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VsevolodXVsevolodX
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Merge pull request #226 from Exabyte-io/feature/SOF-7596-1
feature/SOF-7596 (SOF-7598) chore: rename thickness -> number of layers
2 parents 765acf4 + ddeeb04 commit a673f50

28 files changed

+411
-135
lines changed

‎other/materials_designer/create_adatom_defect.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,7 @@
148148
"slab_config = SlabConfiguration(\n",
149149
" bulk=material,\n",
150150
" miller_indices=MILLER_INDICES,\n",
151-
" thickness=SLAB_THICKNESS,\n",
151+
" number_of_layers=SLAB_THICKNESS,\n",
152152
" vacuum=VACUUM,\n",
153153
" use_orthogonal_z=True,\n",
154154
" xy_supercell_matrix=SUPERCELL_MATRIX\n",

‎other/materials_designer/create_cluster_sphere.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -127,7 +127,7 @@
127127
"slab_config = SlabConfiguration(\n",
128128
" bulk=materials[0],\n",
129129
" miller_indices=Z_ORIENTATION,\n",
130-
" thickness=1,\n",
130+
" number_of_layers=1,\n",
131131
" vacuum=0,\n",
132132
" use_orthogonal_z=True\n",
133133
")\n",

‎other/materials_designer/create_cutout_box.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -138,7 +138,7 @@
138138
"default_slab_config = SlabConfiguration(\n",
139139
" bulk=materials[0],\n",
140140
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
141-
" thickness=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
141+
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
142142
" vacuum=DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
143143
" use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
144144
" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",

‎other/materials_designer/create_cutout_custom_shape.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -251,7 +251,7 @@
251251
"slab_config = SlabConfiguration(\n",
252252
" bulk=material,\n",
253253
" miller_indices=MILLER_INDICES,\n",
254-
" thickness=THICKNESS,\n",
254+
" number_of_layers=THICKNESS,\n",
255255
" vacuum=0,\n",
256256
" xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
257257
" use_orthogonal_z=True,\n",

‎other/materials_designer/create_grain_boundary_crystal.ipynb

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -192,14 +192,14 @@
192192
"phase_1_configuration = SlabConfiguration(\n",
193193
" bulk=material,\n",
194194
" miller_indices=PHASE_1_MILLER_INDICES,\n",
195-
" thickness=PHASE_1_THICKNESS,\n",
195+
" number_of_layers=PHASE_1_THICKNESS,\n",
196196
" use_orthogonal_z=PHASE_1_USE_ORTHOGONAL_Z\n",
197197
")\n",
198198
"\n",
199199
"phase_2_configuration = SlabConfiguration(\n",
200200
" bulk=material,\n",
201201
" miller_indices=PHASE_2_MILLER_INDICES,\n",
202-
" thickness=PHASE_2_THICKNESS,\n",
202+
" number_of_layers=PHASE_2_THICKNESS,\n",
203203
" use_orthogonal_z=PHASE_2_USE_ORTHOGONAL_Z\n",
204204
")"
205205
],
@@ -340,7 +340,7 @@
340340
"slab_configuration = SlabConfiguration(\n",
341341
" bulk=material,\n",
342342
" miller_indices=SLAB_MILLER_INDICES,\n",
343-
" thickness=SLAB_THICKNESS,\n",
343+
" number_of_layers=SLAB_THICKNESS,\n",
344344
" vacuum=SLAB_VACUUM,\n",
345345
")\n",
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"\n",

‎other/materials_designer/create_heterostructure_example.ipynb

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,7 @@
216216
"material1_slab_configuration = SlabConfiguration(\n",
217217
" bulk=material1,\n",
218218
" miller_indices=MATERIAL_1_MILLER_INDICES,\n",
219-
" thickness=MATERIAL_1_THICKNESS, # in atomic layers\n",
219+
" number_of_layers=MATERIAL_1_THICKNESS, # in atomic layers\n",
220220
" vacuum=MATERIAL_1_VACUUM, # in Angstroms\n",
221221
" xy_supercell_matrix=MATERIAL_1_XY_SUPERCELL_MATRIX,\n",
222222
" use_orthogonal_z=MATERIAL_1_USE_ORTHOGONAL_Z\n",
@@ -226,7 +226,7 @@
226226
"material0_slab_configuration = SlabConfiguration(\n",
227227
" bulk=material0,\n",
228228
" miller_indices=MATERIAL_0_MILLER_INDICES,\n",
229-
" thickness=MATERIAL_0_THICKNESS, # in atomic layers\n",
229+
" number_of_layers=MATERIAL_0_THICKNESS, # in atomic layers\n",
230230
" vacuum=MATERIAL_0_VACUUM, # in Angstroms\n",
231231
" xy_supercell_matrix=MATERIAL_0_XY_SUPERCELL_MATRIX,\n",
232232
" use_orthogonal_z=MATERIAL_0_USE_ORTHOGONAL_Z\n",
@@ -474,7 +474,7 @@
474474
"material2_slab_configuration = SlabConfiguration(\n",
475475
" bulk=material2,\n",
476476
" miller_indices=MATERIAL_2_MILLER_INDICES,\n",
477-
" thickness=MATERIAL_2_THICKNESS, # in atomic layers\n",
477+
" number_of_layers=MATERIAL_2_THICKNESS, # in atomic layers\n",
478478
" vacuum=MATERIAL_2_VACUUM, # in atomic layers\n",
479479
" xy_supercell_matrix=MATERIAL_2_XY_SUPERCELL_MATRIX,\n",
480480
" use_orthogonal_z=MATERIAL_2_USE_ORTHOGONAL_Z\n",
@@ -484,7 +484,7 @@
484484
"substrate_second_slab_configuration = SlabConfiguration(\n",
485485
" bulk=substrate_second,\n",
486486
" miller_indices=(0, 0, 1), # Z-orientation for the first interface\n",
487-
" thickness=1, # One unit cell thick\n",
487+
" number_of_layers=1, # One unit cell thick\n",
488488
" vacuum=0, \n",
489489
" xy_supercell_matrix=MATERIAL_0_XY_SUPERCELL_MATRIX, # Adjust if necessary\n",
490490
" use_orthogonal_z=MATERIAL_0_USE_ORTHOGONAL_Z\n",

