Skip to content

Commit

Permalink
Documentation Update for votca/votca@f2e4039
Browse files Browse the repository at this point in the history
  • Loading branch information
@votca-bot
votca-bot committed Oct 18, 2024
1 parent aea4619 commit 9f3d019
Show file tree
Hide file tree
Showing 37 changed files with 14,320 additions and 14,647 deletions.
Binary file modified .doctrees/environment.pickle
View file
Binary file not shown.
104 changes: 52 additions & 52 deletions .doctrees/nbsphinx/xtp-tutorials/DFTGWBSE_ENERGY.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,10 +43,10 @@
"execution_count": 1,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:29.196160Z",
"iopub.status.busy": "2024-10-17T00:47:29.195972Z",
"iopub.status.idle": "2024-10-17T00:47:29.325493Z",
"shell.execute_reply": "2024-10-17T00:47:29.324973Z"
"iopub.execute_input": "2024-10-18T05:15:45.731436Z",
"iopub.status.busy": "2024-10-18T05:15:45.730993Z",
"iopub.status.idle": "2024-10-18T05:15:45.860282Z",
"shell.execute_reply": "2024-10-18T05:15:45.859797Z"
}
},
"outputs": [
Expand All @@ -61,7 +61,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Runs excitation/charge transport tools\r\n",
"\r\n",
Expand Down Expand Up @@ -111,10 +111,10 @@
"execution_count": 2,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:29.328420Z",
"iopub.status.busy": "2024-10-17T00:47:29.328218Z",
"iopub.status.idle": "2024-10-17T00:47:34.193637Z",
"shell.execute_reply": "2024-10-17T00:47:34.192932Z"
"iopub.execute_input": "2024-10-18T05:15:45.862964Z",
"iopub.status.busy": "2024-10-18T05:15:45.862773Z",
"iopub.status.idle": "2024-10-18T05:15:50.746509Z",
"shell.execute_reply": "2024-10-18T05:15:50.745923Z"
}
},
"outputs": [],
Expand Down Expand Up @@ -142,10 +142,10 @@
"execution_count": 3,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:34.197304Z",
"iopub.status.busy": "2024-10-17T00:47:34.196950Z",
"iopub.status.idle": "2024-10-17T00:47:34.431238Z",
"shell.execute_reply": "2024-10-17T00:47:34.430644Z"
"iopub.execute_input": "2024-10-18T05:15:50.749521Z",
"iopub.status.busy": "2024-10-18T05:15:50.749327Z",
"iopub.status.idle": "2024-10-18T05:15:50.982165Z",
"shell.execute_reply": "2024-10-18T05:15:50.981681Z"
}
},
"outputs": [
Expand Down Expand Up @@ -175,10 +175,10 @@
"execution_count": 4,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:34.433931Z",
"iopub.status.busy": "2024-10-17T00:47:34.433744Z",
"iopub.status.idle": "2024-10-17T00:47:34.544773Z",
"shell.execute_reply": "2024-10-17T00:47:34.544176Z"
"iopub.execute_input": "2024-10-18T05:15:50.984669Z",
"iopub.status.busy": "2024-10-18T05:15:50.984489Z",
"iopub.status.idle": "2024-10-18T05:15:51.094691Z",
"shell.execute_reply": "2024-10-18T05:15:51.094129Z"
}
},
"outputs": [
Expand Down Expand Up @@ -222,10 +222,10 @@
"execution_count": 5,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:34.547575Z",
"iopub.status.busy": "2024-10-17T00:47:34.547384Z",
"iopub.status.idle": "2024-10-17T00:47:34.658341Z",
"shell.execute_reply": "2024-10-17T00:47:34.657716Z"
"iopub.execute_input": "2024-10-18T05:15:51.097508Z",
"iopub.status.busy": "2024-10-18T05:15:51.097315Z",
"iopub.status.idle": "2024-10-18T05:15:51.206975Z",
"shell.execute_reply": "2024-10-18T05:15:51.206403Z"
}
},
"outputs": [
Expand Down Expand Up @@ -254,10 +254,10 @@
"execution_count": 6,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:34.661116Z",
"iopub.status.busy": "2024-10-17T00:47:34.660929Z",
"iopub.status.idle": "2024-10-17T00:47:39.062534Z",
"shell.execute_reply": "2024-10-17T00:47:39.061942Z"
"iopub.execute_input": "2024-10-18T05:15:51.209413Z",
"iopub.status.busy": "2024-10-18T05:15:51.209073Z",
"iopub.status.idle": "2024-10-18T05:15:55.572405Z",
"shell.execute_reply": "2024-10-18T05:15:55.571814Z"
