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Develop #325

Merged
merged 49 commits into from
Aug 26, 2024
Merged

Develop #325

merged 49 commits into from
Aug 26, 2024

Commits on Mar 28, 2024

  1. improvement: add Atoms.clone() and remove sites by indices, inclu… 

    …ding 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* 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 <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* 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 <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* 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 <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* 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 <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: Ramya Gurunathan <ramya1006@gmail.com>

* Update tutorials.md

---------

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: Ramya Gurunathan <ramya1006@gmail.com>

* 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 <writetokamal.1989@gmail.com>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: Ramya Gurunathan <ramya1006@gmail.com>
Co-authored-by: Sangjoon Bob Lee <bob@boblee.io>
    @timurbazhirov @knc6
    @wines1 @tavazza @SauravMaheshkar @janosh @RamyaGuru @bobleesj
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  2. Version update.

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  1. QE PSP url updae.

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  2. Remove mkdocs hard dependency.

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  3. Update lammps.

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  4. Lint fix.

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  5. Merge branch 'master' into develop

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  1. Update super.py.

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  3. Describe out.

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  1. Fix surface layers.

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  1. Fix motif and composition.

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