jarvis-tools 2020.11.27

jarvis-tools: an open-source software package for data-driven atomistic materials design. https://jarvis.nist.gov/

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JARVIS-Tools: an open-source software package for data-driven atomistic materials design

NIST-JARVIS (Joint Automated Repository for Various Integrated Simulations) is an integrated framework for computational science using density functional theory, classical force-field/molecular dynamics and machine-learning. The jarvis-tools package consists of scripts used in generating and analyzing the dataset. The NIST-JARVIS official website is: https://jarvis.nist.gov . This project is a part of the Materials Genome Initiative (MGI) at NIST (https://mgi.nist.gov/).

For more details, checkout our latest article: The joint automated repository for various integrated simulations (JARVIS) for data-driven materials design

Some important features

• Software workflow tasks: VASP, Quantum Espresso, Wien2k BoltzTrap, Wannier90, LAMMPS, Scikit-learn, TensorFlow, LightGBM.

• HPC clusters: PBS and SLURM.

• Examples: Notebooks and test scripts to explain the package.

• Available datasets: Summary of several datasets .

Installation

Please see Installation instructions

Example function

>>> from jarvis.core.atoms import Atoms
>>> box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
>>> coords = [[0, 0, 0], [0.25, 0.25, 0.25]]
>>> elements = ["Si", "Si"]
>>> Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
>>> density = round(Si.density,2)
>>> print (density)
2.33
>>>
>>> from jarvis.db.figshare import data
>>> dft_3d = data(dataset='dft_3d')
>>> print (len(dft_3d))
36099
>>> from jarvis.io.vasp.inputs import Poscar
>>> for i in dft_3d:
...     atoms = Atoms.from_dict(i['atoms'])
...     poscar = Poscar(atoms)
...     jid = i['jid']
...     filename = 'POSCAR-'+jid+'.vasp'
...     poscar.write_file(filename)
>>> dft_2d = data(dataset='dft_2d')
>>> print (len(dft_2d))
1070
>>> for i in dft_2d:
...     atoms = Atoms.from_dict(i['atoms'])
...     poscar = Poscar(atoms)
...     jid = i['jid']
...     filename = 'POSCAR-'+jid+'.vasp'
...     poscar.write_file(filename)

Find more examples at

1. https://jarvis-materials-design.github.io/dbdocs/tutorials

2. https://github.com/JARVIS-Materials-Design/jarvis-tools-notebooks

3. https://github.com/usnistgov/jarvis/tree/master/jarvis/tests/testfiles

References

Please see Publications related to JARVIS-Tools

Documentation

https://jarvis-materials-design.github.io/dbdocs/

Correspondence

Please report bugs as Github issues (https://github.com/usnistgov/jarvis/issues) or email to [e-mail].

Funding support

NIST-MGI (https://www.nist.gov/mgi).