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* improvement: add `Atoms.clone()` and `remove sites by indices`, including in-place. Use `develop` branch for the PR. (#315)

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

* Add installation tests (#214)

* QE inputs, XANES, GHAction updates. (#210)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

* Adding folders for nexus setup.

* Update QMOF and hMOF info.

* Fixing auto klength error.

* Adding zeopp surface area.

* Vacancy bug fix, added hmof to docs.

* vacancy update.

* QE inputs update.

* Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details.

* Update Contribution.rst

* Minor lint fix.

* Update action_build.yml

* Update action_build.yml

* Fix qiskit requirements.

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>

* Add installation tests

* Fix codestyle

* Fix codestyle with black

* Add docstrings

* Fix pydocstyle error

* Update __init__.py

* Update __init__.py

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>

* Adding QE super.

* Minor changes to QE module, atoms xyz fix.

* Adding qe_tb info, and version update.

* Update __init__.py

* WIP super QE.

* Working version of ScSi.

* QE inputs and task update.

* Add master super.

* Add master super.

* Lint fix.

* Lint fix.

* Minor fix.

* ET update.

* Fix ET test.

* Update sanitize atoms.

* Additonal checks on supercond.

* Debye bug fix.

* Pressure in QE Super.

* Version fix, publication update, supercond workflow update.

* Lint fix.

* Tensorboard fix.

* Tensorboard fix.

* Tensorboard fix.

* Melting temp fix.

* Update vasp.py (#234)

* Local tetra tmp.

* Version update.

* Lint fix.

* HSE06

* Tmp.

* Vacancy update, Optimade structureand other minor lint updates.

* STEM pytest fix.

* Minor lint fix.

* Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms

* Lint fix.

* Added phononDos class.

* fix pytorch UserWarning in build_undirected_edgedata() (#243)

site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor.
  r = torch.tensor(r).type(torch.get_default_dtype())

* Add PhaseDiagram.

* Add PhaseDiagram.

* PhaseDiagram update.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* Compare atoms, get spg info directly from atoms.

* Flake8 fix.

* Update publications.rst

* Update qiskit.

* Update qiskit.

* Update test_hermsolver.py

* FIix qiskit DOS.

* Update test_hermsolver.py

* Fix linting.

* Develop og (#257)

* Added isotope scattering rate to phonon DOS analysis script.

* Linting fix.

* Linting fix.

* Linting fix.

* Add QE convergence.

* Update converg.py.

* Nexus.

* Super with converg.

* Super with converg.

* SuperCon QE update.

* Figshare DB update.

* Figshare DB update.

* Update alignn ff link.

* Lint fix.

* DB docs update.

* Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy.

* Lint fix.

* Supercon workflow fix.

* Add extra db entires, fix chem in cfid_chem.

* Version update.

* Add figshare datasets.

* Update databases.rst

* codecov fix.

* Version update.

* Lint fix.

* Add FigShare datasets, DOS in QE, Uncertainty.

* Add python 3.9.

* Create README.md

* Update README.

* Add README.md.

* Update action_build.yml

* Update action_lint.yml

* Allow md file, add mode databases.

* Create NISTtheDocs2Death.yml

* Allow md file, add mode databases.

* Add publications.

* Update publications.rst

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Create deploy_nist_pages.yml

* Add mkdocs.

* Update deploy_nist_pages.yml

* Update md.

* Update setup.py

* Update readme.

* Update setup.py

* Remove absl.

* Update dev-requirements.txt

* Update index.md

* Update deploy_nist_pages.yml

* Update index.rst

* Add redirect.

* Update action_build.yml

* Update dev-requirements.txt

* Update dev-requirements.txt

* Update setup.py

* Update dev-requirements.txt

* Fix __repr__ for Atoms.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Use poscar write as string.

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Delete NISTtheDocs2Death.yml

* Delete action_lint.yml

* Use poscar write as string.

* Fix phonopy.

* Update dev-requirements.txt

* Update databases.

* Add eigs.

* Add eigs.