}
},
"outputs": [],
Expand Down Expand Up @@ -285,10 +285,10 @@
"execution_count": 7,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:39.065918Z",
"iopub.status.busy": "2024-10-17T00:47:39.065460Z",
"iopub.status.idle": "2024-10-17T00:47:41.738279Z",
"shell.execute_reply": "2024-10-17T00:47:41.737671Z"
"iopub.execute_input": "2024-10-18T05:15:55.575546Z",
"iopub.status.busy": "2024-10-18T05:15:55.575340Z",
"iopub.status.idle": "2024-10-18T05:15:58.239964Z",
"shell.execute_reply": "2024-10-18T05:15:58.239389Z"
}
},
"outputs": [
Expand All @@ -303,7 +303,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Initializing tool\r\n",
"... partialcharges Evaluating tool\r\n",
Expand All @@ -317,17 +317,17 @@
"output_type": "stream",
"text": [
"\r\n",
"... ... 2024-10-17 0:47:39 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
"... ... 2024-10-17 0:47:39 Calculating ESP at CHELPG grid points"
"... ... 2024-10-18 5:15:55 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
"... ... 2024-10-18 5:15:55 Calculating ESP at CHELPG grid points"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\r\n",
"... ... 2024-10-17 0:47:41 Netcharge constrained to 0\r\n",
"... ... Sum of fitted charges: 2.41716e-14\r\n",
"... ... 2024-10-18 5:15:58 Netcharge constrained to 0\r\n",
"... ... Sum of fitted charges: 2.42167e-14\r\n",
"... ... RMSE of fit: 0.00221585\r\n",
"... ... RRMSE of fit: 0.107179\r\n",
"... ... El Dipole from fitted charges [e*bohr]:\r\n",
Expand Down Expand Up @@ -355,10 +355,10 @@
"execution_count": 8,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:41.741137Z",
"iopub.status.busy": "2024-10-17T00:47:41.740768Z",
"iopub.status.idle": "2024-10-17T00:47:41.877996Z",
"shell.execute_reply": "2024-10-17T00:47:41.877328Z"
"iopub.execute_input": "2024-10-18T05:15:58.242830Z",
"iopub.status.busy": "2024-10-18T05:15:58.242447Z",
"iopub.status.idle": "2024-10-18T05:15:58.376024Z",
"shell.execute_reply": "2024-10-18T05:15:58.375525Z"
}
},
"outputs": [
Expand All @@ -373,7 +373,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Initializing tool\r\n",
"... spectrum Evaluating tool\r\n",
Expand Down Expand Up @@ -415,27 +415,27 @@
"execution_count": 9,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:41.881060Z",
"iopub.status.busy": "2024-10-17T00:47:41.880853Z",
"iopub.status.idle": "2024-10-17T00:47:43.647642Z",
"shell.execute_reply": "2024-10-17T00:47:43.646970Z"
"iopub.execute_input": "2024-10-18T05:15:58.379080Z",
"iopub.status.busy": "2024-10-18T05:15:58.378630Z",
"iopub.status.idle": "2024-10-18T05:16:00.112072Z",
"shell.execute_reply": "2024-10-18T05:16:00.111410Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: seaborn in /usr/lib/python3.12/site-packages (0.13.2)\r\n"
"Requirement already satisfied: seaborn in /usr/lib/python3.12/site-packages (0.13.2)\r\n",
"Requirement already satisfied: numpy!=1.24.0,>=1.20 in /usr/lib64/python3.12/site-packages (from seaborn) (1.26.4)\r\n",
"Requirement already satisfied: pandas>=1.2 in /usr/lib64/python3.12/site-packages (from seaborn) (2.2.1)\r\n",
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.12/site-packages (from seaborn) (3.8.4)\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: numpy!=1.24.0,>=1.20 in /usr/lib64/python3.12/site-packages (from seaborn) (1.26.4)\r\n",
"Requirement already satisfied: pandas>=1.2 in /usr/lib64/python3.12/site-packages (from seaborn) (2.2.1)\r\n",
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.12/site-packages (from seaborn) (3.8.4)\r\n",
"Requirement already satisfied: contourpy>=1.0.1 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (1.2.0)\r\n",
"Requirement already satisfied: cycler>=0.10 in /usr/lib/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (0.11.0)\r\n",
