
class PolySpace(Struct):
"""Abstract polynomial space class."""
_all = None
keys = {
(0, 1) : 'simplex',
(1, 2) : 'simplex',
(2, 3) : 'simplex',
(3, 4) : 'simplex',
(2, 4) : 'tensor_product',
(3, 8) : 'tensor_product',
}
@staticmethod
def any_from_args(name, geometry, order, base='lagrange',
force_bubble=False):
"""
Construct a particular polynomial space classes according to the
arguments passed in.
"""
if name is None:
name = PolySpace.suggest_name(geometry, order, base, force_bubble)
if PolySpace._all is None:
ps_files = | get_paths('sfepy/discrete/fem/poly_spaces.py') | sfepy.get_paths |
from __future__ import absolute_import
import numpy as nm
from sfepy.base.base import load_classes, Struct
from sfepy import get_paths
def transform_basis(transform, bf):
"""
Transform a basis `bf` using `transform` array of matrices.
"""
if bf.ndim == 3:
nbf = nm.einsum('cij,qdj->cqdi', transform, bf, order='C')
elif bf.ndim == 4:
if bf.shape[0] == 1:
nbf = nm.einsum('cij,qdj->cqdi', transform, bf[0], order='C')
else:
nbf = nm.einsum('cij,cqdj->cqdi', transform, bf, order='C')
# Note: the 2nd derivatives are not supported here.
# Workaround for NumPy 1.14.0 - order is ignored(?)
nbf = nm.ascontiguousarray(nbf)
return nbf
class PolySpace(Struct):
"""Abstract polynomial space class."""
_all = None
keys = {
(0, 1) : 'simplex',
(1, 2) : 'simplex',
(2, 3) : 'simplex',
(3, 4) : 'simplex',
(2, 4) : 'tensor_product',
(3, 8) : 'tensor_product',
}
@staticmethod
def any_from_args(name, geometry, order, base='lagrange',
force_bubble=False):
"""
Construct a particular polynomial space classes according to the
arguments passed in.
"""
if name is None:
name = PolySpace.suggest_name(geometry, order, base, force_bubble)
if PolySpace._all is None:
ps_files = get_paths('sfepy/discrete/fem/poly_spaces.py')
ps_files += | get_paths('sfepy/discrete/dg/poly_spaces.py') | sfepy.get_paths |
# This example implements homogenization of porous structures undergoing finite strains.
#
# largedef_porous_mac.py - problem at (global) macroscopic level
# largedef_porous_mic.py - local subproblems, homogenized coefficients
#
# The mathematical model and numerical results are described in:
#
# <NAME>., <NAME>.
# Homogenization of large deforming fluid-saturated porous structures
# https://arxiv.org/abs/2012.03730
#
# Run simulation:
#
# ./simple.py example_largedef_porous-1/largedef_porous_mac.py
#
# The results are stored in `example_largedef_porous-1/results` directory.
#
import numpy as nm
import six
import os.path as osp
from sfepy import data_dir
from sfepy.base.base import Struct, output, debug
from sfepy.terms.terms_hyperelastic_ul import HyperElasticULFamilyData
from sfepy.homogenization.micmac import get_homog_coefs_nonlinear
import sfepy.linalg as la
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.state import State
wdir = osp.dirname(__file__)
hyperelastic_data = {
'update_materials': True,
'state': {'u': None, 'du': None,
'p': None, 'dp': None},
'mapping0': None,
'coors0': None,
'macro_data': None,
}
def post_process(out, pb, state, extend=False):
ts = hyperelastic_data['ts']
if isinstance(state, dict):
pass
else:
stress = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.S, u)',
mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data',
mode='cell',
data=stress)
ret_stress = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.Q, u)',
mode='el_avg')
out['retardation_stress'] = Struct(name='output_data',
mode='cell',
data=ret_stress)
strain = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.E, u)',
mode='el_avg')
out['green_strain'] = Struct(name='output_data',
mode='cell',
data=strain)
he_state = hyperelastic_data['state']
for ch in pb.conf.chs:
plab = 'p%d' % ch
out['p0_%d' % ch] = Struct(name='output_data',
mode='vertex',
data=he_state[plab][:, nm.newaxis])
dvel = pb.evaluate('ev_diffusion_velocity.i.Omega(solid.C%d, %s)' % (ch, plab),
mode='el_avg')
out['w%d' % ch] = Struct(name='output_data',