* Add eigs.

* Fix STM test.

* Delete .travis.yml

* Update README.

* Add python docs.

* GA

* Update action_build.yml

* Atoms class update with props.

* Atoms class update with props.

* Delete .readthedocs.yaml

* Update README.md

* QEjob fix.

* Chang poscar write.

* Add check_polar update, locpot update.

* Locpot pytest.

* X locpot.

* Lint.

* Update figshare.py

* Update tutorials.md for get_chem_only_descriptors (#309)

* Develop (#308)

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

* Adding folders for nexus setup.

* Update QMOF and hMOF info.

* Fixing auto klength error.

* Adding zeopp surface area.

* Vacancy bug fix, added hmof to docs.

* vacancy update.

* QE inputs update.

* Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details.

* Update Contribution.rst

* Minor lint fix.

* Update action_build.yml

* Update action_build.yml

* Fix qiskit requirements.

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

* Add installation tests (#214)

* QE inputs, XANES, GHAction updates. (#210)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

* Adding folders for nexus setup.

* Update QMOF and hMOF info.

* Fixing auto klength error.

* Adding zeopp surface area.

* Vacancy bug fix, added hmof to docs.

* vacancy update.

* QE inputs update.

* Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details.

* Update Contribution.rst

* Minor lint fix.

* Update action_build.yml

* Update action_build.yml

* Fix qiskit requirements.

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>

* Add installation tests

* Fix codestyle

* Fix codestyle with black

* Add docstrings

* Fix pydocstyle error

* Update __init__.py

* Update __init__.py

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>

* Adding QE super.

* Minor changes to QE module, atoms xyz fix.

* Adding qe_tb info, and version update.

* Update __init__.py

* WIP super QE.

* Working version of ScSi.

* QE inputs and task update.

* Add master super.

* Add master super.

* Lint fix.

* Lint fix.

* Minor fix.

* ET update.

* Fix ET test.

* Update sanitize atoms.

* Additonal checks on supercond.

* Debye bug fix.

* Pressure in QE Super.

* Version fix, publication update, supercond workflow update.

* Lint fix.

* Tensorboard fix.

* Tensorboard fix.

* Tensorboard fix.

* Melting temp fix.

* Update vasp.py (#234)

* Local tetra tmp.

* Version update.

* Lint fix.

* HSE06

* Tmp.

* Vacancy update, Optimade structureand other minor lint updates.

* STEM pytest fix.

* Minor lint fix.

* Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms

* Lint fix.

* Added phononDos class.

* fix pytorch UserWarning in build_undirected_edgedata() (#243)

site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor.
  r = torch.tensor(r).type(torch.get_default_dtype())

* Add PhaseDiagram.

* Add PhaseDiagram.

* PhaseDiagram update.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* Compare atoms, get spg info directly from atoms.

* Flake8 fix.

* Update publications.rst

* Update qiskit.

* Update qiskit.

* Update test_hermsolver.py

* FIix qiskit DOS.

* Update test_hermsolver.py

* Fix linting.

* Develop og (#257)

* Added isotope scattering rate to phonon DOS analysis script.

* Linting fix.

* Linting fix.

* Linting fix.

* Add QE convergence.

* Update converg.py.

* Nexus.

* Super with converg.

* Super with converg.

* SuperCon QE update.

* Figshare DB update.

* Figshare DB update.

* Update alignn ff link.

* Lint fix.

* DB docs update.

* Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy.

* Lint fix.

* Supercon workflow fix.

* Add extra db entires, fix chem in cfid_chem.

* Version update.

* Add figshare datasets.

* Update databases.rst

* codecov fix.

* Version update.

* Lint fix.

* Add FigShare datasets, DOS in QE, Uncertainty.

* Add python 3.9.

* Create README.md

* Update README.

* Add README.md.

* Update action_build.yml

* Update action_lint.yml

* Allow md file, add mode databases.

* Create NISTtheDocs2Death.yml

* Allow md file, add mode databases.

* Add publications.