"Requirement already satisfied: fonttools>=4.22.0 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (4.50.0)\r\n",
Expand Down Expand Up @@ -470,10 +470,10 @@
"execution_count": 10,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:43.651208Z",
"iopub.status.busy": "2024-10-17T00:47:43.650807Z",
"iopub.status.idle": "2024-10-17T00:47:44.700428Z",
"shell.execute_reply": "2024-10-17T00:47:44.699816Z"
"iopub.execute_input": "2024-10-18T05:16:00.115476Z",
"iopub.status.busy": "2024-10-18T05:16:00.115038Z",
"iopub.status.idle": "2024-10-18T05:16:01.143989Z",
"shell.execute_reply": "2024-10-18T05:16:01.143265Z"
}
},
"outputs": [
Expand All @@ -483,7 +483,7 @@
"text": [
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11585/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11629/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
" df = pd.read_table(\"methane_spectrum.dat\", comment=\"#\", sep='\\s+',names=columns)\n"
]
},
Expand Down
72 changes: 36 additions & 36 deletions .doctrees/nbsphinx/xtp-tutorials/LAMMPS_KMC.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,10 +35,10 @@
"execution_count": 1,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:47.274794Z",
"iopub.status.busy": "2024-10-17T00:47:47.274412Z",
"iopub.status.idle": "2024-10-17T00:47:48.935503Z",
"shell.execute_reply": "2024-10-17T00:47:48.934929Z"
"iopub.execute_input": "2024-10-18T05:16:03.458929Z",
"iopub.status.busy": "2024-10-18T05:16:03.458751Z",
"iopub.status.idle": "2024-10-18T05:16:05.123226Z",
"shell.execute_reply": "2024-10-18T05:16:05.122588Z"
}
},
"outputs": [
Expand All @@ -49,15 +49,15 @@
"Requirement already satisfied: seaborn in /usr/lib/python3.12/site-packages (0.13.2)\r\n",
"Requirement already satisfied: numpy!=1.24.0,>=1.20 in /usr/lib64/python3.12/site-packages (from seaborn) (1.26.4)\r\n",
"Requirement already satisfied: pandas>=1.2 in /usr/lib64/python3.12/site-packages (from seaborn) (2.2.1)\r\n",
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.12/site-packages (from seaborn) (3.8.4)\r\n"
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.12/site-packages (from seaborn) (3.8.4)\r\n",
"Requirement already satisfied: contourpy>=1.0.1 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (1.2.0)\r\n",
"Requirement already satisfied: cycler>=0.10 in /usr/lib/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (0.11.0)\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: contourpy>=1.0.1 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (1.2.0)\r\n",
"Requirement already satisfied: cycler>=0.10 in /usr/lib/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (0.11.0)\r\n",
"Requirement already satisfied: fonttools>=4.22.0 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (4.50.0)\r\n",
"Requirement already satisfied: kiwisolver>=1.3.1 in /usr/lib64/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (1.4.7)\r\n",
"Requirement already satisfied: packaging>=20.0 in /usr/lib/python3.12/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (23.2)\r\n",
Expand Down Expand Up @@ -108,10 +108,10 @@
"execution_count": 2,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:48.939127Z",
"iopub.status.busy": "2024-10-17T00:47:48.938583Z",
"iopub.status.idle": "2024-10-17T00:47:49.978753Z",
"shell.execute_reply": "2024-10-17T00:47:49.978162Z"
"iopub.execute_input": "2024-10-18T05:16:05.126354Z",
"iopub.status.busy": "2024-10-18T05:16:05.126163Z",
"iopub.status.idle": "2024-10-18T05:16:06.164023Z",
"shell.execute_reply": "2024-10-18T05:16:06.163512Z"
}
},
"outputs": [
Expand All @@ -126,7 +126,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... eanalyze\r\n",
Expand Down Expand Up @@ -191,10 +191,10 @@
"execution_count": 3,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:49.981596Z",
