Skip to content

Commit e352a70

Browse files
committed
Documentation Update for votca/votca@03d5bf1
1 parent 30187b7 commit e352a70

File tree

90 files changed

+39012
-16561
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

90 files changed

+39012
-16561
lines changed

.doctrees/environment.pickle

492 KB
Binary file not shown.

.doctrees/nbsphinx/xtp-tutorials/DFTGWBSE_ENERGY.ipynb

Lines changed: 48 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -43,10 +43,10 @@
4343
"execution_count": 1,
4444
"metadata": {
4545
"execution": {
46-
"iopub.execute_input": "2024-05-31T05:14:00.978301Z",
47-
"iopub.status.busy": "2024-05-31T05:14:00.978100Z",
48-
"iopub.status.idle": "2024-05-31T05:14:01.108490Z",
49-
"shell.execute_reply": "2024-05-31T05:14:01.107826Z"
46+
"iopub.execute_input": "2024-06-03T12:52:08.486411Z",
47+
"iopub.status.busy": "2024-06-03T12:52:08.486044Z",
48+
"iopub.status.idle": "2024-06-03T12:52:08.616902Z",
49+
"shell.execute_reply": "2024-06-03T12:52:08.616204Z"
5050
}
5151
},
5252
"outputs": [
@@ -60,7 +60,7 @@
6060
"\r\n",
6161
"please submit bugs to https://github.com/votca/votca/issues\r\n",
6262
"\r\n",
63-
"xtp_tools, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
63+
"xtp_tools, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
6464
"\r\n",
6565
"Runs excitation/charge transport tools\r\n",
6666
"\r\n",
@@ -110,10 +110,10 @@
110110
"execution_count": 2,
111111
"metadata": {
112112
"execution": {
113-
"iopub.execute_input": "2024-05-31T05:14:01.111629Z",
114-
"iopub.status.busy": "2024-05-31T05:14:01.111423Z",
115-
"iopub.status.idle": "2024-05-31T05:14:06.276369Z",
116-
"shell.execute_reply": "2024-05-31T05:14:06.275769Z"
113+
"iopub.execute_input": "2024-06-03T12:52:08.620257Z",
114+
"iopub.status.busy": "2024-06-03T12:52:08.619869Z",
115+
"iopub.status.idle": "2024-06-03T12:52:13.799688Z",
116+
"shell.execute_reply": "2024-06-03T12:52:13.799097Z"
117117
}
118118
},
119119
"outputs": [],
@@ -141,10 +141,10 @@
141141
"execution_count": 3,
142142
"metadata": {
143143
"execution": {
144-
"iopub.execute_input": "2024-05-31T05:14:06.279671Z",
145-
"iopub.status.busy": "2024-05-31T05:14:06.279279Z",
146-
"iopub.status.idle": "2024-05-31T05:14:06.514631Z",
147-
"shell.execute_reply": "2024-05-31T05:14:06.513969Z"
144+
"iopub.execute_input": "2024-06-03T12:52:13.804783Z",
145+
"iopub.status.busy": "2024-06-03T12:52:13.803581Z",
146+
"iopub.status.idle": "2024-06-03T12:52:14.039094Z",
147+
"shell.execute_reply": "2024-06-03T12:52:14.038540Z"
148148
}
149149
},
150150
"outputs": [
@@ -174,10 +174,10 @@
174174
"execution_count": 4,
175175
"metadata": {
176176
"execution": {
177-
"iopub.execute_input": "2024-05-31T05:14:06.517542Z",
178-
"iopub.status.busy": "2024-05-31T05:14:06.517350Z",
179-
"iopub.status.idle": "2024-05-31T05:14:06.628875Z",
180-
"shell.execute_reply": "2024-05-31T05:14:06.628230Z"
177+
"iopub.execute_input": "2024-06-03T12:52:14.042087Z",
