Molcas parser API

Imports to get the resource files

[1]:
from vibrav.base import resource
from vibrav.util.open_files import uncompress_file
import os

Uncompress the resource file

[2]:
decomp = uncompress_file(resource('molcas-rassi-nien.out.xz'))

Read the output file

[3]:
from vibrav.molcas import Output
[4]:
ed = Output(decomp)

Parse the spin-free dipole moments

[5]:
ed.parse_sf_dipole_moment()
ed.sf_dipole_moment
[5]:
0 1 2 3 4 5 6 7 8 9 ... 16 17 18 19 20 21 22 23 24 component
0 -9.376636e-06 -9.383159e-04 -5.259894e-04 -6.844936e-07 8.287023e-04 5.784427e-04 -3.305595e-08 -7.190377e-08 -8.454175e-04 -4.697420e-04 ... -8.798365e-20 1.388980e-19 -7.326883e-20 2.544445e-18 -1.419502e-18 -1.440886e-21 9.137218e-19 2.811453e-20 4.550291e-18 x
1 -9.383159e-04 4.938038e-03 8.086204e-03 8.956935e-03 -2.483163e-03 -5.127446e-03 -3.889645e-03 -5.159244e-03 3.840473e-03 6.217030e-03 ... 1.989800e-18 1.577644e-18 2.620320e-18 -1.807584e-19 -2.453048e-19 -9.210226e-20 -6.286158e-19 1.502377e-18 5.741586e-20 x
2 -5.259894e-04 8.086204e-03 -4.955820e-03 -1.598368e-02 -5.128130e-03 2.482465e-03 -2.178772e-03 -2.890120e-03 6.220213e-03 -3.840069e-03 ... -1.843977e-18 8.185865e-18 -2.640023e-18 -8.216381e-19 1.244695e-19 -1.027803e-19 -5.960823e-19 -2.427264e-19 2.866196e-19 x
3 -6.844936e-07 8.956935e-03 -1.598368e-02 -5.832545e-06 8.057229e-03 -1.155555e-02 8.588415e-07 -2.991994e-07 -6.062807e-03 1.092611e-02 ... -1.797950e-18 3.197102e-20 1.497748e-18 1.218254e-19 -1.471458e-19 3.094076e-18 -4.012417e-19 6.367794e-18 -1.113868e-19 x
4 8.287023e-04 -2.483163e-03 -5.128130e-03 8.057229e-03 3.184097e-03 8.667119e-03 -2.491305e-03 -2.237622e-03 1.024558e-05 1.718904e-05 ... 4.998033e-18 1.080093e-18 2.621471e-19 -1.356941e-18 4.851931e-18 -4.377820e-19 -2.460354e-19 -2.222575e-18 1.050619e-19 x
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
70 2.798133e-20 -7.494509e-21 1.837413e-19 4.658169e-20 -4.350311e-20 -4.986815e-19 4.598024e-19 -2.752256e-19 3.880373e-20 -2.264951e-19 ... -3.439530e-05 3.746701e-03 4.879674e-05 -4.470660e-06 -1.853061e-08 -5.129429e-07 -2.733188e-04 -3.820681e-07 -4.882723e-07 z
71 1.697245e-19 7.001676e-21 -5.006348e-20 2.464600e-20 4.468406e-20 -1.822131e-19 -6.176509e-19 3.473685e-19 8.654902e-22 2.792257e-20 ... 1.109199e-05 -9.979060e-04 -2.022896e-05 -2.518394e-04 -5.129429e-07 8.667985e-08 2.121827e-05 -2.716501e-06 1.468724e-06 z
72 -1.933543e-22 -1.599636e-19 6.460808e-20 -9.327870e-20 5.560524e-20 1.639681e-20 5.806210e-20 1.996194e-20 1.152501e-19 3.058508e-20 ... 1.010293e-03 1.111767e-05 3.031995e-06 4.642385e-07 -2.733188e-04 2.121827e-05 -8.201143e-08 -1.724641e-05 9.633586e-06 z
73 3.674293e-20 -1.132336e-20 2.856421e-19 4.001355e-21 1.449966e-20 -1.046807e-19 2.573478e-19 -1.295672e-19 7.010531e-21 -3.302352e-19 ... -4.566679e-06 -3.468737e-05 3.051234e-03 2.725762e-06 -3.820681e-07 -2.716501e-06 -1.724641e-05 4.697866e-09 2.735140e-08 z
74 6.389150e-20 -5.825257e-20 4.447751e-20 4.439398e-21 6.247369e-20 1.103016e-18 -1.104416e-18 -6.566795e-19 -1.603367e-20 -7.502357e-20 ... 1.344133e-05 1.051371e-04 -1.062807e-02 2.906158e-06 -4.882723e-07 1.468724e-06 9.633586e-06 2.735140e-08 -1.426067e-08 z