"iopub.status.busy": "2024-10-17T00:47:49.981394Z",
"iopub.status.idle": "2024-10-17T00:47:50.092574Z",
"shell.execute_reply": "2024-10-17T00:47:50.091962Z"
"iopub.execute_input": "2024-10-18T05:16:06.166773Z",
"iopub.status.busy": "2024-10-18T05:16:06.166567Z",
"iopub.status.idle": "2024-10-18T05:16:06.277813Z",
"shell.execute_reply": "2024-10-18T05:16:06.277314Z"
}
},
"outputs": [
Expand Down Expand Up @@ -228,10 +228,10 @@
"execution_count": 4,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:50.095495Z",
"iopub.status.busy": "2024-10-17T00:47:50.095110Z",
"iopub.status.idle": "2024-10-17T00:47:51.149880Z",
"shell.execute_reply": "2024-10-17T00:47:51.149255Z"
"iopub.execute_input": "2024-10-18T05:16:06.280686Z",
"iopub.status.busy": "2024-10-18T05:16:06.280488Z",
"iopub.status.idle": "2024-10-18T05:16:07.311198Z",
"shell.execute_reply": "2024-10-18T05:16:07.310493Z"
}
},
"outputs": [
Expand All @@ -241,7 +241,7 @@
"text": [
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11626/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11670/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
" df = pd.read_table(\"eanalyze.pairhist_e.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n"
]
},
Expand Down Expand Up @@ -300,10 +300,10 @@
"execution_count": 5,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:51.152464Z",
"iopub.status.busy": "2024-10-17T00:47:51.152259Z",
"iopub.status.idle": "2024-10-17T00:47:52.075196Z",
"shell.execute_reply": "2024-10-17T00:47:52.074504Z"
"iopub.execute_input": "2024-10-18T05:16:07.314012Z",
"iopub.status.busy": "2024-10-18T05:16:07.313574Z",
"iopub.status.idle": "2024-10-18T05:16:08.225389Z",
"shell.execute_reply": "2024-10-18T05:16:08.224794Z"
}
},
"outputs": [
Expand All @@ -318,7 +318,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... ianalyze\r\n",
Expand Down Expand Up @@ -358,10 +358,10 @@
"execution_count": 6,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:52.077977Z",
"iopub.status.busy": "2024-10-17T00:47:52.077763Z",
"iopub.status.idle": "2024-10-17T00:47:52.251993Z",
"shell.execute_reply": "2024-10-17T00:47:52.251222Z"
"iopub.execute_input": "2024-10-18T05:16:08.228699Z",
"iopub.status.busy": "2024-10-18T05:16:08.228251Z",
"iopub.status.idle": "2024-10-18T05:16:08.402147Z",
"shell.execute_reply": "2024-10-18T05:16:08.401536Z"
}
},
"outputs": [
Expand All @@ -371,7 +371,7 @@
"text": [
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11626/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11670/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
" df = pd.read_table(\"ianalyze.ihist_h.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n",
"/usr/lib/python3.12/site-packages/seaborn/axisgrid.py:854: FutureWarning: \n",
"\n",
Expand Down Expand Up @@ -421,10 +421,10 @@
"execution_count": 7,
"metadata": {
"execution": {
"iopub.execute_input": "2024-10-17T00:47:52.254533Z",
"iopub.status.busy": "2024-10-17T00:47:52.254328Z",
"iopub.status.idle": "2024-10-17T00:47:53.150261Z",
"shell.execute_reply": "2024-10-17T00:47:53.149593Z"
"iopub.execute_input": "2024-10-18T05:16:08.404659Z",
"iopub.status.busy": "2024-10-18T05:16:08.404463Z",
"iopub.status.idle": "2024-10-18T05:16:09.291697Z",
"shell.execute_reply": "2024-10-18T05:16:09.291179Z"
}
},
"outputs": [
Expand All @@ -439,7 +439,7 @@
"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
"and submit bugs to https://github.com/votca/votca/issues\r\n",
"\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 17 2024, 00:44:28)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Oct 18 2024, 05:12:22)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... kmcmultiple\r\n",
Expand Down
Loading

0 comments on commit 9f3d019

Please sign in to comment.