mode='cell',
data=dvel)
out['u0'] = Struct(name='output_data',
mode='vertex',
data=he_state['u'])
return out
def homog_macro_map(ccoors, macro, nel):
nqpe = ccoors.shape[0] // nel
macro_ = {k: nm.sum(v.reshape((nel, nqpe) + v.shape[1:]), axis=1) / nqpe
for k, v in macro.items()}
macro_['recovery_idxs'] = []
ccoors_ = nm.sum(ccoors.reshape((nel, nqpe) + ccoors.shape[1:]), axis=1) / nqpe
return ccoors_, macro_
def homog_macro_remap(homcf, ncoor):
nqpe = ncoor // homcf['Volume_total'].shape[0]
homcf_ = {k: nm.repeat(v, nqpe, axis=0) for k, v in homcf.items()
if not k == 'Volume_total'}
return homcf_
def get_homog_mat(ts, coors, mode, term=None, problem=None, **kwargs):
hyperela = hyperelastic_data
ts = hyperela['ts']
output('get_homog_mat: mode=%s, update=%s'\
% (mode, hyperela['update_materials']))
if not mode == 'qp':
return
if not hyperela['update_materials']:
out = hyperela['homog_mat']
return {k: nm.array(v) for k, v in six.iteritems(out)}
dim = problem.domain.mesh.dim
nqp = coors.shape[0]
state_u = problem.equations.variables['u']
if len(state_u.field.mappings0) == 0:
state_u.field.get_mapping(term.region, term.integral,
term.integration)
state_u.field.save_mappings()
state_u.field.clear_mappings()
state_u.set_data(hyperela['state']['u'].ravel()) # + state_u.data[-1][state_u.indx]
mtx_f = problem.evaluate('ev_def_grad.i.Omega(u)',
mode='qp').reshape(-1, dim, dim)
# relative deformation gradient
if hasattr(problem, 'mtx_f_prev'):
rel_mtx_f = la.dot_sequences(mtx_f, nm.linalg.inv(problem.mtx_f_prev),
'AB')
else:
rel_mtx_f = mtx_f
problem.mtx_f_prev = mtx_f.copy()
macro_data = {
'mtx_e_rel': rel_mtx_f - nm.eye(dim), # relative macro strain
}
for ch in problem.conf.chs:
plab = 'p%d' % ch
state_p = problem.equations.variables[plab]
state_p.set_data(hyperela['state'][plab])
macro_data['p%d_0' % ch] = \
problem.evaluate('ev_volume_integrate.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, 1, 1)
macro_data['gp%d_0' % ch] = \
problem.evaluate('ev_grad.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, dim, 1)
state_p.set_data(hyperela['state']['d' + plab])
macro_data['dp%d_0' % ch] = \
problem.evaluate('ev_volume_integrate.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, 1, 1)
macro_data['gdp%d_0' % ch] = \
problem.evaluate('ev_grad.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, dim, 1)
nel = term.region.entities[-1].shape[0]
ccoors0, macro_data0 = homog_macro_map(coors, macro_data, nel)
macro_data0['macro_ccoor'] = ccoors0
out0 = get_homog_coefs_nonlinear(ts, ccoors0, mode, macro_data0,
term=term, problem=problem,
iteration=ts.step, **kwargs)
out0['C1'] += nm.eye(2) * 1e-12 # ! auxiliary permeability
out0['C2'] += nm.eye(2) * 1e-12 # ! auxiliary permeability
out = homog_macro_remap(out0, nqp)
# Green strain
out['E'] = 0.5 * (la.dot_sequences(mtx_f, mtx_f, 'ATB') - nm.eye(dim))
for ch in problem.conf.chs:
out['B%d' % ch] = out['B%d' % ch].reshape((nqp, dim, dim))
out['Q'] = out['Q'].reshape((nqp, dim, dim))
hyperela['time'] = ts.step
hyperela['homog_mat'] = \
{k: nm.array(v) for k, v in six.iteritems(out)}
hyperela['update_materials'] = False
hyperela['macro_data'] = macro_data
return out
def incremental_algorithm(pb):
hyperela = hyperelastic_data
chs = pb.conf.chs
ts = pb.conf.ts
hyperela['ts'] = ts
hyperela['ofn_trunk'] = pb.ofn_trunk + '_%03d'
pb.domain.mesh.coors_act = pb.domain.mesh.coors.copy()
pbvars = pb.get_variables()
he_state = hyperela['state']
out = []
out_data ={}
coors0 = pbvars['u'].field.get_coor()
he_state['coors0'] = coors0.copy()
he_state['u'] = nm.zeros_like(coors0)
he_state['du'] = nm.zeros_like(coors0)
for ch in chs:
plab = 'p%d' % ch
press0 = pbvars[plab].field.get_coor()[:, 0].squeeze()
he_state[plab] = nm.zeros_like(press0)
he_state['d' + plab] = nm.zeros_like(press0)
for step, time in ts:
print('>>> step %d (%e):' % (step, time))
hyperela['update_materials'] = True
pb.ofn_trunk = hyperela['ofn_trunk'] % step
