{
"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": {
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"\n",
"[75 rows x 26 columns]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ed.parse_sf_dipole_moment()\n",
"ed.sf_dipole_moment"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Parse the spin-free quadrupole moment\n",
"\n",
"This will only parse the upper triangular elements of the matrix. I.e., the `xx`, `xy`, `xz`, `yy`, `yz`, and `zz` compoenents."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
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150 rows × 26 columns
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" ... 16 17 18 19 \\\n",
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".. ... ... ... ... ... \n",
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"\n",
" component \n",
"0 xx \n",
"1 xx \n",
"2 xx \n",
"3 xx \n",
"4 xx \n",
".. ... \n",
"145 zz \n",
"146 zz \n",
"147 zz \n",
"148 zz \n",
"149 zz \n",
"\n",
"[150 rows x 26 columns]"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ed.parse_sf_quadrupole_moment()\n",
"ed.sf_quadrupole_moment"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Parse the spin-free angular momentum"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
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"\n",
"[75 rows x 26 columns]"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ed.parse_sf_angmom()\n",
"ed.sf_angmom"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Parse the spin-free energies"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
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},
"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": [
{
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"37 -2077.807552 1.468383e-01\n",
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},
"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": [
{
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" 5.124162e-13 | \n",
" 1.784852e-06 | \n",
"
\n",
" \n",
" 146 | \n",
" 21 | \n",
" 24 | \n",
" 2.492648e-06 | \n",
" 2.252458e+02 | \n",
" 5.333962e+02 | \n",
" 4.259893e-05 | \n",
" 7.586421e+02 | \n",
"
\n",
" \n",
" 147 | \n",
" 22 | \n",
" 23 | \n",
" 2.766291e-10 | \n",
" 1.599847e-09 | \n",
" 6.754759e-10 | \n",
" 2.609615e-14 | \n",
" 2.275349e-09 | \n",
"
\n",
" \n",
" 148 | \n",
" 22 | \n",
" 24 | \n",
" 2.512245e-06 | \n",
" 5.361555e+02 | \n",
" 2.263767e+02 | \n",
" 1.825265e-03 | \n",
" 7.625340e+02 | \n",
"
\n",
" \n",
" 149 | \n",
" 23 | \n",
" 24 | \n",
" 6.365324e-11 | \n",
" 3.192207e-03 | \n",
" 1.612189e-02 | \n",
" 1.470600e-08 | \n",
" 1.931411e-02 | \n",
"
\n",
" \n",
"
\n",
"
150 rows × 7 columns
\n",
"
"
],
"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": [
"\n",
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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": []
}
],
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