File size: 17,285 Bytes
f121890
5d45184
f121890
e6e9684
f121890
1366f26
5d45184
1e6e599
5d45184
e6e9684
 
32ed837
 
1e6e599
59575d2
20d40ec
 
 
ddb4a97
20d40ec
00b3ddd
1e6e599
20d40ec
1e6e599
 
00b3ddd
1e6e599
 
00b3ddd
1e6e599
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
f121890
2dd66b7
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
b99c699
2dd66b7
1fcdab3
1e6e599
 
1fcdab3
5d45184
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1fcdab3
5d45184
 
 
 
 
 
 
1fcdab3
f121890
 
 
 
 
 
e6e9684
 
32ed837
 
 
 
 
ddb4a97
 
 
 
 
 
 
32ed837
 
 
 
 
 
ddb4a97
 
32ed837
ddb4a97
32ed837
 
 
 
 
 
 
 
ddb4a97
 
 
 
 
32ed837
ddb4a97
 
32ed837
 
 
 
 
 
 
 
 
ddb4a97
32ed837
 
 
 
 
 
ddb4a97
 
32ed837
 
 
 
 
 
ddb4a97
e6e9684
 
 
 
ddb4a97
b99c699
 
 
 
 
 
 
 
 
 
 
 
 
 
 
32ed837
b99c699
32ed837
b99c699
 
 
 
 
 
 
 
e6e9684
 
 
32ed837
e6e9684
 
 
32ed837
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2dd66b7
32ed837
 
 
 
 
 
 
 
2dd66b7
e6e9684
 
32ed837
 
 
 
 
 
 
e6e9684
ddb4a97
1366f26
 
 
 
 
 
 
 
f121890
b99c699
2dd66b7
 
 
 
 
 
 
 
 
 
 
 
 
 
ddb4a97
2dd66b7
 
 
 
 
 
 
 
f121890
 
 
2dd66b7
a91474f
2dd66b7
a91474f
 
 
 
 
2dd66b7
 
 
 
 
f121890
 
 
 
e6e9684
 
 
 
ddb4a97
2dd66b7
32ed837
f121890
32ed837
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2dd66b7
20d40ec
e6e9684
 
 
 
 
 
1e6e599
 
f121890
59575d2
 
f121890
20d40ec
f121890
 
 
2dd66b7
 
1e6e599
 
 
ce5365e
 
 
59575d2
 
 
ce5365e
 
 
 
59575d2
f121890
 
 
e6e9684
 
 
 
32ed837
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
e6e9684
32ed837
e6e9684
 
 
 
 
32ed837
 
 
e6e9684
 
f121890
 
 
 
32ed837
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
f121890
 
 
e6e9684
3dde8a0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
import os
import re

import crystal_toolkit.components as ctc
import dash
import dash_mp_components as dmp
import numpy as np
import pandas as pd
import periodictable
from crystal_toolkit.settings import SETTINGS
from dash import dcc, html
from dash.dependencies import Input, Output, State
from dash_breakpoints import WindowBreakpoints
from datasets import concatenate_datasets, load_dataset
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pymatgen.core import Structure

HF_TOKEN = os.environ.get("HF_TOKEN")
top_k = 500

subsets = ["compatible_pbe", "compatible_pbesol", "compatible_scan", "non_compatible"]

# Load only the train split of the dataset

datasets = []
for subset in subsets:
    dataset = load_dataset(
        "LeMaterial/leMat-Bulk",
        subset,
        token=HF_TOKEN,
        columns=[
            "lattice_vectors",
            "species_at_sites",
            "cartesian_site_positions",
            "energy",
            # "energy_corrected", # not yet available in LeMat-Bulk
            "immutable_id",
            "elements",
            "functional",
            "stress_tensor",
            "magnetic_moments",
            "forces",
            # "band_gap_direct", #future release
            # "band_gap_indirect", #future release
            "dos_ef",
            # "charges", #future release
            "functional",
            "chemical_formula_reduced",
            "chemical_formula_descriptive",
            "total_magnetization",
        ],
    )
    datasets.append(dataset)

display_columns = [
    "chemical_formula_descriptive",
    "functional",
    "immutable_id",
    "energy",
]
display_names = {
    "chemical_formula_descriptive": "Formula",
    "functional": "Functional",
    "immutable_id": "Material ID",
    "energy": "Energy (eV)",
}

mapping_table_idx_dataset_idx = {}

map_periodic_table = {v.symbol: k for k, v in enumerate(periodictable.elements)}
n_elements = len(map_periodic_table)

