UKRmol-scripts: A Perl-based system for the automated operation of the photoionization and electron/positron scattering suite UKRmol

• Published in: Computer physics communications 2024-05, Vol.298, p.109113, Article 109113
• Main Authors: Houfek, Karel, Benda, Jakub, Mašín, Zdeněk, Harvey, Alex, Meltzer, Thomas, Graves, Vincent, Gorfinkiel, Jimena D.
• Format: Article
• Language: English
• Subjects: Photoionization; R-matrix; Scattering; Transition moments
• ISSN: 0010-4655; 1879-2944
• DOI: 10.1016/j.cpc.2024.109113

UKRmol-scripts is a set of Perl scripts to automatically run the UKRmol+ codes, a complex software suite based on the R-matrix method to model fixed-nuclei photoionization and electron- and positron-scattering for polyatomic molecules. Starting with several basic parameters, the scripts operatively produce all necessary input files and run all codes for electronic structure and scattering calculations as well as gather the more frequently required outputs. The scripts provide a simple way to run such calculations for many molecular geometries concurrently and collect the resulting data for easier post-processing and visualization. We describe the structure of the scripts and the input parameters as well as provide examples for photoionization and electron and positron collisions with molecules. The codes are freely available from Zenodo. Program Title: UKRmol-scripts CPC Library link to program files:https://doi.org/10.17632/cpvc2473pt.1 Developer's repository link:https://gitlab.com/Uk-amor/UKRMol/UKRmol-scripts Licensing provisions: GPLv3 Programming language: Perl Nature of problem: Performing ab initio photoionization and low energy electron- and positron-scattering on polyatomic molecules requires selecting and setting a significant number of input parameters in order to model the physics in a numerically accurate way. These scripts streamline setting up and analyzing calculations based on the R-matrix method [1] using the UKRmol+ suite [2]. Solution method: The scripts provide automatic generation of input files and execution of programs from the UKRmol+ suite [2] using a number of parameters that describe both physical models and machine-dependent settings, and also outputs of the previous programs in the suite which are automatically read and analyzed. The resulting output files are then post-processed to collect target and scattering data for further analysis and simple plotting. Additional comments including restrictions and unusual features: The scripts should be used with releases 3.2 of UKRmol-in and UKRmol-out [3] although they are compatible with earlier versions. [1]P.G. Burke, R-Matrix Theory of Atomic Collisions: Application to Atomic, Molecular and Optical Processes, Springer, Berlin, 2011.[2]Z. Mašín et al., UKRmol+: a suite for modelling electronic processes in molecules interacting with electrons, positrons and photons using the R-matrix method, Comput. Phys. Commum. 249 (2020) 107092.[3]UKRMol+: UKRMol-in 3.2, https://doi.org/10.5281