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PyRad

This script package was developed for the creation and analysis of the radiolysis systems.

The main software to perform all TDDFT calculations: qb@ll (https://github.com/LLNL/qball) You will also need the packmol software to create systems (http://m3g.iqm.unicamp.br/packmol/home.shtml)

This repo includes:

  1. PyRadCreator - creates an enviroment for radyolysis calculation in qb@ll software.

     Usage: PyRadCreator.py input1.ini input2.ini
 .ini files, and the host .xyz files should be placed in the same directory as this script.
 all pseudopotentials should be placed in pseudos directory
 WARNING! qb@ll doesn't respond to windows EOL symbol on unix-based systems!

  2. PyRadTester - H2O radicals searcher with simple gui. Auto output of econst .csv file.

     Usage: PyRadTester.py qball_out.o
 For additional info about econst parameter see the url: 
 https://github.com/LLNL/qball/wiki/Tutorial-TDDFT#finding-the-optimal-time-step

  3. PyRadEDensity - analyses the electron density .cube file and findes all anomalies in it.

     Usage: PyRadTester.py cube_file.o

 on GUI: symbols - atoms
         colored dots - electron density maxima
         sample size and threshold - sliders for maxima searcher
         correlation - slider to filter out electron density maxima that appear near atoms

  4. Utils/PyRadDatAvrg.py is an additional utility for averaging several simulations.

     Usage: PyRadDatAvrg.py 1.sys 2.sys
 .sys-files can be generated by PyRadTester.

  5. Utils/PyRadDatDraw.py is an utility to draw .sys file. It can be generated with PyRadTester

     Usage: PyRadDatDraw.py 1.sys

Please cite, if using:

Andreadi, N, Mitrofanov, A, Eliseev, A, Matveev, P, Kalmykov, S, Petrov, V. PyRad: A software shell for simulating radiolysis with Qball package. J Comput Chem. 2021; 42: 944– 950. https://doi.org/10.1002/jcc.26509