# Preprocessing step to create an index for the dataset
# df = pd.concat([x.to_pandas() for x in datasets])
dataset = concatenate_datasets(datasets)
train_df = dataset.select_columns(["chemical_formula_descriptive"]).to_pandas()

pattern = re.compile(r"(?P<element>[A-Z][a-z]?)(?P<count>\d*)")
extracted = train_df["chemical_formula_descriptive"].str.extractall(pattern)
extracted["count"] = extracted["count"].replace("", "1").astype(int)

wide_df = extracted.reset_index().pivot_table(  # Move index to columns for pivoting
    index="level_0",  # original row index
    columns="element",
    values="count",
    aggfunc="sum",
    fill_value=0,
)

all_elements = [el.symbol for el in periodictable.elements]  # full element list
wide_df = wide_df.reindex(columns=all_elements, fill_value=0)


dataset_index = wide_df.values

dataset_index = dataset_index / np.sum(dataset_index, axis=1)[:, None]
dataset_index = (
    dataset_index / np.linalg.norm(dataset_index, axis=1)[:, None]
)  # Normalize vectors

del train_df, extracted, wide_df

# Initialize the Dash app
app = dash.Dash(__name__, assets_folder=SETTINGS.ASSETS_PATH)
server = app.server  # Expose the server for deployment