* Update publications.rst

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Create deploy_nist_pages.yml

* Add mkdocs.

* Update deploy_nist_pages.yml

* Update md.

* Update setup.py

* Update readme.

* Update setup.py

* Remove absl.

* Update dev-requirements.txt

* Update index.md

* Update deploy_nist_pages.yml

* Update index.rst

* Add redirect.

* Update action_build.yml

* Update dev-requirements.txt

* Update dev-requirements.txt

* Update setup.py

* Update dev-requirements.txt

* Fix __repr__ for Atoms.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Use poscar write as string.

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Delete NISTtheDocs2Death.yml

* Delete action_lint.yml

* Use poscar write as string.

* Fix phonopy.

* Update dev-requirements.txt

* Update databases.

* Add eigs.

* Add eigs.

* Add eigs.

* Fix STM test.

* Delete .travis.yml

* Update README.

* Add python docs.

* GA

* Update action_build.yml

* Atoms class update with props.

* Atoms class update with props.

* Delete .readthedocs.yaml

* Update README.md

* QEjob fix.

* Chang poscar write.

* Add check_polar update, locpot update.

* Locpot pytest.

* X locpot.

* Lint.

---------

Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: Saurav Maheshkar <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>
Co-authored-by: Ramya Gurunathan <[email protected]>

* Update tutorials.md

---------

Co-authored-by: Kamal Choudhary <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: wines1 <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: Saurav Maheshkar <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>
Co-authored-by: Ramya Gurunathan <[email protected]>

* Qsiqskit dversion and CFID chemical feature doc issue.

* Update dev-requirements.txt

* Update dev-requirements.txt

* Update dev-requirements.txt

* Update inputs.py

* Update figshare.py

* Update figshare.py

* chore: update .gitignore to add pycharm .idea

* improvements: clone method and remove multiple sites, including in place

* tests: attempt adding tests for the new functionality

not sure how to run these - some documentation would be good to have in README.md

* Flake8 fix.

* Add pydantic.

* wien2k fix.

* Comment out qiskit related tests.

* Fix OneHotEncoder.

* Check conda

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update action_build.yml

* Update docs.

* Update index.md

* Update index.md

* Minor lint fix.

* Update deploy_nist_pages.yml

* fix: lint

* Fix bug in the PR.

---------

Co-authored-by: knc6 <[email protected]>
Co-authored-by: wines1 <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: Saurav Maheshkar <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>
Co-authored-by: Ramya Gurunathan <[email protected]>
Co-authored-by: Sangjoon Bob Lee <[email protected]>

* Version update.

* QE PSP url updae.

* Remove mkdocs hard dependency.

* Update lammps.

* Lint fix.

* Adding restapi.

* Update super.py.

* Add describer.

* Add describer.

* Add describer.

* Update describe.

* Lint fix.

* Mineral name.

* Add atoms update.

* Add atoms update.

* Update proto pytest.

* Update atoms, old prototype back.

* Update atoms, old prototype back.

* Describe out.

* Fix surface layers.

* Make c surface an option.

* Lint fix.

* Verbose false.

* Parse outcar.

* Outputs fix.

* Update OUTCAR parser.

* Update OUTCAR parser.

* Update OUTCAR parser.

* Update atoms describer.

* Update atoms describer.

* Fix motif and composition.

* Rotate.

* Add additionals DBs.

* PyTest fix.

* DB update.

* Lint fix.

---------

Co-authored-by: Timur Bazhirov <[email protected]>
Co-authored-by: wines1 <[email protected]>
Co-authored-by: tavazza <[email protected]>
Co-authored-by: knc6 <[email protected]>
Co-authored-by: KAMAL CHOUDHARY <[email protected]>
Co-authored-by: Saurav Maheshkar <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>
Co-authored-by: Ramya Gurunathan <[email protected]>
Co-authored-by: Sangjoon Bob Lee <[email protected]>
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10 people authored Jun 28, 2024
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2 changes: 1 addition & 1 deletion jarvis/__init__.py
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""Version number."""

__version__ = "2024.4.30"
__version__ = "2024.5.10"

import os

Expand Down
142 changes: 133 additions & 9 deletions jarvis/core/atoms.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
from sklearn.metrics import mean_absolute_error
import zipfile
import json
from math import cos, pi, sin

amu_gm = 1.66054e-24
ang_cm = 1e-8
Expand Down Expand Up @@ -867,6 +868,128 @@ def get_neighbors_cutoffs(self, max_cut=10, r=5, bond_tol=0.15):
pass
return rcut1, rcut2, neighbors

def rotate_pos(self, phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0)):
"""Rotate atom sites via Euler angles (in degrees).
See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.
Adapted from
https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate
center :
The point to rotate about. A sequence of length 3 with the
coordinates.
phi :
The 1st rotation angle around the z axis.
theta :
Rotation around the x axis.
psi :
2nd rotation around the z axis.
"""
phi *= pi / 180
theta *= pi / 180
psi *= pi / 180

rcoords = self.cart_coords - center
D = np.array(
(
(cos(phi), sin(phi), 0.0),
(-sin(phi), cos(phi), 0.0),
(0.0, 0.0, 1.0),
)
)
# Second Euler rotation about x:
C = np.array(
(
(1.0, 0.0, 0.0),
(0.0, cos(theta), sin(theta)),
(0.0, -sin(theta), cos(theta)),
)
)
# Third Euler rotation, 2nd rotation about z:
B = np.array(
(
(cos(psi), sin(psi), 0.0),
(-sin(psi), cos(psi), 0.0),
(0.0, 0.0, 1.0),
)
)
# Total Euler rotation
A = np.dot(B, np.dot(C, D))
# Do the rotation
rcoords = np.dot(A, np.transpose(rcoords))
positions = np.transpose(rcoords) + center

return Atoms(
lattice_mat=self.lattice_mat,
elements=self.elements,
coords=positions,
cartesian=True,
props=self.props,
)

def rotate_cell(self, phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0)):
"""Rotate atom cell via Euler angles (in degrees).
See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.
Adapted from
https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate
center :
The point to rotate about. A sequence of length 3 with the
coordinates.
phi :
The 1st rotation angle around the z axis.
theta :
Rotation around the x axis.
psi :
2nd rotation around the z axis.
"""
phi *= pi / 180
theta *= pi / 180
psi *= pi / 180

# First move the molecule to the origin In contrast to MATLAB,
# numpy broadcasts the smaller array to the larger row-wise,
# so there is no need to play with the Kronecker product.
# rcoords = atoms.cart_coords - center
# First Euler rotation about z in matrix form
D = np.array(
(
(cos(phi), sin(phi), 0.0),
(-sin(phi), cos(phi), 0.0),
(0.0, 0.0, 1.0),
)
)
# Second Euler rotation about x:
C = np.array(
(
(1.0, 0.0, 0.0),
(0.0, cos(theta), sin(theta)),
(0.0, -sin(theta), cos(theta)),
)
)
# Third Euler rotation, 2nd rotation about z:
B = np.array(
(
(cos(psi), sin(psi), 0.0),
(-sin(psi), cos(psi), 0.0),
(0.0, 0.0, 1.0),
)
)
# Total Euler rotation
A = np.dot(B, np.dot(C, D))
# Do the rotation
r_lattice_mat = np.dot(A, self.lattice_mat)
# Move back to the roactation point
# positions = np.transpose(rcoords) + center
return Atoms(
lattice_mat=r_lattice_mat,
elements=self.elements,
coords=self.frac_coords,
cartesian=False,
props=self.props,
)

def atomwise_angle_and_radial_distribution(
self, r=5, bond_tol=0.15, c_size=10, verbose=False
):
Expand Down Expand Up @@ -1335,6 +1458,7 @@ def hook(model, input, output):
def get_mineral_prototype_name(
self, prim=True, include_c_over_a=False, digits=3
):
"""Get mineral_prototype_name."""
from jarvis.analysis.structure.spacegroup import Spacegroup3D