75 rows × 26 columns

Parse the spin-free quadrupole moment

This will only parse the upper triangular elements of the matrix. I.e., the xx, xy, xz, yy, yz, and zz compoenents.

[6]:
ed.parse_sf_quadrupole_moment()
ed.sf_quadrupole_moment
[6]:
0 1 2 3 4 5 6 7 8 9 ... 16 17 18 19 20 21 22 23 24 component
0 -3.500140e+01 1.173247e-02 6.580265e-03 6.674075e-06 -6.331848e-02 -4.415315e-02 6.546761e-02 7.538489e-02 6.657617e-02 3.695543e-02 ... -1.867184e-18 4.938135e-17 -1.525615e-17 1.081891e-15 -9.495733e-17 2.103179e-17 4.890426e-17 2.152580e-19 8.784260e-17 xx
1 1.173247e-02 -3.545854e+01 3.780688e-02 8.820404e-02 -1.373307e-02 -1.262719e-01 -1.128179e-01 -6.731629e-02 -3.009900e-02 1.232099e-01 ... 5.989637e-16 1.370153e-16 4.590252e-17 -2.581924e-18 9.026816e-18 -2.041515e-16 -1.408774e-16 2.477513e-16 -1.763594e-17 xx
2 6.580265e-03 3.780688e-02 -3.550478e+01 -1.574149e-01 -1.361030e-01 1.133322e-01 -6.321337e-02 -3.770022e-02 1.223889e-01 -1.817725e-01 ... -1.936954e-16 1.032403e-16 6.011572e-16 -9.821624e-17 6.937587e-18 -1.406346e-17 -8.820235e-18 2.148651e-17 -4.197851e-18 xx
3 6.674075e-06 8.820404e-02 -1.574149e-01 -3.536689e+01 1.440698e-01 -2.066119e-01 -1.561867e-06 -1.181690e-06 -1.660243e-01 2.991383e-01 ... 4.826918e-16 2.534805e-17 3.788097e-17 -1.250331e-18 -1.986380e-17 5.757652e-16 1.283977e-17 -2.825176e-16 -9.258153e-18 xx
4 -6.331848e-02 -1.373307e-02 -1.361030e-01 1.440698e-01 -3.560160e+01 1.089867e-01 -1.045581e-01 -2.487637e-01 -3.690626e-01 -1.178888e-01 ... -1.661790e-17 6.268158e-17 1.005471e-17 -1.190769e-17 6.305117e-16 -1.235855e-16 -5.809364e-17 -3.989386e-16 1.953748e-17 xx
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
145 -5.353959e-17 1.553045e-17 -1.791974e-18 -1.280992e-18 4.663912e-16 1.120435e-17 -2.605852e-16 5.946732e-17 2.563243e-16 2.339960e-17 ... 4.950885e-02 4.527462e-04 1.221739e-04 -1.649518e-08 -4.447863e+01 2.213497e-01 -4.169294e-04 1.124140e-03 -9.071752e-04 zz
146 1.213004e-17 -1.731779e-16 -2.041465e-17 4.170898e-16 -1.109232e-16 -5.616328e-18 -9.997202e-17 5.529510e-19 -3.207592e-16 -2.334154e-17 ... -1.656264e-01 -1.831634e-03 -3.086526e-04 -4.184335e-04 2.213497e-01 -4.444879e+01 -4.720966e-06 -1.793273e-03 -1.499529e-03 zz
147 2.583342e-17 -9.382642e-17 -1.365728e-17 1.874459e-17 -2.270473e-17 -3.131737e-16 -8.067280e-16 6.148585e-16 7.953961e-18 5.520967e-16 ... 1.843311e-03 -1.667328e-01 -2.148542e-03 -2.219409e-01 -4.169294e-04 -4.720966e-06 -4.445048e+01 2.823250e-04 2.339333e-04 zz
148 -6.567873e-20 1.772268e-16 2.677679e-17 -3.526988e-16 -2.759673e-16 -1.073295e-16 -1.361126e-18 2.109195e-18 -1.163318e-16 1.769014e-17 ... 2.558363e-05 -1.311877e-06 1.763864e-07 1.743400e-04 1.124140e-03 -1.793273e-03 2.823250e-04 -4.411257e+01 3.167020e-01 zz
149 -1.611504e-18 1.750389e-17 -2.846105e-21 -1.510383e-17 1.040778e-17 -2.532659e-18 2.078083e-19 8.150862e-20 -1.091187e-17 -1.905165e-18 ... 4.111305e-05 -3.663114e-06 1.212405e-06 -1.338341e-04 -9.071752e-04 -1.499529e-03 2.339333e-04 3.167020e-01 -4.388516e+01 zz

