{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Molcas parser API\n", "## Imports to get the resource files" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from vibrav.base import resource\n", "from vibrav.util.open_files import uncompress_file\n", "import os" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Uncompress the resource file" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "decomp = uncompress_file(resource('molcas-rassi-nien.out.xz'))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Read the output file" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "from vibrav.molcas import Output" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "ed = Output(decomp)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Parse the spin-free dipole moments" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " energy rel_energy\n", "0 -2077.953987 0.000000\n", "1 -2077.903019 0.050968\n", "2 -2077.903018 0.050969\n", "3 -2077.902361 0.051626\n", "4 -2077.870278 0.083709\n", "5 -2077.870275 0.083712\n", "6 -2077.868713 0.085274\n", "7 -2077.816677 0.137310\n", "8 -2077.816249 0.137738\n", "9 -2077.816240 0.137747\n", "10 -2077.885925 0.068062\n", "11 -2077.885754 0.068233\n", "12 -2077.835508 0.118479\n", "13 -2077.834321 0.119666\n", "14 -2077.834318 0.119669\n", "15 -2077.834244 0.119743\n", "16 -2077.807731 0.146256\n", "17 -2077.807723 0.146264\n", "18 -2077.807293 0.146694\n", "19 -2077.766660 0.187327\n", "20 -2077.766605 0.187382\n", "21 -2077.763766 0.190221\n", "22 -2077.763634 0.190353\n", "23 -2077.763618 0.190369\n", "24 -2077.666439 0.287548" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ed.parse_sf_energy()\n", "ed.sf_energy" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Parse the spin-orbit energies" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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energyrel_energy
0-2077.9543900.000000e+00
1-2077.9543909.999894e-09
2-2077.9543873.260000e-06
3-2077.9047394.965116e-02
4-2077.9047334.965666e-02
5-2077.9038675.052263e-02
6-2077.9038675.052302e-02
7-2077.9037455.064452e-02
8-2077.9024195.197119e-02
9-2077.9018995.249087e-02
10-2077.9018995.249126e-02
11-2077.9012955.309470e-02
12-2077.8862266.816392e-02
13-2077.8860666.832363e-02
14-2077.8738168.057348e-02
15-2077.8718508.254028e-02
16-2077.8713428.304758e-02
17-2077.8713408.304971e-02
18-2077.8682068.618360e-02
19-2077.8682068.618428e-02
20-2077.8671398.725046e-02
21-2077.8665698.782112e-02
22-2077.8665638.782704e-02
23-2077.8357691.186211e-01
24-2077.8353371.190529e-01
25-2077.8353341.190561e-01
26-2077.8347991.195913e-01
27-2077.8173961.369943e-01
28-2077.8173931.369973e-01
29-2077.8164811.379089e-01
30-2077.8162851.381048e-01
31-2077.8162841.381056e-01
32-2077.8153471.390425e-01
33-2077.8153421.390480e-01
34-2077.8151451.392451e-01
35-2077.8142901.400999e-01
36-2077.8075591.468304e-01
37-2077.8075521.468383e-01
38-2077.8071271.472626e-01
39-2077.7664751.879153e-01
40-2077.7664201.879702e-01
41-2077.7636211.907691e-01
42-2077.7634891.909009e-01
43-2077.7634801.909094e-01
44-2077.6661142.882755e-01
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" ], "text/plain": [ " energy rel_energy\n", "0 -2077.954390 0.000000e+00\n", "1 -2077.954390 9.999894e-09\n", "2 -2077.954387 3.260000e-06\n", "3 -2077.904739 4.965116e-02\n", "4 -2077.904733 4.965666e-02\n", "5 -2077.903867 5.052263e-02\n", "6 -2077.903867 5.052302e-02\n", "7 -2077.903745 5.064452e-02\n", "8 -2077.902419 5.197119e-02\n", "9 -2077.901899 5.249087e-02\n", "10 -2077.901899 5.249126e-02\n", "11 -2077.901295 5.309470e-02\n", "12 -2077.886226 6.816392e-02\n", "13 -2077.886066 6.832363e-02\n", "14 -2077.873816 8.057348e-02\n", "15 -2077.871850 8.254028e-02\n", "16 -2077.871342 8.304758e-02\n", "17 -2077.871340 8.304971e-02\n", "18 -2077.868206 8.618360e-02\n", "19 -2077.868206 8.618428e-02\n", "20 -2077.867139 8.725046e-02\n", "21 -2077.866569 8.782112e-02\n", "22 -2077.866563 8.782704e-02\n", "23 -2077.835769 1.186211e-01\n", "24 -2077.835337 1.190529e-01\n", "25 -2077.835334 1.190561e-01\n", "26 -2077.834799 1.195913e-01\n", "27 -2077.817396 1.369943e-01\n", "28 -2077.817393 1.369973e-01\n", "29 -2077.816481 1.379089e-01\n", "30 -2077.816285 1.381048e-01\n", "31 -2077.816284 1.381056e-01\n", "32 -2077.815347 1.390425e-01\n", "33 -2077.815342 1.390480e-01\n", "34 -2077.815145 1.392451e-01\n", "35 -2077.814290 1.400999e-01\n", "36 -2077.807559 1.468304e-01\n", "37 -2077.807552 1.468383e-01\n", "38 -2077.807127 1.472626e-01\n", "39 -2077.766475 1.879153e-01\n", "40 -2077.766420 1.879702e-01\n", "41 -2077.763621 1.907691e-01\n", "42 -2077.763489 1.909009e-01\n", "43 -2077.763480 1.909094e-01\n", "44 -2077.666114 2.882755e-01" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ed.parse_so_energy()\n", "ed.so_energy" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Parse the spin-free oscillators and the respective Einstein coefficients" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nrowncoloscila_xa_ya_za_tot
0013.930999e-082.496945e+007.840636e-019.657002e-073.281010e+00
1023.933130e-087.846762e-012.498241e+004.025564e-083.282917e+00
2032.102329e-071.380900e-062.857155e-071.800309e+011.800309e+01
3045.696867e-088.628428e+004.197526e+002.811387e-061.282596e+01
4055.706843e-084.204379e+008.644959e+007.061455e-081.284934e+01
........................
