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Adding phono3py input/output modules. Note: need to fix pydocstyle formatting #285

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knc6 and others added 30 commits April 29, 2021 00:43
* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Increase coverage. (usnistgov#137)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (usnistgov#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (usnistgov#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (usnistgov#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (usnistgov#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (usnistgov#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

Co-authored-by: Brian DeCost <brian.decost@nist.gov>
* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Increase coverage. (usnistgov#137)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (usnistgov#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (usnistgov#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (usnistgov#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (usnistgov#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (usnistgov#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

* Version update.

* Version update.

Co-authored-by: Brian DeCost <brian.decost@nist.gov>
* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Increase coverage. (usnistgov#137)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (usnistgov#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (usnistgov#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (usnistgov#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (usnistgov#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (usnistgov#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

* Version update.

* Version update.

* Queue jobs update.

Co-authored-by: Brian DeCost <brian.decost@nist.gov>
* Increase coverage. (usnistgov#137)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (usnistgov#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (usnistgov#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (usnistgov#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (usnistgov#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (usnistgov#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

* Version update.

* Version update.

* Queue jobs update.

* Version ,VASP DB Maker, IR module update.

* Lint fix.

* Remove unnecessary xml files.

* IR test fix.

Co-authored-by: Brian DeCost <brian.decost@nist.gov>
* phonopy TB.

* phonopy TB.

* Versionupdate.

* Wannier TB for phonons (usnistgov#138)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Create CODE_OF_CONDUCT.md (usnistgov#139)

* Update README.rst

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Poscar format fix. (usnistgov#142)

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Minor fix in figshare and spectrum.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor fix in figshare and spectrum. (usnistgov#143)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Fix POSCAR order issue.

* Version change.

* Poscar write fix, CIF reader fix.

* Develop (usnistgov#141)

* Added OQMD, MP, QM9 CFID datasets.

* Added OQMD, MP, QM9 CFID datasets.

* vasp2xml schema update.

* Update config.yml

* XRD DB making bug fix, scattering.json update.

* Minor bug fix in vasp_to_xml.py

* Add license.

* Add license, pin versions

* Remove circle.

* Update shell.nix

* Vasprun single element bug fix.

* Minor updates.

* DB XML and VASP Workflow fix.

* AFLOW CFID added, VASP_PSP_DIR fix.

* Linting fix, new version release.

* Wannier update.

* Version update.

* VASP task update.

* Tempfile for downloading zipfiles.

* Pypi fix.

* Pypi fix.

* Updated wannier, vasp2xml, increased tests.

* Update setup.py

* Update action_build.yml

* Speed up test.

* Update DatasetSummary.rst

* Update outputs.py

* Enforce nk1==nk2 in spillage.

* Update test_spillage.py

* Multiple updates.

* Magtest update.

* Version update.

* Update README.rst

* Update README.rst

* WannierTB Phonons.

* phonopy TB.

* phonopy TB.

* Versionupdate.

* QAlgo

* Atoms POSCAR Order update.

* Qiskit tests.

* Lint fix.

* Wien2K extra test, ene file.

* WT.

* WT added.

* Qiskit depedendence.

* Qiskit version.

* Qiskit version.

* Qiskit version.

* Update requirements-ci.txt

* Update requirements-ci.txt

* Update action_build.yml

* Update shell.nix

* 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

* Ignore QAlgo tests.

* Make qiskit work.

* Make qiskit work.

* 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

* Delete __init__.py

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Qiskit fix attempt.

* Pennylane fix attempt.

* Update test_hermsolver.py

* Test ham.

* Test ham.

* Update inputs.py

* Test ham.

* Update action_build.yml

* Update inputs.py

* Create __init__.py

* Test ham.

* Update test_hermsolver.py

* Update test_hermsolver.py

* Test Circuit.

* Update test_hermsolver.py

* Update action_build.yml

* Aer

* Aer .

* Var circuit added.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Increase test coverage, ASE, Tequila, Qiskit.

* Ready for master branch.

* Update shell.nix

* Update __init__.py

* Version change.

* Minor fix in figshare and spectrum.

* Update README.rst

* Lint fix.

* Minor update.

* Update figshare.py

* Fix build.

* Update README.rst

* docs update.

* Setup requirement change.

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

* Update README.rst

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* develop (usnistgov#147)

* Update version tag. (usnistgov#145)

* Minor fix in figshare and spectrum.

* Setup requirement change.

* Cleanup graph (usnistgov#146)

* revert jarvis.core.graph adjacency matrix weights to interatomic distances

* remove jarvis.core.graph.Graph edges with bond length past threshold max_cut

* fix jarvis.core.graph.Graph.adjacency_matrix to support sparse graphs (with no self edges), and update test file to reflect removal of self edges as well

* Update README.rst

Co-authored-by: Brian DeCost <brian.decost@nist.gov>

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Travis update.

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Update requirements-for-ci-only.txt

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Adding Qiskit.