spg = Spacegroup3D(self)
Expand Down Expand Up @@ -1524,9 +1648,9 @@ def describe(
list(set(spg._dataset["wyckoffs"]))
)
struct_info["natoms_primitive"] = spg.primitive_atoms.num_atoms
struct_info[
"natoms_conventional"
] = spg.conventional_standard_structure.num_atoms
struct_info["natoms_conventional"] = (
spg.conventional_standard_structure.num_atoms
)
info["chemical_info"] = chem_info
info["structure_info"] = struct_info
line = "The number of atoms are: " + str(
Expand Down Expand Up @@ -2276,18 +2400,18 @@ def to_optimade(
info_at["cartesian_site_positions"] = atoms.cart_coords[order].tolist()
info_at["nperiodic_dimensions"] = 3
# info_at["species"] = atoms.elements
info_at[
"species"
] = self.get_optimade_species() # dict(atoms.composition.to_dict())
info_at["species"] = (
self.get_optimade_species()
) # dict(atoms.composition.to_dict())
info_at["elements_ratios"] = list(
atoms.composition.atomic_fraction.values()
)
info_at["structure_features"] = []
info_at["last_modified"] = str(now)
# info_at["more_data_available"] = True
info_at[
"chemical_formula_descriptive"
] = atoms.composition.reduced_formula
info_at["chemical_formula_descriptive"] = (
atoms.composition.reduced_formula
)
info_at["dimension_types"] = [1, 1, 1]
info["attributes"] = info_at
return info
Expand Down
8 changes: 6 additions & 2 deletions jarvis/core/composition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,10 +156,14 @@ def formula(self):
form = ""
for specie, count in self._content.items():
if float(count).is_integer():
form = form + str(specie) + str(int(count))
# form = form + str(specie) + str(int(count))
if count == 1:
form = form + specie
else:
form = form + specie + str(int(count))
else:
form = form + str(specie) + str(count)
return form.replace("1", "")
return form # .replace("1", "")