# Define the app layout
layout = html.Div(
    [
        WindowBreakpoints(
            id="breakpoints",
            widthBreakpointThresholdsPx=[800, 1200],
            widthBreakpointNames=["sm", "md", "lg"],
        ),
        html.H1(
            html.B("Interactive Crystal Viewer"),
            style={"textAlign": "center", "margin-top": "20px"},
        ),
        html.Div(
            [
                html.Div(
                    [
                        html.Div(
                            "Search a material to display its structure and properties",
                            style={"textAlign": "center"},
                        ),
                    ],
                    id="structure-container",
                    style={
                        "width": "44%",
                        "verticalAlign": "top",
                        "boxShadow": "0px 4px 8px rgba(0, 0, 0, 0.1)",
                        "borderRadius": "10px",
                        "backgroundColor": "#f9f9f9",
                        "padding": "20px",
                        "textAlign": "center",
                        "display": "flex",
                        "justifyContent": "center",
                        "alignItems": "center",
                    },
                ),
                html.Div(
                    id="properties-container",
                    style={
                        "width": "55%",
                        "paddingLeft": "4%",
                        "verticalAlign": "top",
                        "boxShadow": "0px 4px 8px rgba(0, 0, 0, 0.1)",
                        "borderRadius": "10px",
                        "backgroundColor": "#f9f9f9",
                        "padding": "20px",
                        "overflow": "auto",
                        "maxHeight": "600px",
                        "display": "flex",
                        "justifyContent": "center",
                        "wordWrap": "break-word",
                    },
                    children=[
                        html.Div(
                            "Properties will be displayed here",
                            style={"textAlign": "center"},
                        ),
                    ],
                ),
            ],
            style={
                "marginTop": "20px",
                "display": "flex",
                "justifyContent": "space-between",  # Ensure the two sections are responsive
                "flexWrap": "wrap",
            },
        ),
        html.Div(
            [
                html.Div(
                    [
                        html.H3("Search Materials (eg. 'Ac,Cd,Ge' or 'Ac2CdGe3')"),
                        html.Div(
                            [
                                html.Div(
                                    [
                                        dmp.MaterialsInput(
                                            allowedInputTypes=["elements", "formula"],
                                            hidePeriodicTable=False,
                                            periodicTableMode="toggle",
                                            hideWildcardButton=True,
                                            showSubmitButton=True,
                                            submitButtonText="Search",
                                            type="elements",
                                            id="materials-input",
                                        ),
                                    ],
                                    id="materials-input-container",
                                    style={
                                        "width": "100%",
                                    },
                                ),
                            ],
                            style={
                                "display": "flex",
                                "justifyContent": "center",
                                "width": "100%",
                            },
                        ),
                    ],
                    style={
                        "width": "48%",
                        "verticalAlign": "top",
                    },
                ),
                html.Div(
                    [
                        html.Label(
                            "Select a row to display the material's structure and properties",
                            style={"margin-bottom": "20px"},
                        ),
                        # dcc.Dropdown(
                        #     id="material-dropdown",
                        #     options=[],  # Empty options initially
                        #     value=None,
                        # ),
                        dash.dash_table.DataTable(
                            id="table",
                            columns=[
                                (
                                    {"name": display_names[col], "id": col}
                                    if col != "energy"
                                    else {
                                        "name": display_names[col],
                                        "id": col,
                                        "type": "numeric",
                                        "format": {"specifier": ".2f"},
                                    }
                                )
                                for col in display_columns
                            ],
                            data=[{}],
                            style_cell={
                                "fontFamily": "Arial",
                                "padding": "10px",
                                "border": "1px solid #ddd",  # Subtle border for elegance
                                "textAlign": "left",
                                "fontSize": "14px",
                            },
                            style_header={
                                "backgroundColor": "#f5f5f5",  # Light grey header
                                "fontWeight": "bold",
                                "textAlign": "left",
                                "borderBottom": "2px solid #ddd",
                            },
                            style_data={
                                "backgroundColor": "#ffffff",
                                "color": "#333333",
                                "borderBottom": "1px solid #ddd",
                            },
                            style_data_conditional=[
                                {
                                    "if": {"state": "active"},
                                    "backgroundColor": "#e6f7ff",
                                    "border": "1px solid #1890ff",
                                },
                            ],
                            style_table={
                                "maxHeight": "400px",
                                "overflowX": "auto",
                                "overflowY": "auto",
                            },
                            style_as_list_view=True,
                            row_selectable="single",
                            selected_rows=[],
                        ),
                    ],
                    style={
                        "width": "48%",
                        # "maxWidth": "800px",
                        "margin": "0 auto",
                        "padding": "20px",
                        "backgroundColor": "#ffffff",
                        "borderRadius": "10px",
                        "boxShadow": "0px 4px 8px rgba(0, 0, 0, 0.1)",
                    },
                ),
            ],
            style={
                "margin-top": "20px",
                "margin-bottom": "20px",
                "display": "flex",
                "flexDirection": "row",
                "alignItems": "center",
            },
        ),
        # html.Button("Display Material", id="display-button", n_clicks=0),
    ],
    style={
        "margin-left": "10px",
        "margin-right": "10px",
    },
)


def search_materials(query):
    query_vector = np.zeros(n_elements)

    if "," in query:
        element_list = [el.strip() for el in query.split(",")]
        for el in element_list:
            query_vector[map_periodic_table[el]] = 1
    else:
        # Formula
        import re

        matches = re.findall(r"([A-Z][a-z]{0,2})(\d*)", query)
        for el, numb in matches:
            numb = int(numb) if numb else 1
            query_vector[map_periodic_table[el]] = numb

    similarity = np.dot(dataset_index, query_vector) / (np.linalg.norm(query_vector))
    indices = np.argsort(similarity)[::-1][:top_k]

    options = [dataset[int(i)] for i in indices]

    mapping_table_idx_dataset_idx.clear()
    for i, idx in enumerate(indices):
        mapping_table_idx_dataset_idx[int(i)] = int(idx)

    return options


# Callback to update the table based on search
@app.callback(
    Output("table", "data"),
    Input("materials-input", "submitButtonClicks"),
    Input("materials-input", "value"),
)
def on_submit_materials_input(n_clicks, query):
    if n_clicks is None or not query:
        return []

    entries = search_materials(query)

    return [{col: entry[col] for col in display_columns} for entry in entries]