150 rows × 26 columns

Parse the spin-free angular momentum

[7]:
ed.parse_sf_angmom()
ed.sf_angmom
[7]:
0 1 2 3 4 5 6 7 8 9 ... 16 17 18 19 20 21 22 23 24 component
0 6.626731e-18 -1.553359e+00 -8.705123e-01 -1.015200e-04 -3.127997e-02 -2.182243e-02 4.095653e-06 1.191905e-06 7.531522e-03 4.182673e-03 ... -1.552690e-16 1.180405e-16 -4.020604e-17 2.068694e-20 5.867911e-18 -7.130628e-17 -2.947106e-17 3.162611e-17 1.128699e-18 x
1 1.553359e+00 -4.571222e-16 -4.233573e-05 2.585774e-01 6.076944e-01 1.254894e+00 -8.535142e-01 2.196790e-01 2.134496e-01 3.456598e-01 ... -1.017408e-16 6.327755e-17 1.062884e-16 -5.816560e-17 1.698517e-17 -1.018386e-16 1.189779e-17 1.037624e-16 5.340634e-17 x
2 8.705123e-01 4.233573e-05 -8.710006e-17 -4.614284e-01 1.254876e+00 -6.077587e-01 -4.782594e-01 1.231310e-01 3.456392e-01 -2.134668e-01 ... -8.478716e-18 -4.990680e-17 -1.430057e-16 -1.092594e-16 9.307636e-17 3.730760e-18 6.864208e-18 5.863639e-17 7.663078e-17 x
3 1.015200e-04 -2.585774e-01 4.614284e-01 9.882260e-17 5.559758e-01 -7.970499e-01 -1.958799e-05 2.570007e-05 1.382345e-01 -2.489937e-01 ... 1.859949e-16 -1.407091e-17 -1.315167e-17 6.863221e-17 -6.336027e-17 -6.016258e-17 1.522854e-16 2.035658e-17 5.194333e-17 x
4 3.127997e-02 -6.076944e-01 -1.254876e+00 -5.559758e-01 7.815008e-16 -4.359339e-05 -9.501658e-01 6.395912e-01 2.098857e-03 4.315184e-03 ... -1.402546e-17 -8.147693e-18 4.681586e-17 -2.209597e-17 8.914598e-17 -1.445746e-17 8.168061e-17 -1.067923e-17 1.460346e-17 x
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
70 1.076297e-18 5.058259e-18 -6.958368e-17 2.276363e-17 -9.803107e-18 -1.241716e-16 1.548133e-16 -1.197104e-16 1.781604e-17 -1.709743e-17 ... -1.553752e-02 1.692434e+00 1.661221e-02 4.493845e-01 -2.242914e-16 2.756765e-03 1.461629e+00 -9.076902e-04 -1.548385e-06 z
71 6.871715e-17 5.650068e-18 1.206950e-17 7.114093e-18 9.970490e-18 1.560849e-16 -1.724995e-16 5.840906e-17 -9.425148e-18 1.035572e-16 ... 4.561864e-03 -4.111893e-01 -9.155088e-03 -1.458302e+00 -2.756765e-03 -4.688703e-16 -1.174555e+00 8.376364e-04 2.041596e-05 z
72 -5.002503e-19 -2.315452e-18 2.365850e-17 -4.725534e-17 7.158064e-17 9.121058e-18 1.574381e-17 -7.206228e-20 -4.742131e-17 7.152212e-18 ... 4.138430e-01 4.560828e-03 1.376082e-03 2.744145e-03 -1.461629e+00 1.174555e+00 4.949914e-17 5.342435e-03 1.209511e-04 z
73 1.875531e-17 -1.439694e-18 9.718745e-17 -8.412248e-19 5.580965e-18 -2.975092e-17 6.093322e-17 -1.302164e-17 1.966598e-18 -9.145873e-17 ... -1.756205e-03 -1.334722e-02 1.224967e+00 -5.833379e-03 9.076902e-04 -8.376364e-04 -5.342435e-03 -6.160120e-16 -1.337943e-06 z
74 4.219490e-18 -2.262157e-17 -8.309751e-18 -1.200748e-19 2.796168e-18 6.910406e-17 -3.962958e-16 -6.394910e-17 3.122763e-18 -2.303865e-17 ... 9.977237e-04 7.759110e-03 -8.003581e-01 -1.392226e-05 1.548385e-06 -2.041596e-05 -1.209511e-04 1.337943e-06 -9.249594e-16 z

75 rows × 26 columns

Parse the spin-free energies

[8]:
ed.parse_sf_energy()
ed.sf_energy
[8]:
energy rel_energy
0 -2077.953987 0.000000
1 -2077.903019 0.050968
2 -2077.903018 0.050969
3 -2077.902361 0.051626
4 -2077.870278 0.083709
5 -2077.870275 0.083712
6 -2077.868713 0.085274
7 -2077.816677 0.137310
8 -2077.816249 0.137738
9 -2077.816240 0.137747
10 -2077.885925 0.068062
11 -2077.885754 0.068233
12 -2077.835508 0.118479
13 -2077.834321 0.119666
14 -2077.834318 0.119669
15 -2077.834244 0.119743
16 -2077.807731 0.146256
17 -2077.807723 0.146264
18 -2077.807293 0.146694
19 -2077.766660 0.187327
20 -2077.766605 0.187382
21 -2077.763766 0.190221
22 -2077.763634 0.190353
23 -2077.763618 0.190369
24 -2077.666439 0.287548

Parse the spin-orbit energies

[9]:
ed.parse_so_energy()
ed.so_energy
[9]:
energy rel_energy
0 -2077.954390 0.000000e+00
1 -2077.954390 9.999894e-09
2 -2077.954387 3.260000e-06
3 -2077.904739 4.965116e-02
4 -2077.904733 4.965666e-02
5 -2077.903867 5.052263e-02
6 -2077.903867 5.052302e-02
7 -2077.903745 5.064452e-02
8 -2077.902419 5.197119e-02
9 -2077.901899 5.249087e-02
10 -2077.901899 5.249126e-02
11 -2077.901295 5.309470e-02
12 -2077.886226 6.816392e-02
13 -2077.886066 6.832363e-02
14 -2077.873816 8.057348e-02
15 -2077.871850 8.254028e-02
16 -2077.871342 8.304758e-02
17 -2077.871340 8.304971e-02
18 -2077.868206 8.618360e-02
19 -2077.868206 8.618428e-02
20 -2077.867139 8.725046e-02
21 -2077.866569 8.782112e-02
22 -2077.866563 8.782704e-02
23 -2077.835769 1.186211e-01
24 -2077.835337 1.190529e-01
25 -2077.835334 1.190561e-01
26 -2077.834799 1.195913e-01
27 -2077.817396 1.369943e-01
28 -2077.817393 1.369973e-01
29 -2077.816481 1.379089e-01
30 -2077.816285 1.381048e-01
31 -2077.816284 1.381056e-01
32 -2077.815347 1.390425e-01
33 -2077.815342 1.390480e-01
34 -2077.815145 1.392451e-01
35 -2077.814290 1.400999e-01
36 -2077.807559 1.468304e-01
37 -2077.807552 1.468383e-01
38 -2077.807127 1.472626e-01
39 -2077.766475 1.879153e-01
40 -2077.766420 1.879702e-01
41 -2077.763621 1.907691e-01
