• Leverage computational simulation to accelerate material discovery through collaboration with experiment team
• Perform DFT geometry optimization and compute properties such as polarizability, electrostatic potential, etc.
• Automate the workflow for upscaling

Personal notes for the automation of DFT calculation and data analysis, including

• [1] Create jobs in batch
• [2] Automate result analysis
• [3] Scripts mainly are written in bash, which is natively supported in Unix environment (some are with their equivalents in Python 3)

Software packages:

• HPC: CentOS Linux 7 3.10.0-957.el7.x86_64
  • PBS 19.1.1
  • ORCA 5.1.0
  • Multiwfn 3.8(dev)
• Windows 11 Pro 26100.4652
  • Avogadro² 1.100.0
  • VMD 1.9.3
  • WSL 2: Ubuntu-24.04

Create shortcuts in Unix via alias (with vim)

• vi ~/.bashrc
• copy below to the end

alias q="qstat"
alias p="pestat"
alias qv="watch --interval=5 qstat"
alias m="orca_2mkl orca.gbw orca.molden -molden -anyorbs"
alias qq="qsub qsub.sh"

• wq write and quite
• source ~/.bashrc to make the change effective

Sections:

• [1] example solo job run (water): https://github.com/er1czz/ORCA-scripts/tree/main/water_example
• [2] scripts for batch job preparation https://github.com/er1czz/ORCA-scripts/tree/main/orca_input
• [3] scripts for batch job data analysis https://github.com/er1czz/ORCA-scripts/tree/main/orca_output

A simple batch .bat to convert xyz format to gjf (GaussView), executable in Windows xyz2gjf.bat

Tips for fast PuTTY login

• Shortcut on Windows
  • From Shortcut property, append the ssh login info
  • Example

     "C:\Program Files\PuTTY\putty.exe" -ssh username@ip_address -pw pa22w0rd -P p0rt

• Passwordless between nodes
  • use ssh-keygen to generate a rsa keypair and then ssh-copy-id userid@hostname to the ssh target