Develop (#313) · usnistgov/jarvis@a4acbdf

Commit

Develop (#313)

* 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.

* 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

* 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.

---------

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]>

Loading branch information

9 people authored Mar 20, 2024

1 parent 02d7716 commit a4acbdf

.github/workflows/action_build.yml

            
                      Original file line number
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    @@ -1,58 +1,116 @@
  
    name: JARVIS-Tools github action

    on: [push, pull_request]

    jobs:

      checks:

        name: Checks

        runs-on: ubuntu-latest

      miniconda:

        name: Miniconda ${{ matrix.os }}

        runs-on: ${{ matrix.os }}

        strategy:

          matrix:

            python-version: ["3.9","3.10"]

            matrix:

                os: ["ubuntu-latest"]

        steps:

        - uses: actions/checkout@v2

        - name: Setup Python ${{ matrix.python-version }}

          uses: actions/setup-python@v2

          with:

            python-version: ${{ matrix.python-version }}

        - uses: actions/cache@v2

          with:

            path: ${{ env.pythonLocation }}

            key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}

        - name: Install requirements

          run: |

            pip install --upgrade pip

            pip install pycodestyle flake8 pydocstyle 

            flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis

            pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis

            pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis

          - uses: actions/checkout@v2

          - uses: conda-incubator/setup-miniconda@v2

            with:

              activate-environment: test

              environment-file: environment.yml

              python-version: "3.10"

              auto-activate-base: false

          - shell: bash -l {0}

            run: |

              conda info

              conda list

          - name: Lint

            shell: bash -l {0}

            run: |

                conda install flake8 pycodestyle pydocstyle

                flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis

                pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis

                pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis

          - name: Run pytest

            shell: bash -l {0}

            run: |

                conda install pytest coverage codecov

                python setup.py develop

                coverage run -m pytest

                coverage report -m -i

                codecov

                codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"

                rm POSCAR* *.png

    # name: JARVIS-Tools github action

    # on: [push, pull_request]

    # jobs:

    #   checks:

    #     name: Checks

    #     runs-on: ubuntu-latest

    #     defaults:

    #       run:

    #         shell: bash -l {0}

    #     strategy:

    #       matrix:

    #         python-version: ["3.10"]

    #     steps:

    #     - uses: actions/checkout@v2

    #     - name: Setup Python ${{ matrix.python-version }}

    #       uses: actions/setup-python@v2

    #       with:

    #         python-version: ${{ matrix.python-version }}

    #     - uses: actions/cache@v2

    #       with:

    #         path: ${{ env.pythonLocation }}

    #         key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}

    #     - name: Install requirements

    #       run: |

    #         source ~/.bashrc

    #         echo "begin: PATH=$PATH;"

    #         find . -type f > before_test_files.txt

    #         conda env create -f environment.yml

    #         conda activate my_jarvis

    #         conda install pandas numpy matplotlib phonopy scikit-learn --quiet

    #         pip install --upgrade pip

    #         pip install pycodestyle flake8 pydocstyle coverage pytest codecov qiskit==0.41.1

    #         flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis

    #         pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis

    #         pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis

    #         #python setup.py develop

    #         #pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .

    #         #conda install -c ambermd pytraj

    #         #pip install numpy scipy matplotlib

    #         #pip install -r dev-requirements.txt

            #python setup.py develop

            #pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .

            #conda install -c ambermd pytraj

            pip install numpy scipy matplotlib

            pip install -r dev-requirements.txt

            pip install -e .

            echo 'CONDA LIST'

            conda list

            echo 'PIP FREEZE'

            pip freeze

            #echo 'PYTEST-COV'

            #pytest --cov-config=.coveragerc --cov=jarvis -n 2

            coverage run -m pytest

            coverage report -m -i

            codecov

            codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"