42 -2077.763489 1.909009e-01
43 -2077.763480 1.909094e-01
44 -2077.666114 2.882755e-01

Parse the spin-free oscillators and the respective Einstein coefficients

[10]:
ed.parse_sf_oscillator()
ed.sf_oscillator
[10]:
nrow ncol oscil a_x a_y a_z a_tot
0 0 1 3.930999e-08 2.496945e+00 7.840636e-01 9.657002e-07 3.281010e+00
1 0 2 3.933130e-08 7.846762e-01 2.498241e+00 4.025564e-08 3.282917e+00
2 0 3 2.102329e-07 1.380900e-06 2.857155e-07 1.800309e+01 1.800309e+01
3 0 4 5.696867e-08 8.628428e+00 4.197526e+00 2.811387e-06 1.282596e+01
4 0 5 5.706843e-08 4.204379e+00 8.644959e+00 7.061455e-08 1.284934e+01
... ... ... ... ... ... ... ...
145 21 23 2.536118e-09 5.299360e-07 1.254916e-06 5.124162e-13 1.784852e-06
146 21 24 2.492648e-06 2.252458e+02 5.333962e+02 4.259893e-05 7.586421e+02
147 22 23 2.766291e-10 1.599847e-09 6.754759e-10 2.609615e-14 2.275349e-09
148 22 24 2.512245e-06 5.361555e+02 2.263767e+02 1.825265e-03 7.625340e+02
149 23 24 6.365324e-11 3.192207e-03 1.612189e-02 1.470600e-08 1.931411e-02

150 rows × 7 columns

Parse the spin-orbit oscillators and the respective Einstein coefficients

[11]:
ed.parse_so_oscillator()
ed.so_oscillator
[11]:
nrow ncol oscil a_x a_y a_z a_tot
0 0 1 4.318828e-18 2.016091e-23 3.312361e-24 2.343992e-30 2.347327e-23
1 0 2 3.911798e-15 4.156324e-16 9.189764e-16 5.844245e-24 1.334609e-15
2 0 3 5.394123e-08 8.279098e-01 1.537588e-01 3.290899e+00 4.272568e+00
3 0 4 1.236666e-08 1.529829e-01 8.254572e-01 1.313496e-03 9.797536e-01
4 0 5 9.356059e-08 4.234016e+00 1.078398e+00 2.360747e+00 7.673160e+00
... ... ... ... ... ... ... ...
985 41 43 2.430109e-09 4.575384e-07 1.079441e-06 4.469775e-13 1.536979e-06
986 41 44 2.508080e-06 2.274764e+02 5.386792e+02 4.296662e-05 7.661557e+02
987 42 43 1.483332e-10 2.427076e-10 1.020911e-10 3.948815e-15 3.448027e-10
988 42 44 2.527732e-06 5.414604e+02 2.286106e+02 1.839430e-03 7.700729e+02
989 43 44 8.138990e-11 1.570466e-03 2.322060e-02 6.346128e-09 2.479108e-02

990 rows × 7 columns

[12]:
os.remove(decomp)
[ ]: