/scripts

Scripts of a Computational Chemist

Primary LanguagePython

Various python / shell scripts created for my work.

Frank Cluster

submit

Generate PBS batch file for a Q-Chem job and submit it, based on CLI flags

best_queue

Find best queue available for job specifications (WIP) submit depends on best_queue (hence the best_queue.py sym link)

multibatch

Create job array for multiple jobs and submit to a distributed queue (WIP)

qs

Queue Status - quick summary of queue, and reveals empty queues

pbsclean

Clean up the trash that pbs and submit script leaves everywhere

General Use

cpg

Cartesian Product Generator - Extension of Python's itertools.product for file text. Primarily used to generate inputs with multiple changed paramaters (e.g. varying bond distances with varying basis sets)

jabget

Convert .ris file format to .bib

ipyr

IPython Remote - Instead of ssh'ing into a machine, access the remote machine through a hosted instance of Jupyter in browser.

search

More code-specific grepping. I mostly use The Silver Searcher these days

pdb

Fetch a pdb file from protein database, given a pdb index

Q-Chem

errors

Quick and dirty error report for Q-Chem jobs, searches for common errors

Personal

eg

Quickly navigate topics in my eg repository

ref

Quickly navigate topics in my ref repository

gitrep

Manage multiple git repositories at once

Undocumented

  • dirtags.sh
  • geomopt
  • plotvfile
  • qchemall
  • qcmake
  • qcmake.py
  • qctags
  • qdelr
  • qfold
  • qgrep
  • rextract
  • rmsd
  • runall
  • search
  • submit
  • submitbatch
  • submitqchemall
  • zmat