FEATURE: define a convention about abinit jobs that have restarted and failed the max number of restarts

atomate2

Atomate2 is a free, open-source software for performing complex materials science workflows using simple Python functions. Features of atomate2 include

It is built on open-source libraries: pymatgen, custodian, jobflow, and FireWorks.
A library of "standard" workflows to compute a wide variety of desired materials properties.
The ability scale from a single material, to 100 materials, or 100,000 materials.
Easy routes to modifying and chaining workflows together.
It can build large databases of output properties that you can query, analyze, and share in a systematic way.
It automatically keeps meticulous records of jobs, their directories, runtime parameters, and more.

Note: Atomate2 is primarily built to work with the VASP electronic structure software, but we are actively working on adding more codes.

Workflows

Some of the workflows available in atomate2 are:

electronic band structures
elastic, dielectric, and piezoelectric tensors
one-shot electron-phonon interactions
electronic transport using AMSET
phonons using phonopy
defect formation energy diagrams
Lobster bonding analysis with lobsterpy

It is easy to customise and compose any of the above workflows.

Quick start

Workflows in atomate2 are written using the jobflow library. Workflows are generated using Maker objects which have a consistent API for modifying input settings and chaining workflows together. Below, we demonstrate how to run a band structure workflow (see the documentation for more details). In total, 4 VASP calculations will be performed:

A structural optimisation.
A self-consistent static calculation on the relaxed geometry.
A non-self-consistent calculation on a uniform k-point mesh (for the density of states).
A non-self-consistent calculation on a high symmetry k-point path (for the line mode band structure).

from atomate2.vasp.flows.core import RelaxBandStructureMaker
from jobflow import run_locally
from pymatgen.core import Structure

# construct a rock salt MgO structure
mgo_structure = Structure(
    lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
    species=["Mg", "O"],
    coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)

# make a band structure flow to optimise the structure and obtain the band structure
bandstructure_flow = RelaxBandStructureMaker().make(mgo_structure)

# run the flow
run_locally(bandstructure_flow, create_folders=True)

Before the above code can run successfully, you'll need to

tell pymatgen where to find your pseudopotential files
tell atomate2 where to find your VASP binary
(optionally) prepare an external database to store the job output

See the installation steps for details how to set all of this up.

In this example, we execute the workflow immediately. In many cases, you might want to perform calculations on several materials simultaneously. To achieve this, all atomate2 workflows can be run using the FireWorks software. See the documentation for more details.

Installation

Atomate2 is a Python 3.8+ library and can be installed using pip. Full installation and configuration instructions are provided in the installation tutorial.

Tutorials

The documentation includes comprehensive tutorials and reference information to get you started:

Need help?

Ask questions about atomate2 on the atomate2 support forum. If you've found an issue with atomate2, please submit a bug report on GitHub Issues.

What’s new?

Track changes to atomate2 through the changelog.

Contributing

We greatly appreciate any contributions in the form of a pull request. Additional information on contributing to atomate2 can be found here. We maintain a list of all contributors here.

License

Atomate2 is released under a modified BSD license; the full text can be found here.

Acknowledgements

The development of atomate2 has benefited from many people across several research groups. A full list of contributors can be found here.

Citing atomate2

A journal submission for atomate2 is planned. In the meantime, please use citation.cff and the Zenodo record to cite atomate2.

@software{ganose_atomate2_2024,
  author = {Ganose, Alex and Riebesell, Janosh and George, J. and Shen, Jimmy and S. Rosen, Andrew and Ashok Naik, Aakash and nwinner and Wen, Mingjian and rdguha1995 and Kuner, Matthew and Petretto, Guido and Zhu, Zhuoying and Horton, Matthew and Sahasrabuddhe, Hrushikesh and Kaplan, Aaron and Schmidt, Jonathan and Ertural, Christina and Kingsbury, Ryan and McDermott, Matt and Goodall, Rhys and Bonkowski, Alexander and Purcell, Thomas and Zügner, Daniel and Qi, Ji},
  doi = {10.5281/zenodo.10677081},
  license = {cc-by-4.0},
  month = jan,
  title = {atomate2},
  url = {https://github.com/materialsproject/atomate2},
  version = {0.0.13},
  year = {2024}
}

	if kconfig.get("line_density"):
	# handle line density generation
	kpath = HighSymmKpath(structure)
	frac_k_points, k_points_labels = kpath.get_kpoints(
	line_density=kconfig["line_density"], coords_are_cartesian=False
	)
	base_kpoints = Kpoints(
	comment="Non SCF run along symmetry lines",
	style=Kpoints.supported_modes.Reciprocal,
	num_kpts=len(frac_k_points),
	kpts=frac_k_points,
	labels=k_points_labels,
	kpts_weights=[1] * len(frac_k_points),
	)

	@pytest.fixture
	def tmp_dir():
	"""Same as clean_dir but is fresh for every test"""
	import os
	import shutil
	import tempfile

	old_cwd = os.getcwd()
	newpath = tempfile.mkdtemp()
	os.chdir(newpath)
	yield
	os.chdir(old_cwd)
	shutil.rmtree(newpath)

materialsproject / atomate2 Goto Github PK

atomate2's Introduction

atomate2

Workflows

Quick start

Installation

Tutorials

Need help?

What’s new?

Contributing

License

Acknowledgements

Citing atomate2

atomate2's People

Stargazers

Watchers

Forkers

atomate2's Issues

Solution

A Few Documentation Suggestions

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