            # git clone https://github.com/QEF/q-e.git

            # cd q-e

            # ./configure

            # make pw

    #         pip install -e .

    #         echo 'CONDA LIST'

    #         conda list

    #         echo 'PIP FREEZE'

    #         pip freeze

    #         #echo 'PYTEST-COV'

    #         #pytest --cov-config=.coveragerc --cov=jarvis -n 2

    #         coverage run -m pytest

    #         coverage report -m -i

    #         codecov

    #         codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"

    #         find . -type f > after_test_files.txt

    #         #comm -13 <(sort before_test_files.txt) <(sort after_test_files.txt) > new_files.txt

    #         #cat new_files.txt | xargs rm

    #         #rm before_test_files.txt after_test_files.txt new_files.txt

    #         # git clone https://github.com/QEF/q-e.git

    #         # cd q-e

    #         # ./configure

    #         # make pw

    # jobs:

    #   checks:

    @@ -149,4 +207,4 @@ jobs:
  
    #             # git clone https://github.com/QEF/q-e.git

    #             # cd q-e

    #             # ./configure

    #             # make pw
      
    #             # make pw

dev-requirements.txt

This file was deleted.

docs/index.md

            
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    @@ -28,9 +28,9 @@ NIST-JARVIS official website is: <https://jarvis.nist.gov> . This
  
    project is a part of the Materials Genome Initiative (MGI) at NIST

    (<https://mgi.nist.gov/>).

    For more details, checkout our latest article: [The joint automated

    For more details, checkout our latest articles: [The joint automated

    repository for various integrated simulations (JARVIS) for data-driven

    materials design](https://www.nature.com/articles/s41524-020-00440-1), [other publications](https://pages.nist.gov/jarvis/publications/) and [YouTube

    materials design](https://www.nature.com/articles/s41524-020-00440-1), [Recent progress in the JARVIS infrastructure for next-generation data-driven materials design](https://pubs.aip.org/aip/apr/article/10/4/041302/2917416), [other publications](https://pages.nist.gov/jarvis/publications/) and [YouTube

    videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel=JARVIS-repository)

    @@ -98,9 +98,9 @@ videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel
  
            bash Miniconda3-latest-Linux-x86_64.sh (for linux)

            bash Miniconda3-latest-MacOSX-x86_64.sh (for Mac)

            Download 32/64 bit python 3.9 miniconda exe and install (for windows)

            Download 32/64 bit python 3.10 miniconda exe and install (for windows)

            Now, let's make a conda environment just for JARVIS::

            conda create --name my_jarvis python=3.9

            conda create --name my_jarvis python=3.10

            source activate my_jarvis

    -   Method-1: Installation using pip:

    @@ -116,12 +116,19 @@ videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel
  
            pip install numpy scipy matplotlib

            git clone https://github.com/usnistgov/jarvis.git

            cd jarvis

            python setup.py install

            python setup.py develop

    -   Note on installing additional dependencies for all modules to

        function:

    -   Method-4: Note on installing additional dependencies (for developers):

            pip install -r dev-requirements.txt

            conda env create --name my_jarvis -f environment.yml

            conda activate my_jarvis

            conda install pytest coverage codecov

            git clone https://github.com/usnistgov/jarvis.git

            cd jarvis

            git checkout develop

            python setup.py develop

            coverage run -m pytest

    <a name="example"></a>

    ## Example function

docs/tutorials.md

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -643,7 +643,7 @@ import numpy as np
  
    from jarvis.core.composition import Composition

    from jarvis.core.specie import Specie

    from jarvis.ai.pkgs.lgbm.regression import regression

    from jarvis.ai.descriptors.cfid import get_chem_only_descriptor

    from jarvis.ai.descriptors.cfid import get_chem_only_descriptors

    # Load a dataset, you can use pandas read_csv also to generte my_data

    # Here is a sample dataset

    @@ -671,7 +671,7 @@ X = []
  
    Y = []

    IDs = []

    for ii, i in enumerate(my_data):

        X.append(get_chem_only_descriptor(i[0]))

        X.append(get_chem_only_descriptors(i[0]))

        Y.append(i[1])

        IDs.append(ii)

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