Skip to content

Commit d31662b

Browse files
nedtaylornedtaylor
committed
Fix file reference
1 parent d3646d9 commit d31662b

File tree

1 file changed

+72
-101
lines changed
  • example/python_pkg/Si-Ge_learn/DRAFFLE

1 file changed

+72
-101
lines changed

‎example/python_pkg/Si-Ge_learn/DRAFFLE/pca.ipynb‎

Lines changed: 72 additions & 101 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"cells": [
33
{
44
"cell_type": "code",
5-
"execution_count": 1,
5+
"execution_count": 6,
66
"metadata": {},
77
"outputs": [],
88
"source": [
@@ -25,7 +25,7 @@
2525
},
2626
{
2727
"cell_type": "code",
28-
"execution_count": 2,
28+
"execution_count": 7,
2929
"metadata": {},
3030
"outputs": [],
3131
"source": [
@@ -38,7 +38,7 @@
3838
},
3939
{
4040
"cell_type": "code",
41-
"execution_count": null,
41+
"execution_count": 8,
4242
"metadata": {},
4343
"outputs": [],
4444
"source": [
@@ -51,7 +51,7 @@
5151
},
5252
{
5353
"cell_type": "code",
54-
"execution_count": 4,
54+
"execution_count": 9,
5555
"metadata": {},
5656
"outputs": [],
5757
"source": [
@@ -66,17 +66,9 @@
6666
},
6767
{
6868
"cell_type": "code",
69-
"execution_count": 5,
69+
"execution_count": 10,
7070
"metadata": {},
7171
"outputs": [
72-
{
73-
"name": "stderr",
74-
"output_type": "stream",
75-
"text": [
76-
"/opt/homebrew/Caskroom/miniconda/base/envs/raffle_env/lib/python3.12/site-packages/e3nn/o3/_wigner.py:10: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.\n",
77-
" _Jd, _W3j_flat, _W3j_indices = torch.load(os.path.join(os.path.dirname(__file__), 'constants.pt'))\n"
78-
]
79-
},
8072
{
8173
"name": "stdout",
8274
"output_type": "stream",
@@ -105,7 +97,7 @@
10597
},
10698
{
10799
"cell_type": "code",
108-
"execution_count": null,
100+
"execution_count": 11,
109101
"metadata": {},
110102
"outputs": [],
111103
"source": [
@@ -120,7 +112,7 @@
120112
},
121113
{
122114
"cell_type": "code",
123-
"execution_count": null,
115+
"execution_count": 12,
124116
"metadata": {},
125117
"outputs": [],
126118
"source": [
@@ -135,7 +127,7 @@
135127
},
136128
{
137129
"cell_type": "code",
138-
"execution_count": null,
130+
"execution_count": 13,
139131
"metadata": {},
140132
"outputs": [],
141133
"source": [
@@ -179,7 +171,7 @@
179171
},
180172
{
181173
"cell_type": "code",
182-
"execution_count": 9,
174+
"execution_count": 14,
183175
"metadata": {},
184176
"outputs": [],
185177
"source": [
@@ -189,7 +181,7 @@
189181
},
190182
{
191183
"cell_type": "code",
192-
"execution_count": 10,
184+
"execution_count": 15,
193185
"metadata": {},
194186
"outputs": [],
195187
"source": [
@@ -207,47 +199,47 @@
207199
},
208200
{
209201
"cell_type": "code",
210-
"execution_count": null,
202+
"execution_count": 16,
211203
"metadata": {},
212204
"outputs": [
213205
{
214206
"name": "stdout",
215207
"output_type": "stream",
216208
"text": [
217209
" Step Time Energy fmax\n",
218-
"FIRE: 0 07:11:23 -404.223419 0.308327\n",
219-
"FIRE: 1 07:11:23 -404.241852 0.287606\n",
220-
"FIRE: 2 07:11:23 -404.272003 0.248617\n",
221-
"FIRE: 3 07:11:24 -404.303772 0.195892\n",
222-
"FIRE: 4 07:11:24 -404.329620 0.135901\n",
223-
"FIRE: 5 07:11:24 -404.347687 0.144643\n",
224-
"FIRE: 6 07:11:24 -404.362213 0.175805\n",
225-
"FIRE: 7 07:11:25 -404.376984 0.175536\n",
226-
"FIRE: 8 07:11:25 -404.394958 0.142853\n",
227-
"FIRE: 9 07:11:25 -404.413055 0.100423\n",
228-
"FIRE: 10 07:11:25 -404.429321 0.129502\n",
229-
"FIRE: 11 07:11:26 -404.447083 0.121732\n",
230-
"FIRE: 12 07:11:26 -404.468384 0.077039\n",
231-
"FIRE: 13 07:11:26 -404.486206 0.055702\n",
