jarvis-tools 2021.2.21

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 and YouTube videos

Capabilities

• Software workflow tasks for preprcessing and post-processing: VASP, Quantum Espresso, Wien2k BoltzTrap, Wannier90, LAMMPS, Scikit-learn, TensorFlow, LightGBM.

• Several examples: Notebooks and test scripts to explain the package.

• Several analysis tools: Atomic structure, Electronic structure, Spacegroup, Diffraction, 2D materials and other vdW bonded systems, Mechanical, Optoelectronic, Topological, Solar-cell, Thermoelectric, Piezoelectric, Dielectric, STM, Phonon, Dark matter, Wannier tight binding models, Point defects, Heterostructures, Magnetic ordering, Images, Spectrum etc.

• Database upload and download: Download JARVIS databases such as JARVIS-DFT, FF, ML, WannierTB, Solar, STM and also external databases such as Materials project, OQMD, AFLOW etc.

• Access raw input/output files: Download input/ouput files for JARVIS-databases to enhance reproducibility.

• Train machine learning models: Use different descriptors, graphs and datasets for training machine learning models.

• HPC clusters: Torque/PBS and SLURM.

• Available datasets: Summary of several datasets .

Installation

>>> pip install -U jarvis-tools

For detailed instructions, 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)
>>> # Example to parse DOS data from JARVIS-DFT webpages
>>> from jarvis.db.webpages import Webpage
>>> from jarvis.core.spectrum import Spectrum
>>> import numpy as np
>>> new_dist=np.arange(-5, 10, 0.05)
>>> all_atoms = []
>>> all_dos_up = []
>>> all_jids = []
>>> for ii,i in enumerate(dft_3d):
      all_jids.append(i['jid'])
...   try:
...     w = Webpage(jid=i['jid'])
...     edos_data = w.get_dft_electron_dos()
...     ens = np.array(edos_data['edos_energies'].strip("'").split(','),dtype='float')
...     tot_dos_up = np.array(edos_data['total_edos_up'].strip("'").split(','),dtype='float')
...     s = Spectrum(x=ens,y=tot_dos_up)
...     interp = s.get_interpolated_values(new_dist=new_dist)
...     atoms=Atoms.from_dict(i['atoms'])
...     all_dos_up.append(interp)
...     all_atoms.append(atoms)
...     all_jids.append(i['jid'])
...     filename=i['jid']+'.cif'
...     atoms.write_cif(filename)
...     break
...   except Exception as exp :
...     print (exp,i['jid'])
...     pass

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).

Code of conduct

Please see Code of conduct