Utility scripts

Felix Plasser

A number of utility scripts are distributed together with TheoDORE. These are found in the $THEODIR/bin directory along with the main programs.

jmol_MOs.py

Prepare a script for automatized orbital rendering of Molden files in Jmol. This script is particularly useful in cases where a large number of orbital files (NOs, NTOs, or NDOs) are produced as is the case for example with libwfa or COLUMBUS. Using this script, it is possible to process the files simultaneously

Call jmol_MOs.py with the names of the Molden files as arguments:

jmol_MOs.py [<mldfile> [<mldfile2> ...]]

For example, if you want to analyze all .molden files call

jmol_MOs.py *.molden

Then choose the required options in the interactive menu.

After running the script, you can either use the fully automatic procedure and simply call

jmol -n multi.jmol_orbitals.spt
firefox multi.orbitals.html

Or use the semi-interactive version

  1. Open Jmol

  2. Run the first few lines of the script to preview the settings (simply copy them into the Jmol console)

  3. Adjust the perspective

  4. Run the remaining lines of the script (by copying into the Jmol console)

  5. Open the file oribtals.html to view the result.

babel.py

Conversion between different types of molecular structure files, using the Open Babel package.

babel.py <intype> <infile> <outtype> <outfile>
---
babel.py tmol coord xyz coord.xyz

extract_molden.py

Extract the hole/particle components from a Molden file and write them into separate Molden files. This utility can be used for plotting hole and particle densities in Molden.

syntax: extract_molden.py <mo_file1> [<mo_file2> ...]
options: -ene          - interpret energies as occupations
         -thresh=0.001 - threshold for print-out

convert_table.py

Convert the data produced by TheoDORE into a table in LaTeX or html format

spectrum.py

Create a convoluted spectrum from the energies and oscillator strengths parsed by analyze_tden.py.

spectrum.py <tden_summ1> [<tden_summ2> ...]

It is also possible to compute the density of states (no weighting by oscillator strengths) and to add restrictions with respect to the states chosen (e.g. only states with CT > 0.5).

cc_check.py

Check whether a file can be parsed with cclib

cc_check.py <logfile>

cc2molden.py

Convert a log-file to Molden format with the help of cclib.

cc2molden.py <logfile>

parse_libwfa.py

Directly parse libwfa output

 parse_libwfa.py <logfile> <type>
   type: qcadc, qctddft, rassi

plot_frag_decomp.py

Interactive script for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py


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