‎other/materials_designer/create_interface_with_min_strain_zsl.ipynb

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,6 @@
4646
},
4747
{
4848
"cell_type": "code",
49-
"outputs": [],
5049
"source": [
5150
"# Enable interactive selection of terminations via UI prompt\n",
5251
"IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
@@ -79,6 +78,7 @@
7978
"metadata": {
8079
"collapsed": false
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},
81+
"outputs": [],
8282
"execution_count": null
8383
},
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{
@@ -93,7 +93,6 @@
9393
},
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{
9595
"cell_type": "code",
96-
"outputs": [],
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"source": [
9897
"import sys\n",
9998
"\n",
@@ -108,6 +107,7 @@
108107
"metadata": {
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"collapsed": false
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},
110+
"outputs": [],
111111
"execution_count": null
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},
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{
@@ -120,7 +120,6 @@
120120
},
121121
{
122122
"cell_type": "code",
123-
"outputs": [],
124123
"source": [
125124
"from utils.jupyterlite import get_materials\n",
126125
"\n",
@@ -135,6 +134,7 @@
135134
"metadata": {
136135
"collapsed": false
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},
137+
"outputs": [],
138138
"execution_count": null
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},
140140
{
@@ -148,14 +148,14 @@
148148
},
149149
{
150150
"cell_type": "code",
151-
"outputs": [],
152151
"source": [
153152
"from utils.visualize import visualize_materials as visualize\n",
154153
"visualize([substrate, film], repetitions=[3, 3, 1], rotation=\"0x\")"
155154
],
156155
"metadata": {
157156
"collapsed": false
158157
},
158+
"outputs": [],
159159
"execution_count": null
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},
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{
@@ -171,14 +171,13 @@
171171
},
172172
{
173173
"cell_type": "code",
174-
"outputs": [],
175174
"source": [
176175
"from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
177176
"\n",
178177
"film_slab_configuration = SlabConfiguration(\n",
179178
" bulk=film,\n",
180179
" miller_indices=FILM_MILLER_INDICES,\n",
181-
" thickness=FILM_THICKNESS, # in atomic layers\n",
180+
" number_of_layers=FILM_THICKNESS, # in atomic layers\n",
182181
" vacuum=FILM_VACUUM, # in angstroms\n",
183182
" xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
184183
" use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n",
@@ -187,13 +186,14 @@
187186
"substrate_slab_configuration = SlabConfiguration(\n",
188187
" bulk=substrate,\n",
189188
" miller_indices=SUBSTRATE_MILLER_INDICES,\n",
190-
" thickness=SUBSTRATE_THICKNESS, # in atomic layers\n",
189+
" number_of_layers=SUBSTRATE_THICKNESS, # in atomic layers\n",
191190
" vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
192191
" xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
193192
" use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n",
194193
")"
195194
],
196195
"metadata": {},
196+
"outputs": [],
197197
"execution_count": null
198198
},
199199
{
@@ -207,14 +207,14 @@
207207
},
208208
{
209209
"cell_type": "code",
210-
"outputs": [],
211210
"source": [
212211
"film_slab_terminations = get_terminations(film_slab_configuration)\n",
213212
"substrate_slab_terminations = get_terminations(substrate_slab_configuration)"
214213
],
215214
"metadata": {
216215
"collapsed": false
217216
},
217+
"outputs": [],
218218
"execution_count": null
219219
},
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{
@@ -228,7 +228,6 @@
228228
},
229229
{
230230
"cell_type": "code",
231-
"outputs": [],
232231
"source": [
233232
"film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n",
234233
"substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n",
@@ -239,6 +238,7 @@
239238
"metadata": {
240239
"collapsed": false
241240
},
241+
"outputs": [],
242242
"execution_count": null
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},
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{
@@ -252,7 +252,6 @@
252252
},
253253
{
254254
"cell_type": "code",
255-
"outputs": [],
256255
"source": [
257256
"from itertools import product\n",
258257
"\n",
@@ -264,6 +263,7 @@