178+
"iopub.status.busy": "2024-06-03T12:52:14.041694Z",
179+
"iopub.status.idle": "2024-06-03T12:52:14.152914Z",
180+
"shell.execute_reply": "2024-06-03T12:52:14.152263Z"
181181
}
182182
},
183183
"outputs": [
@@ -221,10 +221,10 @@
221221
"execution_count": 5,
222222
"metadata": {
223223
"execution": {
224-
"iopub.execute_input": "2024-05-31T05:14:06.632020Z",
225-
"iopub.status.busy": "2024-05-31T05:14:06.631820Z",
226-
"iopub.status.idle": "2024-05-31T05:14:06.742478Z",
227-
"shell.execute_reply": "2024-05-31T05:14:06.741887Z"
224+
"iopub.execute_input": "2024-06-03T12:52:14.155956Z",
225+
"iopub.status.busy": "2024-06-03T12:52:14.155580Z",
226+
"iopub.status.idle": "2024-06-03T12:52:14.265600Z",
227+
"shell.execute_reply": "2024-06-03T12:52:14.265111Z"
228228
}
229229
},
230230
"outputs": [
@@ -253,10 +253,10 @@
253253
"execution_count": 6,
254254
"metadata": {
255255
"execution": {
256-
"iopub.execute_input": "2024-05-31T05:14:06.745507Z",
257-
"iopub.status.busy": "2024-05-31T05:14:06.744882Z",
258-
"iopub.status.idle": "2024-05-31T05:14:11.186317Z",
259-
"shell.execute_reply": "2024-05-31T05:14:11.185740Z"
256+
"iopub.execute_input": "2024-06-03T12:52:14.268317Z",
257+
"iopub.status.busy": "2024-06-03T12:52:14.267949Z",
258+
"iopub.status.idle": "2024-06-03T12:52:18.765140Z",
259+
"shell.execute_reply": "2024-06-03T12:52:18.764496Z"
260260
}
261261
},
262262
"outputs": [],
@@ -284,10 +284,10 @@
284284
"execution_count": 7,
285285
"metadata": {
286286
"execution": {
287-
"iopub.execute_input": "2024-05-31T05:14:11.189801Z",
288-
"iopub.status.busy": "2024-05-31T05:14:11.189315Z",
289-
"iopub.status.idle": "2024-05-31T05:14:13.861137Z",
290-
"shell.execute_reply": "2024-05-31T05:14:13.860466Z"
287+
"iopub.execute_input": "2024-06-03T12:52:18.768353Z",
288+
"iopub.status.busy": "2024-06-03T12:52:18.768025Z",
289+
"iopub.status.idle": "2024-06-03T12:52:21.437874Z",
290+
"shell.execute_reply": "2024-06-03T12:52:21.437197Z"
291291
}
292292
},
293293
"outputs": [
@@ -301,7 +301,7 @@
301301
"\r\n",
302302
"please submit bugs to https://github.com/votca/votca/issues\r\n",
303303
"\r\n",
304-
"xtp_tools, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
304+
"xtp_tools, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
305305
"\r\n",
306306
"Initializing tool\r\n",
307307
"... partialcharges Evaluating tool\r\n",
@@ -315,17 +315,17 @@
315315
"output_type": "stream",
316316
"text": [
317317
"\r\n",
318-
"... ... 2024-5-31 5:14:11 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
319-
"... ... 2024-5-31 5:14:11 Calculating ESP at CHELPG grid points"
318+
"... ... 2024-6-3 12:52:19 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
319+
"... ... 2024-6-3 12:52:19 Calculating ESP at CHELPG grid points"
320320
]
321321
},
322322
{
323323
"name": "stdout",
324324
"output_type": "stream",
325325
"text": [
326326
"\r\n",
327-
"... ... 2024-5-31 5:14:13 Netcharge constrained to 0\r\n",
