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Documentation Update for votca/votca@36ab2c4 
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‎.doctrees/environment.pickle‎

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

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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"and submit bugs to https://github.com/votca/votca/issues\r\n",
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"\r\n",
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"xtp_tools, version 2025.1-dev gitid: 9782ace (compiled Oct 31 2025, 05:46:44)\r\n",
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"xtp_tools, version 2025.1-dev gitid: 36ab2c4 (compiled Oct 31 2025, 19:12:00)\r\n",
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"\r\n",
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"Runs excitation/charge transport tools\r\n",
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"\r\n",
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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"and submit bugs to https://github.com/votca/votca/issues\r\n",
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"\r\n",
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"xtp_tools, version 2025.1-dev gitid: 9782ace (compiled Oct 31 2025, 05:46:44)\r\n",
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"xtp_tools, version 2025.1-dev gitid: 36ab2c4 (compiled Oct 31 2025, 19:12:00)\r\n",
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"\r\n",
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"Initializing tool\r\n",
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"... partialcharges Evaluating tool\r\n",
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"\r\n",
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"... ... 2025-10-31 5:48:32 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
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"... ... 2025-10-31 5:48:32 Calculating ESP at CHELPG grid points"
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"... ... 2025-10-31 19:14:30 Calculated Densities at Numerical Grid, Number of electrons is -2.37461e-08\r\n",
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"... ... 2025-10-31 19:14:30 Calculating ESP at CHELPG grid points"
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"\r\n",
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"... ... 2025-10-31 5:48:34 Netcharge constrained to 0\r\n",
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"... ... Sum of fitted charges: 2.42792e-14\r\n",
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"... ... 2025-10-31 19:14:32 Netcharge constrained to 0\r\n",
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"... ... Sum of fitted charges: 2.41543e-14\r\n",
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"... ... RMSE of fit: 0.00221585\r\n",
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"... ... RRMSE of fit: 0.107179\r\n",
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"... ... El Dipole from fitted charges [e*bohr]:\r\n",
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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"and submit bugs to https://github.com/votca/votca/issues\r\n",
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"\r\n",
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"xtp_tools, version 2025.1-dev gitid: 9782ace (compiled Oct 31 2025, 05:46:44)\r\n",
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"xtp_tools, version 2025.1-dev gitid: 36ab2c4 (compiled Oct 31 2025, 19:12:00)\r\n",
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"\r\n",
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"Initializing tool\r\n",
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"... spectrum Evaluating tool\r\n",
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"Requirement already satisfied: packaging>=20.0 in /usr/lib/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (24.2)\r\n",
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"Requirement already satisfied: pillow>=8 in /usr/lib64/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (11.1.0)\r\n",
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"Requirement already satisfied: pyparsing>=2.3.1 in /usr/lib/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (3.1.2)\r\n",
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"Requirement already satisfied: python-dateutil>=2.7 in /usr/lib/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (2.8.2)\r\n",
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"Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3.13/site-packages (from pandas>=1.2->seaborn) (2025.2)\r\n"
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"Requirement already satisfied: python-dateutil>=2.7 in /usr/lib/python3.13/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn) (2.8.2)\r\n"
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"Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3.13/site-packages (from pandas>=1.2->seaborn) (2025.2)\r\n",
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"Requirement already satisfied: six>=1.5 in /usr/lib/python3.13/site-packages (from python-dateutil>=2.7->matplotlib!=3.6.1,>=3.4->seaborn) (1.17.0)\r\n"
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"<>:5: SyntaxWarning: invalid escape sequence '\\s'\n",
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" df = pd.read_table(\"methane_spectrum.dat\", comment=\"#\", sep='\\s+',names=columns)\n"
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‎.doctrees/nbsphinx/xtp-tutorials/LAMMPS_KMC.ipynb‎

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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"and submit bugs to https://github.com/votca/votca/issues\r\n",
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"\r\n",
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"xtp_run, version 2025.1-dev gitid: 36ab2c4 (compiled Oct 31 2025, 19:12:00)\r\n",
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"Initializing calculator\r\n",
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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"iopub.execute_input": "2025-10-31T19:14:39.586974Z",
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"iopub.status.busy": "2025-10-31T19:14:39.586765Z",
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"iopub.status.idle": "2025-10-31T19:14:39.748529Z",
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"shell.execute_reply": "2025-10-31T19:14:39.747863Z"
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}
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},
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"outputs": [
@@ -353,7 +353,7 @@
353353
"text": [
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"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
355355
"<>:2: SyntaxWarning: invalid escape sequence '\\s'\n",
356-
"/tmp/ipykernel_11427/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
356+
"/tmp/ipykernel_11502/886975016.py:2: SyntaxWarning: invalid escape sequence '\\s'\n",
357357
" df = pd.read_table(\"ianalyze.ihist_h.out\", comment=\"#\", sep='\\s+',names=columns, skiprows=2)\n",
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"/usr/lib/python3.13/site-packages/seaborn/axisgrid.py:854: FutureWarning: \n",
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"\n",
@@ -403,10 +403,10 @@
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"execution_count": 7,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-10-31T05:48:41.598404Z",
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"iopub.status.busy": "2025-10-31T05:48:41.598224Z",
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"iopub.status.idle": "2025-10-31T05:48:41.963022Z",
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"shell.execute_reply": "2025-10-31T05:48:41.962454Z"
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"iopub.execute_input": "2025-10-31T19:14:39.750947Z",
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"iopub.status.busy": "2025-10-31T19:14:39.750766Z",
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"iopub.status.idle": "2025-10-31T19:14:40.116260Z",
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"shell.execute_reply": "2025-10-31T19:14:40.115668Z"
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}
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},
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"outputs": [
@@ -421,7 +421,7 @@
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"please read and cite: https://doi.org/10.21105/joss.06864\r\n",
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"and submit bugs to https://github.com/votca/votca/issues\r\n",
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"\r\n",
424-
"xtp_run, version 2025.1-dev gitid: 9782ace (compiled Oct 31 2025, 05:46:44)\r\n",
424+
"xtp_run, version 2025.1-dev gitid: 36ab2c4 (compiled Oct 31 2025, 19:12:00)\r\n",
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"\r\n",
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"Initializing calculator\r\n",
427427
"... kmcmultiple\r\n",

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