jarvis-tools: an open-source software package for data-driven atomistic materials design. https://jarvis.nist.gov/
Project description
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
References
Please see Publications related to JARVIS-Tools
Documentation
Correspondence
Please report bugs as Github issues (https://github.com/usnistgov/jarvis/issues) or email to kamal.choudhary@nist.gov.
Funding support
NIST-MGI (https://www.nist.gov/mgi).
Code of conduct
Please see Code of conduct
Project details
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