328-
"... ... Sum of fitted charges: 2.41994e-14\r\n",
327+
"... ... 2024-6-3 12:52:21 Netcharge constrained to 0\r\n",
328+
"... ... Sum of fitted charges: 2.41543e-14\r\n",
329329
"... ... RMSE of fit: 0.00221585\r\n",
330330
"... ... RRMSE of fit: 0.107179\r\n",
331331
"... ... El Dipole from fitted charges [e*bohr]:\r\n",
@@ -353,10 +353,10 @@
353353
"execution_count": 8,
354354
"metadata": {
355355
"execution": {
356-
"iopub.execute_input": "2024-05-31T05:14:13.864207Z",
357-
"iopub.status.busy": "2024-05-31T05:14:13.864004Z",
358-
"iopub.status.idle": "2024-05-31T05:14:13.999297Z",
359-
"shell.execute_reply": "2024-05-31T05:14:13.998741Z"
356+
"iopub.execute_input": "2024-06-03T12:52:21.441236Z",
357+
"iopub.status.busy": "2024-06-03T12:52:21.440853Z",
358+
"iopub.status.idle": "2024-06-03T12:52:21.576100Z",
359+
"shell.execute_reply": "2024-06-03T12:52:21.575465Z"
360360
}
361361
},
362362
"outputs": [
@@ -370,7 +370,7 @@
370370
"\r\n",
371371
"please submit bugs to https://github.com/votca/votca/issues\r\n",
372372
"\r\n",
373-
"xtp_tools, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
373+
"xtp_tools, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
374374
"\r\n",
375375
"Initializing tool\r\n",
376376
"... spectrum Evaluating tool\r\n",
@@ -412,10 +412,10 @@
412412
"execution_count": 9,
413413
"metadata": {
414414
"execution": {
415-
"iopub.execute_input": "2024-05-31T05:14:14.002414Z",
416-
"iopub.status.busy": "2024-05-31T05:14:14.001941Z",
417-
"iopub.status.idle": "2024-05-31T05:14:15.704399Z",
418-
"shell.execute_reply": "2024-05-31T05:14:15.703743Z"
415+
"iopub.execute_input": "2024-06-03T12:52:21.579372Z",
416+
"iopub.status.busy": "2024-06-03T12:52:21.579172Z",
417+
"iopub.status.idle": "2024-06-03T12:52:23.295098Z",
418+
"shell.execute_reply": "2024-06-03T12:52:23.294522Z"
419419
}
420420
},
421421
"outputs": [
@@ -467,10 +467,10 @@
467467
"execution_count": 10,
468468
"metadata": {
469469
"execution": {
470-
"iopub.execute_input": "2024-05-31T05:14:15.707592Z",
471-
"iopub.status.busy": "2024-05-31T05:14:15.707186Z",
472-
"iopub.status.idle": "2024-05-31T05:14:16.777501Z",
473-
"shell.execute_reply": "2024-05-31T05:14:16.776919Z"
470+
"iopub.execute_input": "2024-06-03T12:52:23.298040Z",
471+
"iopub.status.busy": "2024-06-03T12:52:23.297852Z",
472+
"iopub.status.idle": "2024-06-03T12:52:24.365870Z",
473+
"shell.execute_reply": "2024-06-03T12:52:24.364866Z"
474474
}
475475
},
476476
"outputs": [
@@ -480,7 +480,7 @@
480480
"text": [
481481
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
482482
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
483-
"/tmp/ipykernel_11593/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
483+
"/tmp/ipykernel_11595/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
484484
" df = pd.read_table(\"methane_spectrum.dat\", comment=\"#\", sep='\\s+',names=columns)\n"
485485
]
486486
},