@property
def atomic_fraction(self):
Expand Down
120 changes: 120 additions & 0 deletions jarvis/core/element_names.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,120 @@
{
"H": "Hydrogen",
"He": "Helium",
"Li": "Lithium",
"Be": "Beryllium",
"B": "Boron",
"C": "Carbon",
"N": "Nitrogen",
"O": "Oxygen",
"F": "Fluorine",
"Ne": "Neon",
"Na": "Sodium",
"Mg": "Magnesium",
"Al": "Aluminum",
"Si": "Silicon",
"P": "Phosphorus",
"S": "Sulfur",
"Cl": "Chlorine",
"Ar": "Argon",
"K": "Potassium",
"Ca": "Calcium",
"Sc": "Scandium",
"Ti": "Titanium",
"V": "Vanadium",
"Cr": "Chromium",
"Mn": "Manganese",
"Fe": "Iron",
"Co": "Cobalt",
"Ni": "Nickel",
"Cu": "Copper",
"Zn": "Zinc",
"Ga": "Gallium",
"Ge": "Germanium",
"As": "Arsenic",
"Se": "Selenium",
"Br": "Bromine",
"Kr": "Krypton",
"Rb": "Rubidium",
"Sr": "Strontium",
"Y": "Yttrium",
"Zr": "Zirconium",
"Nb": "Niobium",
"Mo": "Molybdenum",
"Tc": "Technetium",
"Ru": "Ruthenium",
"Rh": "Rhodium",
"Pd": "Palladium",
"Ag": "Silver",
"Cd": "Cadmium",
"In": "Indium",
"Sn": "Tin",
"Sb": "Antimony",
"Te": "Tellurium",
"I": "Iodine",
"Xe": "Xenon",
"Cs": "Cesium",
"Ba": "Barium",
"La": "Lanthanum",
"Ce": "Cerium",
"Pr": "Praseodymium",
"Nd": "Neodymium",
"Pm": "Promethium",
"Sm": "Samarium",
"Eu": "Europium",
"Gd": "Gadolinium",
"Tb": "Terbium",
"Dy": "Dysprosium",
"Ho": "Holmium",
"Er": "Erbium",
"Tm": "Thulium",
"Yb": "Ytterbium",
"Lu": "Lutetium",
"Hf": "Hafnium",
"Ta": "Tantalum",
"W": "Tungsten",
"Re": "Rhenium",
"Os": "Osmium",
"Ir": "Iridium",
"Pt": "Platinum",
"Au": "Gold",
"Hg": "Mercury",
"Tl": "Thallium",
"Pb": "Lead",
"Bi": "Bismuth",
"Po": "Polonium",
"At": "Astatine",
"Rn": "Radon",
"Fr": "Francium",
"Ra": "Radium",
"Ac": "Actinium",
"Th": "Thorium",
"Pa": "Protactinium",
"U": "Uranium",
"Np": "Neptunium",
"Pu": "Plutonium",
"Am": "Americium",
"Cm": "Curium",
"Bk": "Berkelium",
"Cf": "Californium",
"Es": "Einsteinium",
"Fm": "Fermium",
"Md": "Mendelevium",
"No": "Nobelium",
"Lr": "Lawrencium",
"Rf": "Rutherfordium",
"Db": "Dubnium",
"Sg": "Seaborgium",
"Bh": "Bohrium",
"Hs": "Hassium",
"Mt": "Meitnerium",
"Ds": "Darmstadtium",
"Rg": "Roentgenium",
"Cn": "Copernicium",
"Nh": "Nihonium",
"Fl": "Flerovium",
"Mc": "Moscovium",
"Lv": "Livermorium",
"Ts": "Tennessine",
"Og": "Oganesson"
}
8 changes: 8 additions & 0 deletions jarvis/core/specie.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,14 @@
el_chrg_json.close()
cgcnn_feature_json = os.path.join(os.path.dirname(__file__), "atom_init.json")

element_full_name = os.path.join(
os.path.dirname(__file__), "element_names.json"
)


def get_element_full_names():
return loadjson(element_full_name)


def get_descrp_arr_name(elm="Al"):
"""
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21 changes: 21 additions & 0 deletions jarvis/db/figshare.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -421,6 +421,27 @@ def get_db_info():
"Obtaining m3gnet_mpf dataset 168917...",
"https://github.com/materialsvirtuallab/m3gnet",
],
# https://doi.org/10.6084/m9.figshare.23267852
"m3gnet_mpf_1.5mil": [
"https://figshare.com/ndownloader/files/47281519",
"id_prop.json",
"Obtaining m3gnet_mpf dataset 1.5mil...",
"https://github.com/materialsvirtuallab/m3gnet",
],
# https://doi.org/10.6084/m9.figshare.23531523
"mxene275": [
"https://figshare.com/ndownloader/files/41266233",
"mxene275.json",
"Obtaining mxene dataset 275...",
"https://cmr.fysik.dtu.dk/c2db/c2db.html",
],
# https://doi.org/10.6084/m9.figshare.26117998
"cccbdb": [
"https://figshare.com/ndownloader/files/47283808",
"cccbdb.json",
"Obtaining CCCBDB dataset 1333...",
"https://cccbdb.nist.gov/",
],
# https://doi.org/10.6084/m9.figshare.13154159
"raw_files": [
"https://ndownloader.figshare.com/files/25295732",
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2 changes: 2 additions & 0 deletions jarvis/tests/testfiles/core/test_atoms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,6 +132,8 @@ def test_basic_atoms():
rem = (Si.make_supercell([2, 2, 2]).remove_site_by_index(site=0)).num_atoms
prim = Si.get_primitive_atoms
print(prim.cart_coords)
#print(prim.get_pos())
#print(prim.get_cell())
conv = Si.get_conventional_atoms
spgn = Si.get_spacegroup
comp = compare_atoms(atoms1=prim, atoms2=conv)
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