Command-line utilities

Useful command-line utilities for research in HANS group.

Installation

First, make sure that cargo is installed.

git clone https://github.com/hans-group/cli-utils
cd cli-utils
./install.sh

If it fails, reinstall the latest rustup and try again.

List of commands

• gotojob: Go to SLURM job submission directory
• animate_vibmode_orca: Animate the normal mode of molecule to .xyz file from orca frequency calculation.
• submit_orca: Submit ORCA job to SLURM in one line
• submit_vasp: Submit VASP job to SLURM in one line
• vasp_mdstat: Plot potential/kinetic/total energy and temperature profile of VASP MD run.
• check_ef_vasp: Check convergence of energy and force from VASP geometry optimization run.
• kpointsgen: Generate KPOINTS file for VASP calculation, either from explicit grid or from density of k-points.
• pos2pot: Generate POTCAR file from POSCAR file.
• ndstat: Prettier version of pestat
• qst: Prettier version of qst
• symmetrize_poscar: Symmetrize POSCAR
• vasp_set: Generate VASP inputs from POSCAR file and input_params.toml. Example of input_params.toml can be found in wiki.

See wiki for detailed usage.

For developers & contributors

Bash scripts

• Write a command as function definition.
• If it is short, append to src/bash/cli_utils_bash.sh. Otherwise, write to separate file and add source $source_dir/filename to cli_utils_bash.sh.

Python scripts

• In the directory src/python, only executable scripts are allowed. Do not put the library code in it.
• The library codes should be placed in src/python/lib.
• Check the errors with flake8 and format the code with black.