.doctrees/nbsphinx/xtp-tutorials/LAMMPS_KMC.ipynb

Lines changed: 35 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -35,10 +35,10 @@
3535
"execution_count": 1,
3636
"metadata": {
3737
"execution": {
38-
"iopub.execute_input": "2024-05-31T05:14:19.384208Z",
39-
"iopub.status.busy": "2024-05-31T05:14:19.383785Z",
40-
"iopub.status.idle": "2024-05-31T05:14:21.012431Z",
41-
"shell.execute_reply": "2024-05-31T05:14:21.011885Z"
38+
"iopub.execute_input": "2024-06-03T12:52:26.943452Z",
39+
"iopub.status.busy": "2024-06-03T12:52:26.943268Z",
40+
"iopub.status.idle": "2024-06-03T12:52:28.575824Z",
41+
"shell.execute_reply": "2024-06-03T12:52:28.575238Z"
4242
}
4343
},
4444
"outputs": [
@@ -108,10 +108,10 @@
108108
"execution_count": 2,
109109
"metadata": {
110110
"execution": {
111-
"iopub.execute_input": "2024-05-31T05:14:21.016037Z",
112-
"iopub.status.busy": "2024-05-31T05:14:21.015637Z",
113-
"iopub.status.idle": "2024-05-31T05:14:22.056717Z",
114-
"shell.execute_reply": "2024-05-31T05:14:22.056160Z"
111+
"iopub.execute_input": "2024-06-03T12:52:28.579418Z",
112+
"iopub.status.busy": "2024-06-03T12:52:28.579021Z",
113+
"iopub.status.idle": "2024-06-03T12:52:29.633555Z",
114+
"shell.execute_reply": "2024-06-03T12:52:29.632930Z"
115115
}
116116
},
117117
"outputs": [
@@ -125,7 +125,7 @@
125125
"\r\n",
126126
"please submit bugs to https://github.com/votca/votca/issues\r\n",
127127
"\r\n",
128-
"xtp_run, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
128+
"xtp_run, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
129129
"\r\n",
130130
"Initializing calculator\r\n",
131131
"... eanalyze\r\n",
@@ -153,15 +153,15 @@
153153
"output_type": "stream",
154154
"text": [
155155
"\r\n",
156-
"... ... excited state h\r\n",
157-
"... ... excited state s"
156+
"... ... excited state h"
158157
]
159158
},
160159
{
161160
"name": "stdout",
162161
"output_type": "stream",
163162
"text": [
164163
"\r\n",
164+
"... ... excited state s\r\n",
165165
"... ... excited state t"
166166
]
167167
},
@@ -190,10 +190,10 @@
190190
"execution_count": 3,
191191
"metadata": {
192192
"execution": {
193-
"iopub.execute_input": "2024-05-31T05:14:22.060041Z",
194-
"iopub.status.busy": "2024-05-31T05:14:22.059558Z",
195-
"iopub.status.idle": "2024-05-31T05:14:22.171419Z",
196-
"shell.execute_reply": "2024-05-31T05:14:22.170698Z"
193+
"iopub.execute_input": "2024-06-03T12:52:29.636512Z",
194+
"iopub.status.busy": "2024-06-03T12:52:29.636317Z",
195+
"iopub.status.idle": "2024-06-03T12:52:29.748310Z",
196+
"shell.execute_reply": "2024-06-03T12:52:29.747620Z"
197197
}
198198
},
199199
"outputs": [
@@ -227,10 +227,10 @@
227227
"execution_count": 4,
228228
"metadata": {
229229
"execution": {
230-
"iopub.execute_input": "2024-05-31T05:14:22.174898Z",
231-
"iopub.status.busy": "2024-05-31T05:14:22.174665Z",
232-
"iopub.status.idle": "2024-05-31T05:14:23.245200Z",
233-
"shell.execute_reply": "2024-05-31T05:14:23.244020Z"
230+
"iopub.execute_input": "2024-06-03T12:52:29.751884Z",
231+
"iopub.status.busy": "2024-06-03T12:52:29.751508Z",
232+
"iopub.status.idle": "2024-06-03T12:52:30.838364Z",
233+
"shell.execute_reply": "2024-06-03T12:52:30.837697Z"
234234
}
235235
},
236236
"outputs": [
@@ -240,7 +240,7 @@
240240
"text": [
241241
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
242242
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