232-
"FIRE: 14 07:11:26 -404.490448 0.068700\n",
233-
"FIRE: 15 07:11:27 -404.491364 0.059904\n",
234-
"FIRE: 16 07:11:27 -404.493073 0.043546\n",
210+
"FIRE: 0 09:37:36 -404.223419 0.308327\n",
211+
"FIRE: 1 09:37:36 -404.241852 0.287606\n",
212+
"FIRE: 2 09:37:36 -404.272003 0.248617\n",
213+
"FIRE: 3 09:37:37 -404.303772 0.195892\n",
214+
"FIRE: 4 09:37:37 -404.329620 0.135901\n",
215+
"FIRE: 5 09:37:37 -404.347687 0.144643\n",
216+
"FIRE: 6 09:37:37 -404.362213 0.175805\n",
217+
"FIRE: 7 09:37:38 -404.376984 0.175536\n",
218+
"FIRE: 8 09:37:38 -404.394958 0.142853\n",
219+
"FIRE: 9 09:37:38 -404.413055 0.100423\n",
220+
"FIRE: 10 09:37:39 -404.429321 0.129503\n",
221+
"FIRE: 11 09:37:39 -404.447083 0.121735\n",
222+
"FIRE: 12 09:37:39 -404.468445 0.077042\n",
223+
"FIRE: 13 09:37:40 -404.486176 0.055705\n",
224+
"FIRE: 14 09:37:40 -404.490448 0.068701\n",
225+
"FIRE: 15 09:37:40 -404.491455 0.059911\n",
226+
"FIRE: 16 09:37:40 -404.493134 0.043550\n",
235227
" Step Time Energy fmax\n",
236-
"FIRE: 0 07:11:27 -346.881958 0.666953\n",
237-
"FIRE: 1 07:11:27 -346.957520 0.634437\n",
238-
"FIRE: 2 07:11:28 -347.092957 0.572620\n",
239-
"FIRE: 3 07:11:28 -347.262268 0.487324\n",
240-
"FIRE: 4 07:11:28 -347.436462 0.385976\n",
241-
"FIRE: 5 07:11:28 -347.591003 0.276925\n",
242-
"FIRE: 6 07:11:28 -347.711609 0.213073\n",
243-
"FIRE: 7 07:11:29 -347.796143 0.225150\n",
244-
"FIRE: 8 07:11:29 -347.859192 0.209056\n",
245-
"FIRE: 9 07:11:29 -347.912292 0.221024\n",
246-
"FIRE: 10 07:11:29 -347.974304 0.227086\n",
247-
"FIRE: 11 07:11:30 -348.062683 0.211165\n",
248-
"FIRE: 12 07:11:30 -348.180664 0.205920\n",
249-
"FIRE: 13 07:11:30 -348.289246 0.142311\n",
250-
"FIRE: 14 07:11:30 -348.345886 0.030842\n"
228+
"FIRE: 0 09:37:41 -346.881958 0.666953\n",
229+
"FIRE: 1 09:37:41 -346.957520 0.634437\n",
230+
"FIRE: 2 09:37:41 -347.092957 0.572620\n",
231+
"FIRE: 3 09:37:41 -347.262268 0.487324\n",
232+
"FIRE: 4 09:37:42 -347.436462 0.385976\n",
233+
"FIRE: 5 09:37:42 -347.591003 0.276925\n",
234+
"FIRE: 6 09:37:42 -347.711609 0.213073\n",
235+
"FIRE: 7 09:37:42 -347.796143 0.225150\n",
236+
"FIRE: 8 09:37:43 -347.859192 0.209056\n",
237+
"FIRE: 9 09:37:43 -347.912292 0.221024\n",
238+
"FIRE: 10 09:37:43 -347.974304 0.227086\n",
239+
"FIRE: 11 09:37:43 -348.062683 0.211165\n",
240+
"FIRE: 12 09:37:43 -348.180664 0.205920\n",
241+
"FIRE: 13 09:37:44 -348.289246 0.142311\n",
242+
"FIRE: 14 09:37:44 -348.345886 0.030842\n"
251243
]
252244
},
253245
{
@@ -256,7 +248,7 @@
256248
"True"
257249
]
258250
},
259-
"execution_count": 11,
251+
"execution_count": 16,
260252
"metadata": {},
261253
"output_type": "execute_result"
262254
}
@@ -275,48 +267,27 @@
275267
},
276268
{
277269
"cell_type": "code",
278-
"execution_count": 12,
270+
"execution_count": null,
279271
"metadata": {},
280272
"outputs": [
281273
{
282-
"name": "stdout",
283-
"output_type": "stream",
284-
"text": [
285-
" Step Time Energy fmax\n",
286-
"FIRE: 0 07:11:31 -789.081665 0.573500\n",
287-
"FIRE: 1 07:11:31 -789.132935 0.505219\n",
288-
"FIRE: 2 07:11:32 -789.219177 0.382348\n",
289-
"FIRE: 3 07:11:32 -789.312744 0.240137\n",
290-
"FIRE: 4 07:11:33 -789.400818 0.241156\n",
291-
"FIRE: 5 07:11:33 -789.483398 0.250259\n",
292-
"FIRE: 6 07:11:34 -789.572144 0.231571\n",
293-
"FIRE: 7 07:11:34 -789.668152 0.197278\n",
294-
"FIRE: 8 07:11:35 -789.775635 0.172412\n",
295-
"FIRE: 9 07:11:35 -789.887451 0.148718\n",
296-
"FIRE: 10 07:11:36 -790.001465 0.144370\n",
297-
"FIRE: 11 07:11:36 -790.117432 0.108855\n",
298-
