santoshkumarradha/pyquestaal

Python class to interface with QUESTAAL Quantum codes which is a suite of electronic structure programs.

PyQUESTAAL

This is a calculator class that has been written to interface calculations done using QUESTAAL with highthroughput calculators like ASE.

Note: The module can be used as a stand alone python controller for questaal jobs as well.

Features

• make symmetry line files supported by QUESTAAL on the fly with a given structure
• plot bands directly (requires plotquestaal.py)
• relaxations included
• can read forces from output files
• Control number of processors

Installation

1. Copy the files lmf.py to the working directory
2. Import them and use !
3. Make sure "lmf" is recognizable in the path and also modify the type of mpi call. default "mpirun"

Examples

Simple example usage shown in simple_examples.ipynb Comprehensive example shown in tutorial_example.ipynb

To use it with ASE, one can do something like

from lmf import lmf #load the lmf calculator
import numpy as np
from ase.io import read
from ase.units import kJ
from ase.eos import EquationOfState
from ase import Atoms
from ase.io.trajectory import Trajectory
def test():
    a = 4.0  # approximate lattice constant
    b = a / 2
    ag = Atoms('Ag',
               cell=[(0, b, b), (b, 0, b), (b, b, 0)],
               pbc=1,
               calculator=lmf()) # Use QUESTAAL's LMF as calculator
    cell = ag.get_cell()
    traj = Trajectory('Ag.traj', 'w')
    for x in np.linspace(0.95, 1.05, 5):
        ag.set_cell(cell * x, scale_atoms=True)
        ag.get_potential_energy()
        traj.write(ag)
    

    configs = read('Ag.traj@0:5')  # read 5 configurations
    # Extract volumes and energies:
    volumes = [ag.get_volume() for ag in configs]
    energies = [ag.get_potential_energy() for ag in configs]
    eos = EquationOfState(volumes, energies)
    v0, e0, B = eos.fit()
    print(B / kJ * 1.0e24, 'GPa')
    eos.plot('Ag-eos.png')
test()

Citation

If you find this work useful, please cite using

@misc{https://doi.org/10.5281/zenodo.4292415,
  doi = {10.5281/ZENODO.4292415},
  url = {https://zenodo.org/record/4292415},
  author = {Radha, Santosh Kumar},
  title = {pyQuestaal: An python interface or Questaal quantum codes.},
  publisher = {Zenodo},
  year = {2020},
  copyright = {Open Access}
}

To Do

• control over all variables
• Interface with pyamtgen
• Add the developed lattice relaxation module which uses Genetic Algorithm
• Make more standalone
• More complex parser for questaal output (look for questaal-reader repo)

pyquestaal's Issues

Specifying cif2cell as a prerequisite

lmf() as is written cannot be run unless cif2cell is installed. I installed it using pip install cif2cell as suggested here (https://github.com/torbjornbjorkman/cif2cell) and now lmf is working. I think stating cif2cell as a requirement and adding a line to install it in setup.py is probably a good idea.