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Description:

pyquestaal 0.2.3

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

Copy the files lmf.py to the working directory
Import them and use !
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)