https://github.com/santoshkumarradha/pyquestaal

Python class to interface with QUESTAAL Quantum codes which is a suite of electronic structure programs.
https://github.com/santoshkumarradha/pyquestaal

ase atomic-simulation-environment condensed-matter-physics dft electronic-structure gw physics pymatgen python qsgw questaal

Last synced: 3 months ago
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Python class to interface with QUESTAAL Quantum codes which is a suite of electronic structure programs.

• Host: GitHub
• URL: https://github.com/santoshkumarradha/pyquestaal
• Owner: santoshkumarradha
• License: mit
• Created: 2020-04-25T00:41:22.000Z (over 4 years ago)
• Default Branch: pyquestaal
• Last Pushed: 2022-07-05T00:24:19.000Z (over 2 years ago)
• Last Synced: 2024-09-18T13:52:30.693Z (4 months ago)
• Topics: ase, atomic-simulation-environment, condensed-matter-physics, dft, electronic-structure, gw, physics, pymatgen, python, qsgw, questaal
• Language: Python
• Homepage:
• Size: 1.27 MB
• Stars: 3
• Watchers: 3
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.rst

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README

        
# PyQUESTAAL

[![DOI](https://zenodo.org/badge/258655688.svg)](https://zenodo.org/badge/latestdoi/258655688)

This is a calculator class that has been written to interface calculations done using [QUESTAAL](http://questaal.org) with highthroughput calculators like [ASE](https://wiki.fysik.dtu.dk/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](https://github.com/santoshkumarradha/pyquestaal/blob/pyquestaal/simple_example.ipynb) 

Comprehensive example shown in [ tutorial_example.ipynb](https://github.com/santoshkumarradha/pyquestaal/blob/pyquestaal/tutorial_example.ipynb)

To use it with ASE, one can do something like

```python

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)