* Version update.

* Version update.

* Adding Qiskit.

* Adding Qiskit.

* Fix travis.

* Fix travis.

* Fix travis.

* Fix travis.

* VASP outputs bug fix.

* Optics module and Dos module of VASP fixed.

* Fixing commit.

* Lint fix.

* Update inputs.py

* Version update.

* README update.

* Graph and dataset update.

* Graph and dataset update.

* Graph and dataset update.

* Graph module update.

* More datasets added.

* Update .travis.yml

* Update .travis.yml

* Exclude tequila tests.

* Exclude tequila tests.

* Extra tests.

* Pytest-cov added.

* Update action_build.yml

* Update action_build.yml

* Covergae update.

* Covergae update.

* StructureDataset test added.

* Graph tests fixed.

* Figshare update.

* STM image links added.

* Update test_figshare.py

* Update test_figshare.py

* Update .travis.yml

* Update .travis.yml

* Cache github action attempt.

* DB update.

* Update action.

* DB update.

* Figshare test update.

* JARVIS-FF DB added.

* Try to increase coverage.

* Polymer genome added.

* Graph update.

* Graph update.

* Graph update.

* Figshare update.

* Version update.

* Figshare update.

* Hot encoded species.

* STEM with Convolution and Pyprismatic added.

* STEM Conv update.

* Atoms module update.

* Lorentzian fix.

* Digitized features added.

* Graph angle,prdf added. QE parser update.

* Update outputs.py

* Graph angle update and cif2cell added.

* Reduced formula fix and linting fix.

* Test minor fix.

* Graph tests update.

* Pytestfix.

* See also check url in xml

* See also check url in xml

* Phonopy run update.

* Graph update with torch angle.

* Get all neighbors routine bug fix.

* Figshare lint fix.

* Version update, IR extended, graph torch fix.

* Fix IR pytest.

* IR test fix.

* Cache graph dataset (usnistgov#161)

* modify graph StructureDataset to enable/disable computation of atomistic line graph.

* fix line length setting in black configuration and fix jarvis.core.specie and jarvis.core.graphs

* pin pennylane version to 0.14.1 in GH build action.

* update graph dataloader test.

* fix pennylane version pinning and fix missing pandas.DataFrame in dataloader test.

* bump version number.

* README update.

* Bandgap based on occupation tolerance added to Vasprun.

* id_tag update.

* Version update

* Remove cif2cell dependence.

* Version update.

* Version update.

* Queue jobs update.

* Version ,VASP DB Maker, IR module update.

* Lint fix.

* Remove unnecessary xml files.

* IR test fix.

* Image blob angle analysis for STM,figshare STM.

* MAD added.

* Remove XSD.

* Update .travis.yml

* Delete .travis.yml

Co-authored-by: Brian DeCost <brian.decost@nist.gov>
RamyaGuru and others added 29 commits February 23, 2022 12:56
* 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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#214)

* QE inputs, XANES, GHAction updates. (usnistgov#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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#234)

* Local tetra tmp.

* Version update.

* Lint fix.

* HSE06

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>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
Bumps [numpy](https://github.com/numpy/numpy) from 1.20.0 to 1.21.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](numpy/numpy@v1.20.0...v1.21.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.7.0 to 2.8.0.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](tensorflow/tensorflow@v2.7.0...v2.8.0)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* 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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#214)

* QE inputs, XANES, GHAction updates. (usnistgov#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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#234)

* Local tetra tmp.

* Version update.

* Lint fix.

* HSE06

* Tmp.

* Vacancy update, Optimade structureand other minor lint updates.

* STEM pytest fix.

* Minor lint fix.

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>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
* 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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#214)

* QE inputs, XANES, GHAction updates. (usnistgov#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 (usnistgov#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. (usnistgov#197)

* Develop (usnistgov#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 (usnistgov#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 (usnistgov#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.

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>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
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codecov-commenter commented Mar 2, 2023

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.50 ⚠️

Comparison is base (bc4b20f) 89.48% compared to head (54224f6) 88.99%.

📣 This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

Additional details and impacted files
@@            Coverage Diff             @@
##            tcond     #285      +/-   ##
==========================================
- Coverage   89.48%   88.99%   -0.50%     
==========================================
  Files          61       61              
  Lines       10512    10600      +88     
==========================================
+ Hits         9407     9433      +26     
- Misses       1105     1167      +62     
Impacted Files Coverage Δ
jarvis/analysis/elastic/tensor.py 97.08% <ø> (ø)
jarvis/io/phonopy/fcmat2hr.py 100.00% <ø> (ø)
jarvis/io/phonopy/inputs.py 83.19% <ø> (-8.48%) ⬇️
jarvis/io/phonopy/outputs.py 68.35% <ø> (-22.86%) ⬇️
jarvis/core/kpoints.py 86.58% <100.00%> (-1.99%) ⬇️

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5 participants