"FIRE: 12 07:11:37 -790.208984 0.092348\n",
299-
"FIRE: 13 07:11:37 -790.255676 0.084902\n",
300-
"FIRE: 14 07:11:38 -790.259705 0.098246\n",
301-
"FIRE: 15 07:11:38 -790.263000 0.086857\n",
302-
"FIRE: 16 07:11:38 -790.267517 0.065695\n",
303-
"FIRE: 17 07:11:39 -790.272095 0.037790\n"
274+
"ename": "FileNotFoundError",
275+
"evalue": "[Errno 2] No such file or directory: 'SiGe_abrupt_interface.vasp'",
276+
"output_type": "error",
277+
"traceback": [
278+
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
279+
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
280+
"Cell \u001b[0;32mIn[17], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m## Get abrupt interface energetics\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m SiGe_abrupt \u001b[38;5;241m=\u001b[39m \u001b[43mread\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSiGe_abrupt_interface.vasp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3\u001b[0m SiGe_abrupt\u001b[38;5;241m.\u001b[39mcalc \u001b[38;5;241m=\u001b[39m calc\n\u001b[1;32m 4\u001b[0m SiGe_abrupt\u001b[38;5;241m.\u001b[39mset_cell(rlxd_structures[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mget_cell(), scale_atoms\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n",
281+
"File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/envs/raffle_env/lib/python3.12/site-packages/ase/io/formats.py:793\u001b[0m, in \u001b[0;36mread\u001b[0;34m(filename, index, format, parallel, do_not_split_by_at_sign, **kwargs)\u001b[0m\n\u001b[1;32m 791\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m index \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 792\u001b[0m index \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m\n\u001b[0;32m--> 793\u001b[0m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;129;01mor\u001b[39;00m \u001b[43mfiletype\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mread\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43misinstance\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 795\u001b[0m io \u001b[38;5;241m=\u001b[39m get_ioformat(\u001b[38;5;28mformat\u001b[39m)\n\u001b[1;32m 796\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(index, (\u001b[38;5;28mslice\u001b[39m, \u001b[38;5;28mstr\u001b[39m)):\n",
282+
"File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/envs/raffle_env/lib/python3.12/site-packages/ase/io/formats.py:965\u001b[0m, in \u001b[0;36mfiletype\u001b[0;34m(filename, read, guess)\u001b[0m\n\u001b[1;32m 962\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ext\n\u001b[1;32m 964\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m orig_filename \u001b[38;5;241m==\u001b[39m filename:\n\u001b[0;32m--> 965\u001b[0m fd \u001b[38;5;241m=\u001b[39m \u001b[43mopen_with_compression\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mrb\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 966\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 967\u001b[0m fd \u001b[38;5;241m=\u001b[39m orig_filename \u001b[38;5;66;03m# type: ignore[assignment]\u001b[39;00m\n",
283+
"File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/envs/raffle_env/lib/python3.12/site-packages/ase/io/formats.py:597\u001b[0m, in \u001b[0;36mopen_with_compression\u001b[0;34m(filename, mode)\u001b[0m\n\u001b[1;32m 594\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m lzma\u001b[38;5;241m.\u001b[39mopen(filename, mode)\n\u001b[1;32m 595\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 596\u001b[0m \u001b[38;5;66;03m# Either None or unknown string\u001b[39;00m\n\u001b[0;32m--> 597\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m)\u001b[49m\n",