# Callback to display the selected material
@app.callback(
    [
        Output("structure-container", "children"),
        Output("properties-container", "children"),
    ],
    # Input("display-button", "n_clicks"),
    Input("table", "active_cell"),
    Input("table", "derived_virtual_selected_rows"),
)
def display_material(active_cell, selected_rows):
    if not active_cell and not selected_rows:
        return (
            html.Div(
                "Search a material to display its structure and properties",
                style={"textAlign": "center"},
            ),
            html.Div(
                "Properties will be displayed here",
                style={"textAlign": "center"},
            ),
        )

    if len(selected_rows) > 0:
        idx_active = selected_rows[0]
    else:
        idx_active = active_cell["row"]
    row = dataset[mapping_table_idx_dataset_idx[idx_active]]

    structure = Structure(
        [x for y in row["lattice_vectors"] for x in y],
        row["species_at_sites"],
        row["cartesian_site_positions"],
        coords_are_cartesian=True,
    )
    if row["magnetic_moments"]:
        structure.add_site_property("magmom", row["magnetic_moments"])

    sga = SpacegroupAnalyzer(structure)

    # Create the StructureMoleculeComponent
    structure_component = ctc.StructureMoleculeComponent(structure)

    # Extract key properties
    properties = {
        "Material ID": row["immutable_id"],
        "Formula": row["chemical_formula_descriptive"],
        "Energy per atom (eV/atom)": round(
            row["energy"] / len(row["species_at_sites"]), 3
        ),
        # "Band Gap (eV)": row["band_gap_direct"] or row["band_gap_indirect"], #future release
        "Total Magnetization (μB)": row["total_magnetization"],
        "Density (g/cm^3)": round(structure.density, 3),
        "Fermi energy level (eV)": row["dos_ef"],
        "Crystal system": sga.get_crystal_system(),
        "International Spacegroup": sga.get_symmetry_dataset().international,
        "Magnetic moments (μB/f.u.)": np.round(row["magnetic_moments"], 3),
        "Stress tensor (kB)": row["stress_tensor"],
        "Forces on atoms (eV/A)": np.round(row["forces"], 3),
        # "Bader charges (e-)": np.round(row["charges"], 3), # future release
        "DFT Functional": row["functional"],
    }

    # Format properties as an HTML table
    properties_html = html.Table(
        [
            html.Tbody(
                [
                    html.Tr(
                        [
                            html.Th(
                                key,
                                style={
                                    "padding": "10px",
                                    "verticalAlign": "middle",
                                },
                            ),
                            html.Td(
                                str(value),
                                style={
                                    "padding": "10px",
                                    "borderBottom": "1px solid #ddd",
                                },
                            ),
                        ],
                    )
                    for key, value in properties.items()
                ],
            )
        ],
        style={
            "width": "100%",
            "borderCollapse": "collapse",
            "fontFamily": "'Arial', sans-serif",
            "fontSize": "14px",
            "color": "#333333",
        },
    )

    return structure_component.layout(), properties_html


@app.callback(
    Output("materials-input-container", "children"),
    Input("breakpoints", "widthBreakpoint"),
    State("breakpoints", "width"),
)
def update_materials_input_layout(breakpoint_name, width):
    if breakpoint_name in ["lg", "md"]:
        # Default layout if no page size is detected
        return dmp.MaterialsInput(
            allowedInputTypes=["elements", "formula"],
            hidePeriodicTable=False,
            periodicTableMode="toggle",
            hideWildcardButton=True,
            showSubmitButton=True,
            submitButtonText="Search",
            type="elements",
            id="materials-input",
        )
    elif breakpoint_name == "sm":
        return dmp.MaterialsInput(
            allowedInputTypes=["elements", "formula"],
            hidePeriodicTable=True,
            periodicTableMode="none",
            hideWildcardButton=False,
            showSubmitButton=False,
            # submitButtonText="Search",
            type="elements",
            id="materials-input",
        )


# Register crystal toolkit with the app
ctc.register_crystal_toolkit(app, layout)

if __name__ == "__main__":
    app.run_server(debug=True, port=7860, host="0.0.0.0")