pyvasptools

Provides Python scripts for analyzing the:

• Radial distribution function (RDF) — calculated directly from VASP structure files (POSCAR)
• Density of states (DOS) — calculated directly from VASP output files (vaspout.h5)
• Crystal orbital Hamilton population analysis — analyzed beforehand with LOBSTER
• Electron localization function partitioning — analyzed beforehand with critic2

Installation

Requires Python ≥ 3.10.14.

1. Create a Python environment to isolate the package dependencies:

   python3 -m venv ~/envs/pyvasp_tools
   

2. Activate the Python environment:

   source ~/envs/pyvasp_tools/bin/activate
   

3. Install the package from PyPI:

   pip install pyvasptools
   

   Or install from a local clone (for development):

   cd /path/to/pyvasptools/
   pip install .
   

Sample data

The example VASP outputs used by the tests and demos are too large for git and are hosted on Zenodo: https://doi.org/10.5281/zenodo.22182966

Download the archive and unzip its contents into the repository root so that a sample_data/ folder sits next to this README:

cd /path/to/pyvasptools/
# download sample_data.zip from the Zenodo record above, then:
unzip sample_data.zip

Example - Density of States calculated from ab initio molecular dynamics (AIMD) simulation VASP output files

from pyvasptools.dataset import *
from pyvasptools.dos.dos import *  
from pyvasptools.compound import * 

current_dir = Path(__file__).parent
root_dir = current_dir.parents[1]

# 1. Sample data set 1: Compare the density of states of two (100)-NbTaMoW and (100)-NbTaMoWV slabs 
NbTaMoW = Dataset(path=root_dir / 'sample_data/NbTaMoW/10ps/DOS', lc='black', label='NbTaMoW')
NbTaMoWV = Dataset(path=root_dir / 'sample_data/NbTaMoWV/10ps/DOS', lc='purple', label='NbTaMoWV')

# 1. Plot the total density of states of a single (100)-NbTaMoW alloy
NbTaMoW.plot_total_DOS(output_dir=current_dir, output_name='DOS_NbTaMoW')
# 2. Zoom in near the Fermi level (zoom_in=True)
NbTaMoW.plot_total_DOS(output_dir=current_dir, zoom_in=True, output_name='DOS_NbTaMoW_Fermi')

# 3. Compare the density of states of two (100)-NbTaMoW and (100)-NbTaMoWV slabs. zoom_in=True zooms in close to the Fermi level. 
plot_multi_overlaid_dos(NbTaMoW, NbTaMoWV, zoom_in=True, output_dir=current_dir, output_name='DOS_NbTaMoW_vs_NbTaMoWV')



# 3. Now compare the partial density of states of a NbTaMoW-H2O-FLiBe and NbTaMoWV-H2O-FLiBe interface. 
elements = ['Nb', 'Ta', 'Mo', 'W', 'F']

NbTaMoW = Dataset(path=root_dir / 'sample_data/NbTaMoW-FLiBe/10ps/DOS', lc="blue", ls="solid", label=f'')
NbTaMoWV = Dataset(path=root_dir / 'sample_data/NbTaMoWV-FLiBe/10ps/DOS', lc="purple", ls="solid", label=f'V')

plot_pdos_modified(elements, {'d': 'solid', 'p': 'dashed', 's': 'dotted'}, NbTaMoW, NbTaMoWV, x_lim=(-10, 10), y_lim=(((-5, 100),) + ((-1, 20),) * 4 + ((-5, 50),)), labels=("", "V"), path_to_fig=current_dir / 'pDOS_NbTaMoW_vs_NbTaMoWV')

The script above produces the following plots (see tests/dos/):

1. Total DOS of a single NbTaMoW alloy

2. Same DOS, zoomed in near the Fermi level

3. Total DOS of NbTaMoW vs. NbTaMoWV

4. Partial DOS of the NbTaMoW-FLiBe vs. NbTaMoWV-FLiBe interfaces