284+
"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: 'SiGe_abrupt_interface.vasp'"
304285
]
305-
},
306-
{
307-
"data": {
308-
"text/plain": [
309-
"True"
310-
]
311-
},
312-
"execution_count": 12,
313-
"metadata": {},
314-
"output_type": "execute_result"
315286
}
316287
],
317288
"source": [
318289
"## Get abrupt interface energetics\n",
319-
"SiGe_abrupt = read(\"SiGe_abrupt_interface.vasp\")\n",
290+
"SiGe_abrupt = read(\"../SiGe_abrupt_interface.vasp\")\n",
320291
"SiGe_abrupt.calc = calc\n",
321292
"SiGe_abrupt.set_cell(rlxd_structures[0].get_cell(), scale_atoms=True)\n",
322293
"optimizer = FIRE(SiGe_abrupt)\n",
@@ -325,7 +296,7 @@
325296
},
326297
{
327298
"cell_type": "code",
328-
"execution_count": 13,
299+
"execution_count": null,
329300
"metadata": {},
330301
"outputs": [
331302
{
@@ -344,7 +315,7 @@
344315
},
345316
{
346317
"cell_type": "code",
347-
"execution_count": 14,
318+
"execution_count": null,
348319
"metadata": {},
349320
"outputs": [],
350321
"source": [
@@ -364,7 +335,7 @@
364335
},
365336
{
366337
"cell_type": "code",
367-
"execution_count": 15,
338+
"execution_count": null,
368339
"metadata": {},
369340
"outputs": [],
370341
"source": [
@@ -374,7 +345,7 @@
374345
},
375346
{
376347
"cell_type": "code",
377-
"execution_count": 16,
348+
"execution_count": null,
378349
"metadata": {},
379350
"outputs": [
380351
{
@@ -392,7 +363,7 @@
392363
},
393364
{
394365
"cell_type": "code",
395-
"execution_count": 17,
366+
"execution_count": null,
396367
"metadata": {},
397368
"outputs": [
398369
{
@@ -411,7 +382,7 @@
411382
},
412383
{
413384
"cell_type": "code",
414-
"execution_count": 18,
385+
"execution_count": null,
415386
"metadata": {},
416387
"outputs": [
417388
{
@@ -430,7 +401,7 @@
430401
},
431402
{
432403
"cell_type": "code",
433-
"execution_count": 19,
404+
"execution_count": null,
434405
"metadata": {},
435406
"outputs": [],
436407
"source": [
@@ -440,7 +411,7 @@
440411
},
441412
{
442413
"cell_type": "code",
443-
"execution_count": 20,
414+
"execution_count": null,
444415
"metadata": {},
445416
"outputs": [],
446417
"source": [
@@ -452,7 +423,7 @@
452423
},
453424
{
454425
"cell_type": "code",
455-
"execution_count": 21,
426+
"execution_count": null,
456427
"metadata": {},
457428
"outputs": [],
458429
"source": [
@@ -464,7 +435,7 @@
464435
},
465436
{
466437
"cell_type": "code",
467-
"execution_count": 22,
438+
"execution_count": null,
468439
"metadata": {},
469440
"outputs": [],
470441
"source": [
@@ -474,7 +445,7 @@
474445
},
475446
{
476447
"cell_type": "code",
477-
"execution_count": 23,
448+
"execution_count": null,
478449
"metadata": {},
479450
"outputs": [],
480451
"source": [
@@ -492,7 +463,7 @@
492463
},
493464
{
494465
"cell_type": "code",
495-
"execution_count": 24,
466+
"execution_count": null,
496467
"metadata": {},
497468
"outputs": [],
498469
"source": [
@@ -503,7 +474,7 @@
503474
},
504475
{
505476
"cell_type": "code",
506-
"execution_count": 25,
477+
"execution_count": null,
507478
"metadata": {},
508479
"outputs": [],
509480
"source": [
@@ -515,7 +486,7 @@
515486
},
516487
{
517488
"cell_type": "code",
518-
"execution_count": 26,
489+
"execution_count": null,
519490
"metadata": {},
520491
"outputs": [
521492
{
@@ -534,7 +505,7 @@
534505
},
535506
{
536507
"cell_type": "code",
537-
"execution_count": 68,
508+
"execution_count": null,
538509
"metadata": {},
539510
"outputs": [
540511
{

0 commit comments

Comments
 (0)