14521232.536118e-095.299360e-071.254916e-065.124162e-131.784852e-06
14621242.492648e-062.252458e+025.333962e+024.259893e-057.586421e+02
14722232.766291e-101.599847e-096.754759e-102.609615e-142.275349e-09
14822242.512245e-065.361555e+022.263767e+021.825265e-037.625340e+02
14923246.365324e-113.192207e-031.612189e-021.470600e-081.931411e-02
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150 rows × 7 columns

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" ], "text/plain": [ " nrow ncol oscil a_x a_y a_z \\\n", "0 0 1 3.930999e-08 2.496945e+00 7.840636e-01 9.657002e-07 \n", "1 0 2 3.933130e-08 7.846762e-01 2.498241e+00 4.025564e-08 \n", "2 0 3 2.102329e-07 1.380900e-06 2.857155e-07 1.800309e+01 \n", "3 0 4 5.696867e-08 8.628428e+00 4.197526e+00 2.811387e-06 \n", "4 0 5 5.706843e-08 4.204379e+00 8.644959e+00 7.061455e-08 \n", ".. ... ... ... ... ... ... \n", "145 21 23 2.536118e-09 5.299360e-07 1.254916e-06 5.124162e-13 \n", "146 21 24 2.492648e-06 2.252458e+02 5.333962e+02 4.259893e-05 \n", "147 22 23 2.766291e-10 1.599847e-09 6.754759e-10 2.609615e-14 \n", "148 22 24 2.512245e-06 5.361555e+02 2.263767e+02 1.825265e-03 \n", "149 23 24 6.365324e-11 3.192207e-03 1.612189e-02 1.470600e-08 \n", "\n", " a_tot \n", "0 3.281010e+00 \n", "1 3.282917e+00 \n", "2 1.800309e+01 \n", "3 1.282596e+01 \n", "4 1.284934e+01 \n", ".. ... \n", "145 1.784852e-06 \n", "146 7.586421e+02 \n", "147 2.275349e-09 \n", "148 7.625340e+02 \n", "149 1.931411e-02 \n", "\n", "[150 rows x 7 columns]" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ed.parse_sf_oscillator()\n", "ed.sf_oscillator" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Parse the spin-orbit oscillators and the respective Einstein coefficients" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nrowncoloscila_xa_ya_za_tot
0014.318828e-182.016091e-233.312361e-242.343992e-302.347327e-23
1023.911798e-154.156324e-169.189764e-165.844245e-241.334609e-15
2035.394123e-088.279098e-011.537588e-013.290899e+004.272568e+00
3041.236666e-081.529829e-018.254572e-011.313496e-039.797536e-01
4059.356059e-084.234016e+001.078398e+002.360747e+007.673160e+00
........................
98541432.430109e-094.575384e-071.079441e-064.469775e-131.536979e-06
98641442.508080e-062.274764e+025.386792e+024.296662e-057.661557e+02
98742431.483332e-102.427076e-101.020911e-103.948815e-153.448027e-10
98842442.527732e-065.414604e+022.286106e+021.839430e-037.700729e+02
98943448.138990e-111.570466e-032.322060e-026.346128e-092.479108e-02
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990 rows × 7 columns

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" ], "text/plain": [ " nrow ncol oscil a_x a_y a_z \\\n", "0 0 1 4.318828e-18 2.016091e-23 3.312361e-24 2.343992e-30 \n", "1 0 2 3.911798e-15 4.156324e-16 9.189764e-16 5.844245e-24 \n", "2 0 3 5.394123e-08 8.279098e-01 1.537588e-01 3.290899e+00 \n", "3 0 4 1.236666e-08 1.529829e-01 8.254572e-01 1.313496e-03 \n", "4 0 5 9.356059e-08 4.234016e+00 1.078398e+00 2.360747e+00 \n", ".. ... ... ... ... ... ... \n", "985 41 43 2.430109e-09 4.575384e-07 1.079441e-06 4.469775e-13 \n", "986 41 44 2.508080e-06 2.274764e+02 5.386792e+02 4.296662e-05 \n", "987 42 43 1.483332e-10 2.427076e-10 1.020911e-10 3.948815e-15 \n", "988 42 44 2.527732e-06 5.414604e+02 2.286106e+02 1.839430e-03 \n", "989 43 44 8.138990e-11 1.570466e-03 2.322060e-02 6.346128e-09 \n", "\n", " a_tot \n", "0 2.347327e-23 \n", "1 1.334609e-15 \n", "2 4.272568e+00 \n", "3 9.797536e-01 \n", "4 7.673160e+00 \n", ".. ... \n", "985 1.536979e-06 \n", "986 7.661557e+02 \n", "987 3.448027e-10 \n", "988 7.700729e+02 \n", "989 2.479108e-02 \n", "\n", "[990 rows x 7 columns]" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ed.parse_so_oscillator()\n", "ed.so_oscillator" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [], "source": [ "os.remove(decomp)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.6" } }, "nbformat": 4, "nbformat_minor": 4 }