yield pb, out
state = out[-1][1]
result = state.get_parts()
du = result['u']
he_state['u'] += du.reshape(he_state['du'].shape)
he_state['du'][:] = du.reshape(he_state['du'].shape)
pb.set_mesh_coors(he_state['u'] + he_state['coors0'],
update_fields=True, actual=True, clear_all=False)
for ch in chs:
plab = 'p%d' % ch
dp = result[plab]
he_state[plab] += dp
he_state['d' + plab][:] = dp
out_data = post_process(out_data, pb, state, extend=False)
filename = pb.get_output_name()
pb.save_state(filename, out=out_data)
yield None
print('<<< step %d finished' % step)
def move(ts, coor, problem=None, ramp=0.4, **kwargs):
ts = problem.conf.ts
nrs = round(ts.n_step * ramp)
switch = 1 if (ts.step <= nrs) and (ts.step > 0) else 0
displ = nm.ones((coor.shape[0],)) * problem.conf.move_val / nrs * switch
return displ
def define():
chs = [1, 2]
ts = | TimeStepper(0, 0.15, n_step=30) | sfepy.solvers.ts.TimeStepper |
# This example implements homogenization of porous structures undergoing finite strains.
#
# largedef_porous_mac.py - problem at (global) macroscopic level
# largedef_porous_mic.py - local subproblems, homogenized coefficients
#
# The mathematical model and numerical results are described in:
#
# <NAME>., <NAME>.
# Homogenization of large deforming fluid-saturated porous structures
# https://arxiv.org/abs/2012.03730
#
# Run simulation:
#
# ./simple.py example_largedef_porous-1/largedef_porous_mac.py
#
# The results are stored in `example_largedef_porous-1/results` directory.
#
import numpy as nm
import six
import os.path as osp
from sfepy import data_dir
from sfepy.base.base import Struct, output, debug
from sfepy.terms.terms_hyperelastic_ul import HyperElasticULFamilyData
from sfepy.homogenization.micmac import get_homog_coefs_nonlinear
import sfepy.linalg as la
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.state import State
wdir = osp.dirname(__file__)
hyperelastic_data = {
'update_materials': True,
'state': {'u': None, 'du': None,
'p': None, 'dp': None},
'mapping0': None,
'coors0': None,
'macro_data': None,
}
def post_process(out, pb, state, extend=False):
ts = hyperelastic_data['ts']
if isinstance(state, dict):
pass
else:
stress = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.S, u)',
mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data',
mode='cell',
data=stress)
ret_stress = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.Q, u)',
mode='el_avg')
out['retardation_stress'] = Struct(name='output_data',
mode='cell',
data=ret_stress)
strain = pb.evaluate('ev_volume_integrate_mat.i.Omega(solid.E, u)',
mode='el_avg')
out['green_strain'] = Struct(name='output_data',
mode='cell',
data=strain)
he_state = hyperelastic_data['state']
for ch in pb.conf.chs:
plab = 'p%d' % ch
out['p0_%d' % ch] = Struct(name='output_data',
mode='vertex',
data=he_state[plab][:, nm.newaxis])
dvel = pb.evaluate('ev_diffusion_velocity.i.Omega(solid.C%d, %s)' % (ch, plab),
mode='el_avg')
out['w%d' % ch] = Struct(name='output_data',
mode='cell',
data=dvel)
out['u0'] = Struct(name='output_data',
mode='vertex',
data=he_state['u'])
return out
def homog_macro_map(ccoors, macro, nel):
nqpe = ccoors.shape[0] // nel
macro_ = {k: nm.sum(v.reshape((nel, nqpe) + v.shape[1:]), axis=1) / nqpe
for k, v in macro.items()}
macro_['recovery_idxs'] = []
ccoors_ = nm.sum(ccoors.reshape((nel, nqpe) + ccoors.shape[1:]), axis=1) / nqpe
return ccoors_, macro_
def homog_macro_remap(homcf, ncoor):
nqpe = ncoor // homcf['Volume_total'].shape[0]
homcf_ = {k: nm.repeat(v, nqpe, axis=0) for k, v in homcf.items()
if not k == 'Volume_total'}
return homcf_
def get_homog_mat(ts, coors, mode, term=None, problem=None, **kwargs):
hyperela = hyperelastic_data
ts = hyperela['ts']
output('get_homog_mat: mode=%s, update=%s'\
% (mode, hyperela['update_materials']))
if not mode == 'qp':
return
if not hyperela['update_materials']:
out = hyperela['homog_mat']
return {k: nm.array(v) for k, v in six.iteritems(out)}
dim = problem.domain.mesh.dim
