QCP - Quantum Chemical Processor
Automate processes such as
- creating input and job files
- recursive parsing of log files
- recursive submission of jobs, deletion of queued jobs
- Finding bond distances of xyz files
Currently installed on Raijin, Magnus, Monarch, Massive and Stampede. Implemented for GAMESS, PSI4 and Gaussian calculations
Scripts to generate a LAMMPS input file, along with a data file containing the appropriate force field parameters, given an xyz file with numbered atoms. Uses a python script to fill a blank data file generated by vmd, with a dictionary populated with the required force field parameters. See the readme in the folder for more details.
Takes a GAMESS log file as an input and produces an infrared spectra along with a molecule viewer to view all the vibrational modes of files generated using the FMO approach.
Parse GAMESS log files for use with molden, allowing for easy viewing of geometries, convergence, frequencies and vibrational modes generated using the FMO approach (also works with non-FMO).
Useful when generating IR spectra as molden automatically fits Lorentzian curves to the intensities found from the Hessian.
Run as gamess_to_molden.py input.log
Use this script to obtain the sizes of each folder in the current directory. Useful for logging scratch space usage. (May throw errors if directory names contain spaces)
Use clean_scratch.sh to remove all files that are not required for currently running jobs.
NB: Do NOT use this script if you run jobs from the scratch folder and have no local backups. This script will delete all of your work!
To remove temporary files in the group scratch folder, run the following command:
cd /scratch/sn29; ls -l | grep $USER | awk '{print $NF}' | grep ^[0-9] | xargs rm -r; cd -
This will remove folders written by SLURM i.e. folders named with the SLURM job id.
Gaussview 5 cannot read a Gaussian 16 frequency output. A fix is described here.