JARVIS-Tools

2026.4.2 verified Mon Apr 27 auth: no python

jarvis-tools is an open-source Python package for data-driven atomistic materials design, developed by NIST. It provides modules for crystal structure analysis, high-throughput DFT workflows, machine learning descriptors, and access to the JARVIS-DFT and JARVIS-FF databases. Current version is 2026.4.2, released monthly (around end of each month).

pip install jarvis-tools

Common errors

error ModuleNotFoundError: No module named 'jarvis.core.atoms' ↓

cause Importing from jarvis.core.atoms but the version is old (<2022) or package not installed correctly.

fix

Upgrade: pip install --upgrade jarvis-tools. Also ensure you have correct import path: from jarvis.core.atoms import Atoms.

error AttributeError: 'Atoms' object has no attribute 'coords' ↓

cause Trying to access atoms.coords directly but newer version uses atoms.cart_coords or requires utility function.

fix

Use atoms.cart_coords or from jarvis.core.utils import get_fractional_coordinates for coordinates.

error ValueError: Could not parse POSCAR file ↓

cause Using an outdated reader for VASP files. The POSCAR parser has been updated and expects specific format.

fix

Use 'from jarvis.io.vasp.inputs import Poscar' and call Poscar.from_file('POSCAR').atoms.

error TypeError: lattice_mat must be a 3x3 list or array ↓

cause Passing lattice vectors incorrectly (e.g., 1D array or wrong shape).

fix

Provide lattice as a list of three vectors, each a list of three floats: [[a1,a2,a3],[b1,b2,b3],[c1,c2,c3]].

Warnings

breaking The 'Atoms' class was moved from jarvis.io.vasp.outputs to jarvis.core.atoms in 2022. Old imports will break. ↓

fix Use 'from jarvis.core.atoms import Atoms' instead.

breaking The 'Graph' class is not directly importable from jarvis.core; must be imported from jarvis.core.graphs. ↓

fix Use 'from jarvis.core.graphs import Graph'.

deprecated Functions like 'jarvis.core.utils.get_fractional_coordinates' replaced older methods on Atoms (e.g., atoms.fractional_coords). Check deprecation warnings. ↓

fix Use jarvis.core.utils functions as needed; check documentation for new API.

gotcha The package 'jarvis-tools' should be installed with exact hyphen, not underscore (jarvis_tools). pip install jarvis_tools will fail if not found. ↓

fix Install via 'pip install jarvis-tools'.

gotcha Many JARVIS-DFT database functions require an internet connection and may cache data in ~/.cache/atomgptlab/ by default. If you get connection errors, check network or set JARVIS_CACHE_DIR. ↓

fix Set environment variable JARVIS_CACHE_DIR to a different path.

Install

pip install git+https://github.com/atomgptlab/jarvis-tools.git

Imports

Atoms
wrong
```
from jarvis.io.vasp.outputs import Atoms
```
correct
```
from jarvis.core.atoms import Atoms
```
Atoms class moved to jarvis.core.atoms around version 2022.x. Old import path from VASP is incorrect.
Graph
wrong
```
from jarvis.core import Graph
```
correct
```
from jarvis.core.graphs import Graph
```
Graph is not directly in core; must import from jarvis.core.graphs.
get_fractional_coordinates
```
from jarvis.core.utils import get_fractional_coordinates
```
Utility functions are under jarvis.core.utils, not directly on Atoms object in older API.

Quickstart

Create a simple atomic structure and print basic properties.

from jarvis.core.atoms import Atoms
from jarvis.core.specie import Specie

# Create an atomistic structure (diamond silicon)
coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
elements = ["Si", "Si"]
lattice = [[0.0, 0.0, 1.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]  # cubic, a=1.0

atoms = Atoms(lattice_mat=lattice, coords=coords, elements=elements)
print(atoms)
print("Lattice:", atoms.lattice_mat)
print("Number of atoms:", len(atoms))

# Convert to fractional coordinates (using utility)
from jarvis.core.utils import get_fractional_coordinates
frac = get_fractional_coordinates(atoms.coords, atoms.lattice_mat)
print("Fractional coords:", frac)