nqp = coors.shape[0]
state_u = problem.equations.variables['u']
if len(state_u.field.mappings0) == 0:
state_u.field.get_mapping(term.region, term.integral,
term.integration)
state_u.field.save_mappings()
state_u.field.clear_mappings()
state_u.set_data(hyperela['state']['u'].ravel()) # + state_u.data[-1][state_u.indx]
mtx_f = problem.evaluate('ev_def_grad.i.Omega(u)',
mode='qp').reshape(-1, dim, dim)
# relative deformation gradient
if hasattr(problem, 'mtx_f_prev'):
rel_mtx_f = la.dot_sequences(mtx_f, nm.linalg.inv(problem.mtx_f_prev),
'AB')
else:
rel_mtx_f = mtx_f
problem.mtx_f_prev = mtx_f.copy()
macro_data = {
'mtx_e_rel': rel_mtx_f - nm.eye(dim), # relative macro strain
}
for ch in problem.conf.chs:
plab = 'p%d' % ch
state_p = problem.equations.variables[plab]
state_p.set_data(hyperela['state'][plab])
macro_data['p%d_0' % ch] = \
problem.evaluate('ev_volume_integrate.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, 1, 1)
macro_data['gp%d_0' % ch] = \
problem.evaluate('ev_grad.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, dim, 1)
state_p.set_data(hyperela['state']['d' + plab])
macro_data['dp%d_0' % ch] = \
problem.evaluate('ev_volume_integrate.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, 1, 1)
macro_data['gdp%d_0' % ch] = \
problem.evaluate('ev_grad.i.Omega(p%d)' % ch,
mode='qp').reshape(-1, dim, 1)
nel = term.region.entities[-1].shape[0]
ccoors0, macro_data0 = homog_macro_map(coors, macro_data, nel)
macro_data0['macro_ccoor'] = ccoors0
out0 = get_homog_coefs_nonlinear(ts, ccoors0, mode, macro_data0,
term=term, problem=problem,
iteration=ts.step, **kwargs)
out0['C1'] += nm.eye(2) * 1e-12 # ! auxiliary permeability
out0['C2'] += nm.eye(2) * 1e-12 # ! auxiliary permeability
out = homog_macro_remap(out0, nqp)
# Green strain
out['E'] = 0.5 * ( | la.dot_sequences(mtx_f, mtx_f, 'ATB') | sfepy.linalg.dot_sequences |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = | FEDomain('d1', m1) | sfepy.discrete.fem.FEDomain |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = | FEDomain('d2', m2) | sfepy.discrete.fem.FEDomain |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf( | transform_variables(variables) | sfepy.base.conf.transform_variables |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf( | transform_variables(variables) | sfepy.base.conf.transform_variables |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = | Mesh('source mesh', data_dir + '/meshes/3d/block.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = | Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = | FEDomain('d1', m1) | sfepy.discrete.fem.FEDomain |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = | FEDomain('d2', m2) | sfepy.discrete.fem.FEDomain |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = | Mesh('source mesh', data_dir + '/meshes/3d/block.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
bbox = mesh.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1])
variables = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
domain = | FEDomain('domain', mesh) | sfepy.discrete.fem.FEDomain |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
bbox = mesh.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1])
variables = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
field = Field.from_args('scalar_tp', nm.float64, 1, omega,
approx_order=1)
ff = {field.name : field}
vv = Variables.from_conf(transform_variables(variables), ff)
u = vv['u']
u.set_from_mesh_vertices(data)
integral = | Integral('i', order=2) | sfepy.discrete.Integral |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
bbox = mesh.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1])
variables = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
field = Field.from_args('scalar_tp', nm.float64, 1, omega,
approx_order=1)
ff = {field.name : field}
vv = Variables.from_conf(transform_variables(variables), ff)
u = vv['u']
u.set_from_mesh_vertices(data)
