orca-uv

A Python 3 script for (hassle-free) plotting of absorption spectra from ORCA output files with peak dectection and annotation. It combines the stick spectrum with the convoluted spectrum (gaussian line shape). The script supports energy (wave number, cm^-1) and wavelength (λ, nm) plots. The full spectrum or parts of the spectrum can be plotted.

Please also have a look at the interactive Jupyter Notebook edition. It offers a sligthly reduced functionality without the need to maintain a local Python installation. Please upload an orca.out file to the same directory and adjust the code to abs_data = imp_data('my_orca_calc_with_abs_data.out').
Note: The interactive Matplotlib window does not work very well with colab. Replace %matplotlib widget with %matplotlib inline for a better performance. However, this change removes the ability to select a specific region and save the spectrum bitmap.

External modules

numpy scipy matplotlib

Quick start

Start the script with:

python3 orca-uv.py filename

it will save the plot as PNG bitmap: filename-abs.png

Command-line options

• filename , required: filename
• -s , optional: shows the matplotlib window
• -n , optional: do not save the spectrum
• -e , optional: export the line spectrum in a csv-like fashion; filename of the export is input filename + "-mod.dat"
• -pwn , optional: plot the wave number (energy, cm^-1) spectrum
• -wnm N , optional: line width of the gaussian for the nm scale (default is N = 20)
• -wwn N , optional: line width of the gaussian for the cm^-1 scale (default is N = 1000)
• -x0 N , optional: start spectrum at N nm or N cm^-1 (x0 => 0)
• -x1 N , optional: end spectrum at N nm or N cm^-1 (x1 => 0)

Script options

There are numerous ways to configure the spectrum in the script: Check # plot config section - configure here in the script. You can even configure the script to plot of the single gaussian functions.

The delimiter for the line spectrum export can be changed by changing the value of export_delim =.

Code options

Colors, line thickness, line styles, level of peak detection and more can be changed in the code directly.

Remarks

The PNG file will be replaced everytime you start the script with the same output file. If you want to keep the file, you have to rename it. The data are taken from the section "ABSORPTION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS".

Examples: