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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.

---------

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 Mar 31, 2024
1 parent 90d7d7e commit 24b7266
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Showing 8 changed files with 52 additions and 16 deletions.
2 changes: 1 addition & 1 deletion jarvis/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""Version number."""

__version__ = "2024.3.24"
__version__ = "2024.3.30"

import os

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20 changes: 20 additions & 0 deletions jarvis/db/restapi.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""Module to access or upload data in JARVIS-API."""

import requests
import pprint
import os
Expand All @@ -9,6 +10,25 @@
import json


def jarvisdft_optimade(
prefix="https://jarvis.nist.gov/optimade/jarvisdft/v1/structures/?filter=",
query="elements HAS ALL C,Si",
):
url = prefix + query
vals = []
while True:
if url is not None:
# print('url', url)
response = requests.get(url)
data = response.json()["data"]
for i in data:
vals.append(i)
url = response.json()["links"]["next"]
else:
break
return vals


class Api(object):
"""Class for handling functions for JARVIS-API."""

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8 changes: 4 additions & 4 deletions jarvis/io/lammps/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,10 @@ def atoms_to_lammps(self, atoms, origin=(0, 0, 0)):
xhi = a + xlo
m = atoms.lattice._lat
xy = np.dot(m[1], m[0] / a)
yhi = np.sqrt(b ** 2 - xy ** 2) + ylo
yhi = np.sqrt(b**2 - xy**2) + ylo
xz = np.dot(m[2], m[0] / a)
yz = (np.dot(m[1], m[2]) - xy * xz) / (yhi - ylo)
zhi = np.sqrt(c ** 2 - xz ** 2 - yz ** 2) + zlo
zhi = np.sqrt(c**2 - xz**2 - yz**2) + zlo
rot_matrix = np.linalg.solve(
[[xhi - xlo, 0, 0], [xy, yhi - ylo, 0], [xz, yz, zhi - zlo]], m
)
Expand Down Expand Up @@ -94,7 +94,7 @@ def read_data(
filename="lammps.data",
element_order=[],
potential_file="pot.mod",
verbose=True,
verbose=False,
has_charges=True,
):
"""Read Lammps data file."""
Expand Down Expand Up @@ -179,7 +179,7 @@ def read_data(
y[j] = float((lines[i + j + 2]).split()[it + 2])
z[j] = float((lines[i + j + 2]).split()[it + 3])
coords.append([x[j], y[j], z[j]])
print(coords[-1])
# print(coords[-1])
f.close()
# print ("info",(typ),'coo',(coords),'latt',lat)
typ_sp = [str(i, "utf-8") for i in typ]
Expand Down
8 changes: 6 additions & 2 deletions jarvis/io/lammps/outputs.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
"""Function to analze LAMMPS output."""

import numpy as np
import glob
import os
from jarvis.analysis.elastic.tensor import ElasticTensor
from jarvis.io.lammps.inputs import LammpsData
from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos
from jarvis.core.atoms import Atoms


Expand Down Expand Up @@ -251,6 +251,8 @@ def parse_material_calculation_folder(
with optimization, vacancy, phonon, surface etc.
"""
from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos

cwd = os.getcwd()
jid_file = os.path.join(path, "JARVISFF-ID")
if os.path.exists(jid_file):
Expand Down Expand Up @@ -375,7 +377,9 @@ def parse_material_calculation_folder(
return info


def parse_full_ff_folder(path="Mishin-Ni-Al-2009.eam.alloy_nist",):
def parse_full_ff_folder(
path="Mishin-Ni-Al-2009.eam.alloy_nist",
):
"""Parse complete FF calculation folder."""
cwd = os.getcwd()
os.chdir(path)
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2 changes: 1 addition & 1 deletion jarvis/io/qe/inputs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def __init__(
# Download GBRV PSPs by default
if url is None:
url = (
"http://www.physics.rutgers.edu/"
"https://www.physics.rutgers.edu/"
"gbrv/all_pbesol_UPF_v1.5.tar.gz"
)
print("Please cite for PSPs:")
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14 changes: 9 additions & 5 deletions jarvis/tasks/lammps/lammps.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -142,11 +142,15 @@ def phonons(
self, atoms=None, lammps_cmd="", enforce_c_size=15.0, parameters={}
):
"""Make Phonon calculation setup."""
from phonopy import Phonopy
from phonopy.file_IO import (
# parse_FORCE_CONSTANTS,
write_FORCE_CONSTANTS,
)
try:
from phonopy import Phonopy
from phonopy.file_IO import (
# parse_FORCE_CONSTANTS,
write_FORCE_CONSTANTS,
)
except Exception as exp:
print("Phonopy check", exp)
pass

bulk = atoms.phonopy_converter()

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8 changes: 8 additions & 0 deletions jarvis/tests/testfiles/db/test_restapi.py
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
from jarvis.db.restapi import jarvisdft_optimade


def test_optimade():
x = jarvisdft_optimade()
print(x)
print(len(x))
assert len(x) > 1
6 changes: 3 additions & 3 deletions setup.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

setup(
name="jarvis-tools",
version="2024.3.24",
version="2024.3.30",
long_description=long_d,
install_requires=[
"numpy>=1.20.1",
Expand All @@ -24,8 +24,8 @@
"toolz>=0.9.0",
"xmltodict>=0.11.0",
"tqdm>=4.41.1",
"mkdocs-material>=9.0.5",
"markdown>=3.2.1",
# "mkdocs-material>=9.0.5",
# "markdown>=3.2.1",
# "absl-py==1.4.0",
],
package_data={
Expand Down

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