integral = Integral('i', order=2)
term = | Term.new('ev_volume_integrate(u)', integral, omega, u=u) | sfepy.terms.Term.new |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
bbox = mesh.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1])
variables = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
field = Field.from_args('scalar_tp', nm.float64, 1, omega,
approx_order=1)
ff = {field.name : field}
vv = Variables.from_conf(transform_variables(variables), ff)
u = vv['u']
u.set_from_mesh_vertices(data)
integral = Integral('i', order=2)
term = Term.new('ev_volume_integrate(u)', integral, omega, u=u)
term.setup()
val1, _ = term.evaluate(mode='qp')
val1 = val1.ravel()
qps = | get_physical_qps(omega, integral) | sfepy.discrete.common.mappings.get_physical_qps |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : | Mesh('original mesh', data_dir + '/meshes/3d/block.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : | Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf( | transform_variables(variables1) | sfepy.base.conf.transform_variables |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf( | transform_variables(variables2) | sfepy.base.conf.transform_variables |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : | Mesh('original mesh', data_dir + '/meshes/3d/block.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : | Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh') | sfepy.discrete.fem.Mesh |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh')
m2.coors *= 2.0
bbox = m1.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1])
variables1 = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
variables2 = {
'u' : ('unknown field', 'scalar_si', 0),
'v' : ('test field', 'scalar_si', 'u'),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1,
approx_order=1)
ff1 = {field1.name : field1}
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2,
approx_order=0)
ff2 = {field2.name : field2}
vv1 = Variables.from_conf(transform_variables(variables1), ff1)
u1 = vv1['u']
u1.set_from_mesh_vertices(data)
vv2 = Variables.from_conf(transform_variables(variables2), ff2)
u2 = vv2['u']
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.1)
fname = in_dir(self.options.out_dir)
u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk'))
u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk'))
return True
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh')
bbox = mesh.get_bounding_box()
dd = bbox[1,:] - bbox[0,:]
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \
* nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1])
variables = {
'u' : ('unknown field', 'scalar_tp', 0),
'v' : ('test field', 'scalar_tp', 'u'),
}
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
field = Field.from_args('scalar_tp', nm.float64, 1, omega,
approx_order=1)
ff = {field.name : field}
vv = Variables.from_conf( | transform_variables(variables) | sfepy.base.conf.transform_variables |
import os.path as op
import numpy as nm
from sfepy.base.conf import transform_variables
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x)
def gen_datas(meshes):
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
return datas
def do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
fields = {
'scalar_si' : ((1,1), 'Omega', 2),
'vector_si' : ((3,1), 'Omega', 2),
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
d1 = FEDomain('d1', m1)
omega1 = d1.create_region('Omega', 'all')
f = fields[field_name]
field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]],
approx_order=f[2])
ff = {field1.name : field1}
vv = Variables.from_conf(transform_variables(variables), ff)
u1 = vv['u']
u1.set_from_mesh_vertices(data)
d2 = FEDomain('d2', m2)
omega2 = d2.create_region('Omega', 'all')
field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]],
approx_order=f[2])
ff2 = {field2.name : field2}
vv2 = Variables.from_conf(transform_variables(variables), ff2)
u2 = vv2['u']
if not force:
