UKRmol-scripts: A Perl-based system for the automated operation of the photoionization and electron/positron scattering suite UKRmol+
UKRmol-scripts: A Perl-based system for the automated operation of the photoionization and electron/positron scattering suite UKRmol+
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DOI：
10.1016/j.cpc.2024.109113
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发表时间：
2023-04
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通讯作者：
K. Houfek;J. Benda;Z. Mašín;A. Harvey;T. Meltzer;V. Graves;J. Gorfinkiel
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作者：
K. Houfek;J. Benda;Z. Mašín;A. Harvey;T. Meltzer;V. Graves;J. Gorfinkiel
UKRmol-scripts是一组Perl脚本，用于自动运行UKRmol+代码，这是一个复杂的软件套件，基于R矩阵方法，用于模拟多原子分子的固定核光电离和电子和正电子散射。从几个基本参数开始，脚本可操作地产生所有必要的输入文件，并运行所有用于电子结构和散射计算的代码，以及收集更频繁需要的输出。这些脚本提供了一种简单的方法来同时运行许多分子几何形状的计算，并收集结果数据，以便于后处理和可视化。我们描述的脚本和输入参数的结构，以及提供的例子，光电离和电子和正电子与分子碰撞。程序概要程序标题：UKRmol-scriptsCPC Library程序文件链接：https：//doi.org/10.17632/cpvc2473pt.1开发者仓库链接：https://gitlab.com/Uk-amor/UKRMol/UKRmol-scriptsLicensing条款：GPL v3编程语言：Perl问题性质：在多原子分子上执行ab initiphotoionization和低能电子和正电子散射需要选择和设置大量的输入参数，以便以数值精确的方式模拟物理。这些脚本使用UKRmol+套件[2]简化了基于R-矩阵方法[1]的设置和分析计算。解决方案方法：脚本提供自动生成输入文件和执行UKRmol+套件[2]中的程序，使用许多参数描述物理模型和机器相关设置，以及套件中以前程序的输出，这些输出可以自动读取和分析。然后对生成的输出文件进行后处理，以收集目标和散射数据，用于进一步分析和简单绘图。其他注释包括限制和不寻常的功能：这些脚本应该与UKRmol-in和UKRmol-out的3.2版本一起使用[3]，尽管它们与早期版本兼容。Burke，原子碰撞的R矩阵理论：应用于原子、分子和光学过程，Springer，柏林，2011年。[2]Z. Mašín等人，UKRmol+：一套用于模拟分子与电子，正电子和光子相互作用的电子过程的R矩阵方法，COMPUT。公共物理学249（2020）107092. [3]UKRMol+：UKRMol-in 3.2，https：//doi.org/10.5281/zenodo.5799110，2021; UKRMol+：UKRMol-out 3.2，https：//doi.org/10.5281/zenodo.5799134，2020.
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 summaryProgram Title:UKRmol-scriptsCPC Library link to program files:https://doi.org/10.17632/cpvc2473pt.1Developer's repository link:https://gitlab.com/Uk-amor/UKRMol/UKRmol-scriptsLicensing provisions:GPLv3Programming language:PerlNature of problem:Performingab initiophotoionization 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.References[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/zenodo.5799110, 2021; UKRMol+: UKRMol-out 3.2, https://doi.org/10.5281/zenodo.5799134, 2020.