/comp-chem-scripts

Primary LanguagePython

Adrea's comp chem scripts (that are worth sharing)

compoundScripts/fieldGen

This tool allows you to generate an electric field based on the grid points surrounding the molecules, and with the help of plotVecField.py, allows you to visualise the fiueld in PyMOL. since Psi4's generation of properties on a grid is serial in nature, I've also parallelised that process.

Tips:

  • If your wavefunction is going to take up lots of memory, make sure to run your psi4 job specifying only a small amount (~16GB) but allow the slurm job to take as much memory as you need. This will force the calculation to use disk-based algorithms, instead of in-memory ones, that can otherwise explode in memory during density fitting procedures.
  • Make sure that you specify the same number of threads in the psi4 job as you do in the slurm script.
  • There are two flavours of the script, one in which the script generates the Psi4 wavefunction object internally form the molecule and theory specified in the input file, and the other in which the geometry and wavefunction are read from an exported wfn.npy object. This is useful if you want to generate the wavefunction with different slurm properties (more or less threads/mem), since the generation of the vector field is heavily threaded and not that memory intensive.

compoundScripts/miniFMO

This praticular project was a failiure, but attempted ot re-implement the FMO1+2 method in Psi4, using point charge genration of the ESP and optimisation. The process has been documented on my website.

I've included both the partial charge version and the charge cloud (ESP) version, which is based heavily on the CHELPG method. The included iPython notebook just allows for the interactive visualisation of the point cloud from the exported .npy matrix.

slmUtilities/2slm.py (formerly 2slm.sh)

A job submitter for MonARCH and M3 that supports the automatic generation and submisison of slm files from ORCA, Psi4, and Gaussian input files. All the slurm settings are fully customisable, but where possible it will automatically detect the settings from the input file itself.

It also supports a few more advanced tricks, like IFTTT notificaitons, file copying, software version selection, dependencies, working form the projects forlder instead of scratch, switching between normal and partner QoS, etc.

fileConverters/lpg2prm.py

This script is designed as a simple tool to help build Q-Chem inputs that require MM parameters. It's set up so that you can download and extract the output from ligpargen and run the script as lpg2prm.py tmp/* pointing to the folder of all the output files.

The only files it really needs are the .xyz (which is output with atom types and adjacency list), and the .prm.

It will print the $molecule section of the Q-Chem input to the terminal and will write the .prm to the directory it obtained the .xyz file from as <filename>-qchem.prm

fileConverters/lpg2qchemlj.py

Based on the redacted above script, this prints the .xyz with adjacency and negative atom types to the temrinal as well as a $force_field_params section that can be pasted into the Q-Chem input file. This is appropriate for QM ONLY atoms.

compoundScripts/orcaIRCMax.py

Brings the functionality of the Gaussian IRCmax process to ORCA.

  • It will create a directory called scratch in the location that it's called from, so cd where you want it before you call it
  • Takes the ORCA_ROOT environment variable, so be sure to source ORCA or load the orca module in your slurm script
  • Outputs the resutls to 00-ircmax_results.out. These include the IRC and IRCmax energies for the specified range
  • The IRC job files are prefixed with irc_ and the IRCmax jobfiles are prefixed with ircmax_##.

energyExtractors/gsolv.py and gsolv-z.py

These jobs just take ORCA 4/5 output files that have been solvated with CPCM (With or without SMD) and adds on the solvation cavitation and surface charge enrgies into the appropriate Total SCF energy or Gibbs Free Energy.

gsolv-z.py is a modification that prints out the Final SCF energy + ZPVE corrections + solvation corrections. (yes I could have integrated this into gsolv.py with a flag, but I cbf...)

energyExtractors/visualise_neb.py

This does exactly what it says, it takes an ORCA NEB .interp file and plots it in a nice neat way that doesn't rely on interpolation through spline fitting.

energyExtractors/orcaOrbs.py

A useful tool to plot orbital energy levels from ORCA output files, and will also show occupancy numbers for multirefernce calculations.

energyExtractors/pltSpectrum.py

Plots the .spectrum files that are output from ORCA's ESD module.

optUtilities/chkopt.py (formerly chkopt.sh, chkoptenergy.py, chkoptprogress.sh, and chkopttransition.py)

Takes the output from an ORCA/Psi4/Gaussian/Q-Chem/XTB opt job and plots the energy so that you you can see the optimiser progress.

  • Optional -t flag to plot the transition energy of ORCA/Q-Chem jobs with optional -r flag to set the root (uses root 1 by default)
  • Optional -p flag to print the optimisation convergence progress

optUtilities/rmsdGeom.py

Takes two .xyz and compares them atom for atom.

  • Does not orient the molecues on top of each toher
  • Assumes all atoms are in the same order
  • If multi-geom XYZ file is used, it will read the last geom