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Documentation Update for votca/votca@f2e4039
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votca-bot committed Nov 22, 2024
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104 changes: 52 additions & 52 deletions .doctrees/nbsphinx/xtp-tutorials/DFTGWBSE_ENERGY.ipynb
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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 Nov 15 2024, 05:24:10)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\r\n",
"\r\n",
"Runs excitation/charge transport tools\r\n",
"\r\n",
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"execution_count": 4,
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"execution_count": 5,
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"execution_count": 6,
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"execution_count": 7,
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"execution": {
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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 Nov 15 2024, 05:24:10)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\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",
"... ... 2024-11-15 5:26:13 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
"... ... 2024-11-15 5:26:13 Calculating ESP at CHELPG grid points"
"... ... 2024-11-22 5:14:41 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
"... ... 2024-11-22 5:14:41 Calculating ESP at CHELPG grid points"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\r\n",
"... ... 2024-11-15 5:26:15 Netcharge constrained to 0\r\n",
"... ... Sum of fitted charges: 2.40849e-14\r\n",
"... ... 2024-11-22 5:14:44 Netcharge constrained to 0\r\n",
"... ... Sum of fitted charges: 2.41925e-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",
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"execution_count": 8,
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"outputs": [
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"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 Nov 15 2024, 05:24:10)\r\n",
"xtp_tools, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\r\n",
"\r\n",
"Initializing tool\r\n",
"... spectrum Evaluating tool\r\n",
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"execution_count": 9,
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: seaborn in /usr/lib/python3.13/site-packages (0.13.2)\r\n",
"Requirement already satisfied: numpy!=1.24.0,>=1.20 in /usr/lib64/python3.13/site-packages (from seaborn) (1.26.4)\r\n",
"Requirement already satisfied: pandas>=1.2 in /usr/lib64/python3.13/site-packages (from seaborn) (2.2.1)\r\n",
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.13/site-packages (from seaborn) (3.9.1)\r\n"
"Requirement already satisfied: seaborn in /usr/lib/python3.13/site-packages (0.13.2)\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: numpy!=1.24.0,>=1.20 in /usr/lib64/python3.13/site-packages (from seaborn) (1.26.4)\r\n",
"Requirement already satisfied: pandas>=1.2 in /usr/lib64/python3.13/site-packages (from seaborn) (2.2.1)\r\n",
"Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /usr/lib64/python3.13/site-packages (from seaborn) (3.9.1)\r\n",
"Requirement already satisfied: contourpy>=1.0.1 in /usr/lib64/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (1.3.0)\r\n",
"Requirement already satisfied: cycler>=0.10 in /usr/lib/python3.13/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/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (4.53.1)\r\n",
Expand All @@ -458,10 +458,10 @@
"execution_count": 10,
"metadata": {
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}
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"outputs": [
Expand All @@ -471,7 +471,7 @@
"text": [
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11533/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11538/3151737206.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
" df = pd.read_table(\"methane_spectrum.dat\", comment=\"#\", sep='\\s+',names=columns)\n"
]
},
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66 changes: 33 additions & 33 deletions .doctrees/nbsphinx/xtp-tutorials/LAMMPS_KMC.ipynb
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"execution_count": 2,
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"outputs": [
Expand All @@ -114,7 +114,7 @@
"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 Nov 15 2024, 05:24:10)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... eanalyze\r\n",
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"execution_count": 3,
"metadata": {
"execution": {
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}
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"outputs": [
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"execution_count": 4,
"metadata": {
"execution": {
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Expand All @@ -229,7 +229,7 @@
"text": [
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11574/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11579/2362228021.py:5: SyntaxWarning: invalid escape sequence '\\s'\n",
" df = pd.read_table(\"eanalyze.pairhist_e.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n"
]
},
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"execution_count": 5,
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-15T05:26:23.082562Z",
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}
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"outputs": [
Expand All @@ -306,7 +306,7 @@
"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 Nov 15 2024, 05:24:10)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... ianalyze\r\n",
Expand Down Expand Up @@ -346,10 +346,10 @@
"execution_count": 6,
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-15T05:26:24.001559Z",
"iopub.status.busy": "2024-11-15T05:26:24.001370Z",
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}
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"outputs": [
Expand All @@ -359,7 +359,7 @@
"text": [
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11574/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
"/tmp/ipykernel_11579/886975016.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/python3.13/site-packages/seaborn/axisgrid.py:854: FutureWarning: \n",
"\n",
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"execution_count": 7,
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-15T05:26:24.162365Z",
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}
},
"outputs": [
Expand All @@ -427,7 +427,7 @@
"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 Nov 15 2024, 05:24:10)\r\n",
"xtp_run, version 2024.2-dev gitid: f2e4039 (compiled Nov 22 2024, 05:12:38)\r\n",
"\r\n",
"Initializing calculator\r\n",
"... kmcmultiple\r\n",
Expand Down
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