264263
"metadata": {
265264
"collapsed": false
266265
},
266+
"outputs": [],
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"execution_count": null
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},
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{
@@ -277,7 +277,6 @@
277277
},
278278
{
279279
"cell_type": "code",
280-
"outputs": [],
281280
"source": [
282281
"from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
283282
"\n",
@@ -293,6 +292,7 @@
293292
"metadata": {
294293
"collapsed": false
295294
},
295+
"outputs": [],
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"execution_count": null
297297
},
298298
{
@@ -308,7 +308,6 @@
308308
},
309309
{
310310
"cell_type": "code",
311-
"outputs": [],
312311
"source": [
313312
"from mat3ra.made.tools.build.interface import InterfaceConfiguration\n",
314313
"\n",
@@ -325,6 +324,7 @@
325324
"metadata": {
326325
"collapsed": false
327326
},
327+
"outputs": [],
328328
"execution_count": null
329329
},
330330
{
@@ -339,7 +339,6 @@
339339
},
340340
{
341341
"cell_type": "code",
342-
"outputs": [],
343342
"source": [
344343
"from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
345344
"zsl_strain_matching_parameters = ZSLStrainMatchingParameters(\n",
@@ -352,6 +351,7 @@
352351
"metadata": {
353352
"collapsed": false
354353
},
354+
"outputs": [],
355355
"execution_count": null
356356
},
357357
{
@@ -366,7 +366,6 @@
366366
},
367367
{
368368
"cell_type": "code",
369-
"outputs": [],
370369
"source": [
371370
"from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, ZSLStrainMatchingInterfaceBuilderParameters\n",
372371
"\n",
@@ -377,6 +376,7 @@
377376
"metadata": {
378377
"collapsed": false
379378
},
379+
"outputs": [],
380380
"execution_count": null
381381
},
382382
{
@@ -390,7 +390,6 @@
390390
},
391391
{
392392
"cell_type": "code",
393-
"outputs": [],
394393
"source": [
395394
"from utils.plot import plot_strain_vs_atoms\n",
396395
"\n",
@@ -405,6 +404,7 @@
405404
"metadata": {
406405
"collapsed": false
407406
},
407+
"outputs": [],
408408
"execution_count": null
409409
},
410410
{
@@ -420,7 +420,6 @@
420420
},
421421
{
422422
"cell_type": "code",
423-
"outputs": [],
424423
"source": [
425424
"# select the first interface with the lowest strain and the smallest number of atoms\n",
426425
"interfaces_slice_range_or_index = slice(0, 1)\n",
@@ -429,6 +428,7 @@
429428
"metadata": {
430429
"collapsed": false
431430
},
431+
"outputs": [],
432432
"execution_count": null
433433
},
434434
{
@@ -442,14 +442,14 @@
442442
},
443443
{
444444
"cell_type": "code",
445-
"outputs": [],
446445
"source": [
447446
"visualize(selected_interfaces, repetitions=[3, 3, 1])\n",
448447
"visualize(selected_interfaces, repetitions=[3, 3, 1], rotation=\"-90x\")"
449448
],
450449
"metadata": {
451450
"collapsed": false
452451
},
452+
"outputs": [],
453453
"execution_count": null
454454
},
455455
{
@@ -461,13 +461,13 @@
461461
},
462462
{
463463
"cell_type": "code",
464-
"execution_count": null,
465464
"metadata": {},
466-
"outputs": [],
467465
"source": [
468466
"from utils.jupyterlite import set_materials\n",
469467
"set_materials(selected_interfaces)"
470-
]
468+
],
469+
"outputs": [],
470+
"execution_count": null
471471
}
472472
],
473473
"metadata": {

‎other/materials_designer/create_interface_with_no_strain_matching.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -172,7 +172,7 @@
172172
"film_slab_configuration = SlabConfiguration(\n",
173173
" bulk=film,\n",
174174
" miller_indices=FILM_MILLER_INDICES,\n",
175-
" thickness=FILM_THICKNESS, # in atomic layers\n",
175+
" number_of_layers=FILM_THICKNESS, # in atomic layers\n",
176176
" vacuum=FILM_VACUUM, # in angstroms\n",
177177
" xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
178178
" use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n",
@@ -181,7 +181,7 @@
181181
"substrate_slab_configuration = SlabConfiguration(\n",
182182
" bulk=substrate,\n",
183183
" miller_indices=SUBSTRATE_MILLER_INDICES,\n",
184-
" thickness=SUBSTRATE_THICKNESS, # in atomic layers\n",
184+
" number_of_layers=SUBSTRATE_THICKNESS, # in atomic layers\n",
185185
" vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
186186
" xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
187187
" use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n",

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