# Performs interpolation, if other field differs from self.field
# or, in particular, is defined on a different mesh.
u2.set_from_other(u1, strategy='interpolation', close_limit=0.5)
else:
coors = u2.field.get_coor()
vals = u1.evaluate_at(coors, close_limit=0.5)
u2.set_data(vals)
return u1, u2
class Test(TestCommon):
@staticmethod
def from_conf(conf, options):
test = Test(conf=conf, options=options)
return test
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = | make_axis_rotation_matrix([0, 1, 0], angle) | sfepy.linalg.make_axis_rotation_matrix |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = | plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False) | sfepy.postprocess.plot_dofs.plot_mesh |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = | plot_global_dofs(ax, gel.coors, [gel.conn], show=show) | sfepy.postprocess.plot_dofs.plot_global_dofs |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = plot_global_dofs(ax, gel.coors, [gel.conn], show=show)
return ax
def plot_edges(ax, gel, length, show=False):
"""
Plot edges of a geometry element as numbered arrows.
"""
dim = gel.dim
ax = | _get_axes(ax, dim) | sfepy.postprocess.plot_dofs._get_axes |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = plot_global_dofs(ax, gel.coors, [gel.conn], show=show)
return ax
def plot_edges(ax, gel, length, show=False):
"""
Plot edges of a geometry element as numbered arrows.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
l2 = 0.5 * length
for ii, edge in enumerate(gel.edges):
cc = gel.coors[edge]
centre = 0.5 * cc.sum(axis=0)
vdir = (cc - centre)
normalize_vectors(vdir)
cc = l2 * vdir + centre
draw_arrow(ax, cc, length=0.3*length, linewidth=3, color='b')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='b', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='b', fontsize=10, weight='light')
return ax
def plot_faces(ax, gel, radius, n_point, show=False):
"""
Plot faces of a 3D geometry element as numbered oriented arcs. An arc
centre corresponds to the first node of a face. It points from the first
edge towards the last edge of the face.
"""
dim = gel.dim
ax = | _get_axes(ax, dim) | sfepy.postprocess.plot_dofs._get_axes |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = plot_global_dofs(ax, gel.coors, [gel.conn], show=show)
return ax
def plot_edges(ax, gel, length, show=False):
"""
Plot edges of a geometry element as numbered arrows.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
l2 = 0.5 * length
for ii, edge in enumerate(gel.edges):
cc = gel.coors[edge]
centre = 0.5 * cc.sum(axis=0)
vdir = (cc - centre)
normalize_vectors(vdir)
cc = l2 * vdir + centre
draw_arrow(ax, cc, length=0.3*length, linewidth=3, color='b')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='b', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='b', fontsize=10, weight='light')
return ax
def plot_faces(ax, gel, radius, n_point, show=False):
"""
Plot faces of a 3D geometry element as numbered oriented arcs. An arc
centre corresponds to the first node of a face. It points from the first
edge towards the last edge of the face.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
if dim < 3: return ax
for ii, face in enumerate(gel.faces):
cc = gel.coors[face]
t1 = cc[1, :] - cc[0, :]
t2 = cc[-1, :] - cc[0, :]
n = nm.cross(t1, t2)
nt1 = nm.linalg.norm(t1)
nt2 = nm.linalg.norm(t2)
angle = nm.arccos(nm.dot(t1, t2) / (nt1 * nt2))
da = angle / (n_point - 1)
mtx = make_axis_rotation_matrix(n, da)
rt = cc[0] + radius * t1 / nt1
coors = [rt]
for ip in range(n_point - 1):
rt = nm.dot(mtx.T, (rt - cc[0])) + cc[0]
coors.append(rt)
coors = nm.array(coors, dtype=nm.float64)
centre = coors.sum(axis=0) / coors.shape[0]
draw_arrow(ax, coors, length=0.3*radius, linewidth=3, color='r')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='r', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='r', fontsize=10, weight='light')
return ax
def draw_arrow(ax, coors, angle=20.0, length=0.3, **kwargs):
"""
Draw a line ended with an arrow head, in 2D or 3D.
