PYSORP

Generate QE input files

In examples/qe_input_source are some example files to set up a series of QE input files. .pos files contain positions of surface atoms or molecule. In these files those atoms are marked by a number 1(atom in molecule or surface top side), 2(surface bridge side), 3(surface hollow side) which will be used for positioning of the molecule above the surface. qe_template contains all options to run a QE calculation except the atom positions. generate_files.params tells the script which template files to combine and how to generate the different configurations.

python2 pysorb_mkqein.py -i examples/qe_input_source/generate_files.params -o examples/qe_input_generated

This files can then be used for QE calculation runs:

pw.x < file.in > file.out

Extract information from QE outputfiles

Place a series of QE output files inside of a directory. This script will extract atom positions and energies from these files and generate a single file which contains all required information to do further analysis or generate a GULP input file.

python2 pysorb_dump.py -qe examples/qe_output -e_ref -7425.27983804 -o examples/test.qedump

Generate GULP input files

Simple energy calculation with GULP

to get adsorption energies for a given set of potentials.

python2 pysorb_compare.py -d examples/test.qedump -p examples/gulp_compare/model1.param -o examples/compare_run.gin

Parameter optimisation with GULP

python2 pysorb_fit.py -d examples/test.qedump -p examples/gulp_compare/model1.param -o examples/fit_run.gin

# or

python2 pysorb_fit.py -d examples/test.qedump -p examples/gulp_compare/model1.param -o examples/fit_run.gin -w -t 310

Run GULP

gulp < file.gin > file.gout