Links

This page contains a number of links to resources that I find useful.

• SeeK-path - find k-point paths for band structure and phonon dispersion plots using crystal structure
• atomsk - easily generate different types of crystallographic defects
• Colby Energy Converter - useful conversions between different energy units
• Halas Energy Converter - this one gives you energy to natural frequencies too
• matgenie - generate slab model given Miller index and vacuum/slab size
• Molecular structures - cartesian coordinates for a bunch of molecules
• Phonon calculations in QE - a practical introduction
• XC functionals in QE - DFT functionals in QE
• Markdown Cheatsheet - a great reference for Markdown formatting

These are some books that I highly recommend.

• Materials Modelling using Density Functional Theory - great introduction to practical DFT calculations
• Fundamental Concepts in Heterogeneous Catalysis - a compact but comprehensive introduction to theoretical and computational catalysis

Codes I’ve written to automate some processes. Please let me know if you encounter any difficulties.

• VASP to xsf structure file converter - just type python vasp2xsf.py <filename>.POSCAR.vasp
• cfg to xsf structure file converter - just type python cfg2xsf.py <filename>.cfg
• Restart QE vc-relax - first change <filename>.in to <filename>.in.old, then run python re-vc-relax.py <filename>.out (note: PBS script should be called runscript)
• k-convergence in QE - modify values and then type python k-pt-conv.py <filename>.in
• plane wave convergence in QE - modify values and then type python pw-conv.py <filename>.in
• csv of Lowdin charges - wrangles Lowdin charges in a csv file, just type python lowdin-csv.py <filename>.out with projwfc.x output
• Phonon free energy - calculates the phonon free energy for a range of temperatures using QE ph.x output, just type python harmonic.py dynmat.out
• QE to xsf converter - just type python qe2xsf.py <filename prefix> where the prefix is everything that comes before the .
• Restart QE relax - run python re-relax.py <filename prefix> (currently doesn’t support fixed atoms)

Here are some tools I use on a regular basis.

• VESTA - static crystal structure visualization
• VMD - efficient visualization of molecular dynamics simulations
• FileZilla - GUI for file transfers
• Inkscape - free vector graphics software
• RStudio - environment for R programming
• Avogadro - static molecular structure visualization
• Octave - free alternative to MATLAB
• Mercury - molecule/crystal visualization software that can also count bonds/angles/dihedrals and calculate the BFDH morphology
• Anaconda - powerful software manager for Python
• USPEX - evolutionary algorithm for crystal structure prediction

Here are some tools that look cool but I haven’t used yet

• PyChemia - global optimization of structures, magnetic moments, and density matrices for DFT+U
• atomate - VASP workflows for electronic band structures, piezoelectric tensor, dielectric tensor, ferroelectricity, nudged elastic band, Raman spectroscopy, and more…
• abipy - Python package for analyzing ABINIT results
• abiflows - ABINIT workflows
• AiiDA - framework for reproducible workflows
• PyTorch - machine learning library for GPUs
• QCArchive - quantum chemistry data archive