"""
color = kwargs.get('color', 'b')
c0 = coors[-2]
c1 = coors[-1]
vd = c1 - c0
nvd = nm.linalg.norm(vd)
vd /= nvd
c0 = c1 - length * vd
ps = | get_perpendiculars(vd) | sfepy.linalg.get_perpendiculars |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = plot_global_dofs(ax, gel.coors, [gel.conn], show=show)
return ax
def plot_edges(ax, gel, length, show=False):
"""
Plot edges of a geometry element as numbered arrows.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
l2 = 0.5 * length
for ii, edge in enumerate(gel.edges):
cc = gel.coors[edge]
centre = 0.5 * cc.sum(axis=0)
vdir = (cc - centre)
normalize_vectors(vdir)
cc = l2 * vdir + centre
draw_arrow(ax, cc, length=0.3*length, linewidth=3, color='b')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='b', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='b', fontsize=10, weight='light')
return ax
def plot_faces(ax, gel, radius, n_point, show=False):
"""
Plot faces of a 3D geometry element as numbered oriented arcs. An arc
centre corresponds to the first node of a face. It points from the first
edge towards the last edge of the face.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
if dim < 3: return ax
for ii, face in enumerate(gel.faces):
cc = gel.coors[face]
t1 = cc[1, :] - cc[0, :]
t2 = cc[-1, :] - cc[0, :]
n = nm.cross(t1, t2)
nt1 = nm.linalg.norm(t1)
nt2 = nm.linalg.norm(t2)
angle = nm.arccos(nm.dot(t1, t2) / (nt1 * nt2))
da = angle / (n_point - 1)
mtx = make_axis_rotation_matrix(n, da)
rt = cc[0] + radius * t1 / nt1
coors = [rt]
for ip in range(n_point - 1):
rt = nm.dot(mtx.T, (rt - cc[0])) + cc[0]
coors.append(rt)
coors = nm.array(coors, dtype=nm.float64)
centre = coors.sum(axis=0) / coors.shape[0]
draw_arrow(ax, coors, length=0.3*radius, linewidth=3, color='r')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='r', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='r', fontsize=10, weight='light')
return ax
def draw_arrow(ax, coors, angle=20.0, length=0.3, **kwargs):
"""
Draw a line ended with an arrow head, in 2D or 3D.
"""
color = kwargs.get('color', 'b')
c0 = coors[-2]
c1 = coors[-1]
vd = c1 - c0
nvd = nm.linalg.norm(vd)
vd /= nvd
c0 = c1 - length * vd
ps = get_perpendiculars(vd)
rangle = nm.deg2rad(min(angle, 60.0))
plength = length * nm.arctan(rangle)
if coors.shape[1] == 2:
from matplotlib.patches import Polygon
cx, cy = coors[:, 0], coors[:, 1]
ax.plot(cx, cy, **kwargs)
p0 = c0 + plength * ps
p1 = c0 - plength * ps
pol = Polygon([p0, p1, c1], color=color)
ax.add_artist(pol)
else:
import mpl_toolkits.mplot3d as plt3
cx, cy, cz = coors[:, 0], coors[:, 1], coors[:, 2]
ax.plot(cx, cy, cz, **kwargs)
p00 = c0 + plength * ps[0]
p01 = c0 - plength * ps[0]
p10 = c0 + plength * ps[1]
p11 = c0 - plength * ps[1]
arr = plt3.art3d.Poly3DCollection([[p00, p01, c1],
[p10, p11, c1]], color=color)
ax.add_collection3d(arr)
if __name__ == '__main__':
from sfepy.discrete.fem.geometry_element import GeometryElement, geometry_data
for key, gd in | geometry_data.iteritems() | sfepy.discrete.fem.geometry_element.geometry_data.iteritems |
"""
Functions to visualize the geometry elements and numbering and orientation of
their facets (edges and faces).
The standard geometry elements can be plotted by running::
$ python sfepy/postprocess/plot_facets.py
"""
import numpy as nm
import matplotlib.pyplot as plt
from sfepy.linalg import (get_perpendiculars, normalize_vectors,
make_axis_rotation_matrix)
from sfepy.postprocess.plot_dofs import _get_axes, plot_mesh, plot_global_dofs
def plot_geometry(ax, gel, show=False):
"""
Plot a geometry element as a wireframe.
"""
ax = plot_mesh(ax, gel.coors, [gel.conn], gel.edges, show=False)
ax = plot_global_dofs(ax, gel.coors, [gel.conn], show=show)
return ax
def plot_edges(ax, gel, length, show=False):
"""
Plot edges of a geometry element as numbered arrows.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
l2 = 0.5 * length
for ii, edge in enumerate(gel.edges):
cc = gel.coors[edge]
centre = 0.5 * cc.sum(axis=0)
vdir = (cc - centre)
| normalize_vectors(vdir) | sfepy.linalg.normalize_vectors |