243-
"/tmp/ipykernel_11634/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
243+
"/tmp/ipykernel_11636/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
244244
" df = pd.read_table(\"eanalyze.pairhist_e.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n"
245245
]
246246
},
@@ -299,10 +299,10 @@
299299
"execution_count": 5,
300300
"metadata": {
301301
"execution": {
302-
"iopub.execute_input": "2024-05-31T05:14:23.248388Z",
303-
"iopub.status.busy": "2024-05-31T05:14:23.247971Z",
304-
"iopub.status.idle": "2024-05-31T05:14:24.176628Z",
305-
"shell.execute_reply": "2024-05-31T05:14:24.176055Z"
302+
"iopub.execute_input": "2024-06-03T12:52:30.841405Z",
303+
"iopub.status.busy": "2024-06-03T12:52:30.841050Z",
304+
"iopub.status.idle": "2024-06-03T12:52:31.760862Z",
305+
"shell.execute_reply": "2024-06-03T12:52:31.760191Z"
306306
}
307307
},
308308
"outputs": [
@@ -316,7 +316,7 @@
316316
"\r\n",
317317
"please submit bugs to https://github.com/votca/votca/issues\r\n",
318318
"\r\n",
319-
"xtp_run, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
319+
"xtp_run, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
320320
"\r\n",
321321
"Initializing calculator\r\n",
322322
"... ianalyze\r\n",
@@ -356,10 +356,10 @@
356356
"execution_count": 6,
357357
"metadata": {
358358
"execution": {
359-
"iopub.execute_input": "2024-05-31T05:14:24.179649Z",
360-
"iopub.status.busy": "2024-05-31T05:14:24.179427Z",
361-
"iopub.status.idle": "2024-05-31T05:14:24.355699Z",
362-
"shell.execute_reply": "2024-05-31T05:14:24.354816Z"
359+
"iopub.execute_input": "2024-06-03T12:52:31.764136Z",
360+
"iopub.status.busy": "2024-06-03T12:52:31.763715Z",
361+
"iopub.status.idle": "2024-06-03T12:52:31.937146Z",
362+
"shell.execute_reply": "2024-06-03T12:52:31.936388Z"
363363
}
364364
},
365365
"outputs": [
@@ -369,7 +369,7 @@
369369
"text": [
370370
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
371371
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
372-
"/tmp/ipykernel_11634/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
372+
"/tmp/ipykernel_11636/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
373373
" df = pd.read_table(\"ianalyze.ihist_h.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n",
374374
"/usr/lib/python3.12/site-packages/seaborn/axisgrid.py:854: FutureWarning: \n",
375375
"\n",
@@ -419,10 +419,10 @@
419419
"execution_count": 7,
420420
"metadata": {
421421
"execution": {
422-
"iopub.execute_input": "2024-05-31T05:14:24.358453Z",
423-
"iopub.status.busy": "2024-05-31T05:14:24.358088Z",
424-
"iopub.status.idle": "2024-05-31T05:14:25.250005Z",
425-
"shell.execute_reply": "2024-05-31T05:14:25.249382Z"
422+
"iopub.execute_input": "2024-06-03T12:52:31.939998Z",
423+
"iopub.status.busy": "2024-06-03T12:52:31.939629Z",
424+
"iopub.status.idle": "2024-06-03T12:52:32.825456Z",
425+
"shell.execute_reply": "2024-06-03T12:52:32.824842Z"
426426
}
427427
},
428428
"outputs": [
@@ -436,7 +436,7 @@
436436
"\r\n",
437437
"please submit bugs to https://github.com/votca/votca/issues\r\n",
438438
"\r\n",
439-
"xtp_run, version 2024-dev gitid: 421d44d (compiled May 31 2024, 05:12:12)\r\n",
439+
"xtp_run, version 2024-dev gitid: 03d5bf1 (compiled Jun 3 2024, 12:50:20)\r\n",
440440
"\r\n",
441441
"Initializing calculator\r\n",
442442
"... kmcmultiple\r\n",

0 commit comments

Comments
 (0)