Files for running representative sampling for Nuclear ensemble method
Contains all of the scripts, split into 3 stages
LAUNCH - launch ORCA calculations from MD movie or wigner sampling
PROCESS - calculate UV-vis spectra, perform representative sampling, extract ORCA calculation results
POSTPROCESS - plotting scripts for postprocessing data
There is also a WORKFLOW folder containing
- a SLURM submission script with SBATCH settings
- a runscript which acts as a wrapper and calls the different LAUNCH and PROCESSSING scripts
- a config file, which intialises variables required for the script
Requirements:
- a "movie" of geometries, see the example movies for format details
- ORCA QC software
- Access to HPC (QC calculations are costly for personal machines)
Most of the configuration is done in the config file, however, to use different QC methods, they need to be added to calc.ORCA.sh. A simplified Hartree-Fock semi-empirical method, and TDDFT B3LYP 6-311*G are given as an example
Scripts from https://github.com/PHOTOX/photoxrepo, https://github.com/stepan-srsen/PyNEAppLES have been used in this repository
The mol directory is initialised by the programme in the LaunchNEM directory, with seperate mol directories created for each seperate run. All of the spectrum data, ORCA files and geometry data is found here after the program has been run.