Develop (#318)

* improvement: add `Atoms.clone()` and `remove sites by indices`, including in-place. Use `develop` branch for the PR. (#315) * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. * Add installation tests (#214) * QE inputs, XANES, GHAction updates. (#210) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Add installation tests * Fix codestyle * Fix codestyle with black * Add docstrings * Fix pydocstyle error * Update __init__.py * Update __init__.py Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py * WIP super QE. * Working version of ScSi. * QE inputs and task update. * Add master super. * Add master super. * Lint fix. * Lint fix. * Minor fix. * ET update. * Fix ET test. * Update sanitize atoms. * Additonal checks on supercond. * Debye bug fix. * Pressure in QE Super. * Version fix, publication update, supercond workflow update. * Lint fix. * Tensorboard fix. * Tensorboard fix. * Tensorboard fix. * Melting temp fix. * Update vasp.py (#234) * Local tetra tmp. * Version update. * Lint fix. * HSE06 * Tmp. * Vacancy update, Optimade structureand other minor lint updates. * STEM pytest fix. * Minor lint fix. * Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms * Lint fix. * Added phononDos class. * fix pytorch UserWarning in build_undirected_edgedata() (#243) site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. r = torch.tensor(r).type(torch.get_default_dtype()) * Add PhaseDiagram. * Add PhaseDiagram. * PhaseDiagram update. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * Compare atoms, get spg info directly from atoms. * Flake8 fix. * Update publications.rst * Update qiskit. * Update qiskit. * Update test_hermsolver.py * FIix qiskit DOS. * Update test_hermsolver.py * Fix linting. * Develop og (#257) * Added isotope scattering rate to phonon DOS analysis script. * Linting fix. * Linting fix. * Linting fix. * Add QE convergence. * Update converg.py. * Nexus. * Super with converg. * Super with converg. * SuperCon QE update. * Figshare DB update. * Figshare DB update. * Update alignn ff link. * Lint fix. * DB docs update. * Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy. * Lint fix. * Supercon workflow fix. * Add extra db entires, fix chem in cfid_chem. * Version update. * Add figshare datasets. * Update databases.rst * codecov fix. * Version update. * Lint fix. * Add FigShare datasets, DOS in QE, Uncertainty. * Add python 3.9. * Create README.md * Update README. * Add README.md. * Update action_build.yml * Update action_lint.yml * Allow md file, add mode databases. * Create NISTtheDocs2Death.yml * Allow md file, add mode databases. * Add publications. * Update publications.rst * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Create deploy_nist_pages.yml * Add mkdocs. * Update deploy_nist_pages.yml * Update md. * Update setup.py * Update readme. * Update setup.py * Remove absl. * Update dev-requirements.txt * Update index.md * Update deploy_nist_pages.yml * Update index.rst * Add redirect. * Update action_build.yml * Update dev-requirements.txt * Update dev-requirements.txt * Update setup.py * Update dev-requirements.txt * Fix __repr__ for Atoms. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Use poscar write as string. * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Delete NISTtheDocs2Death.yml * Delete action_lint.yml * Use poscar write as string. * Fix phonopy. * Update dev-requirements.txt * Update databases. * Add eigs. * Add eigs. * Add eigs. * Fix STM test. * Delete .travis.yml * Update README. * Add python docs. * GA * Update action_build.yml * Atoms class update with props. * Atoms class update with props. * Delete .readthedocs.yaml * Update README.md * QEjob fix. * Chang poscar write. * Add check_polar update, locpot update. * Locpot pytest. * X locpot. * Lint. * Update figshare.py * Update tutorials.md for get_chem_only_descriptors (#309) * Develop (#308) * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. * Add installation tests (#214) * QE inputs, XANES, GHAction updates. (#210) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Add installation tests * Fix codestyle * Fix codestyle with black * Add docstrings * Fix pydocstyle error * Update __init__.py * Update __init__.py Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> * Adding QE super. * Minor changes to QE module, atoms xyz fix. * Adding qe_tb info, and version update. * Update __init__.py * WIP super QE. * Working version of ScSi. * QE inputs and task update. * Add master super. * Add master super. * Lint fix. * Lint fix. * Minor fix. * ET update. * Fix ET test. * Update sanitize atoms. * Additonal checks on supercond. * Debye bug fix. * Pressure in QE Super. * Version fix, publication update, supercond workflow update. * Lint fix. * Tensorboard fix. * Tensorboard fix. * Tensorboard fix. * Melting temp fix. * Update vasp.py (#234) * Local tetra tmp. * Version update. * Lint fix. * HSE06 * Tmp. * Vacancy update, Optimade structureand other minor lint updates. * STEM pytest fix. * Minor lint fix. * Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms * Lint fix. * Added phononDos class. * fix pytorch UserWarning in build_undirected_edgedata() (#243) site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. r = torch.tensor(r).type(torch.get_default_dtype()) * Add PhaseDiagram. * Add PhaseDiagram. * PhaseDiagram update. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * STM image pytest increase, requirements upgrade. * Compare atoms, get spg info directly from atoms. * Flake8 fix. * Update publications.rst * Update qiskit. * Update qiskit. * Update test_hermsolver.py * FIix qiskit DOS. * Update test_hermsolver.py * Fix linting. * Develop og (#257) * Added isotope scattering rate to phonon DOS analysis script. * Linting fix. * Linting fix. * Linting fix. * Add QE convergence. * Update converg.py. * Nexus. * Super with converg. * Super with converg. * SuperCon QE update. * Figshare DB update. * Figshare DB update. * Update alignn ff link. * Lint fix. * DB docs update. * Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy. * Lint fix. * Supercon workflow fix. * Add extra db entires, fix chem in cfid_chem. * Version update. * Add figshare datasets. * Update databases.rst * codecov fix. * Version update. * Lint fix. * Add FigShare datasets, DOS in QE, Uncertainty. * Add python 3.9. * Create README.md * Update README. * Add README.md. * Update action_build.yml * Update action_lint.yml * Allow md file, add mode databases. * Create NISTtheDocs2Death.yml * Allow md file, add mode databases. * Add publications. * Update publications.rst * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Create deploy_nist_pages.yml * Add mkdocs. * Update deploy_nist_pages.yml * Update md. * Update setup.py * Update readme. * Update setup.py * Remove absl. * Update dev-requirements.txt * Update index.md * Update deploy_nist_pages.yml * Update index.rst * Add redirect. * Update action_build.yml * Update dev-requirements.txt * Update dev-requirements.txt * Update setup.py * Update dev-requirements.txt * Fix __repr__ for Atoms. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Update requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Fix requirements. * Use poscar write as string. * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Update action_build.yml * Use poscar write as string. * Use poscar write as string. * Delete NISTtheDocs2Death.yml * Delete action_lint.yml * Use poscar write as string. * Fix phonopy. * Update dev-requirements.txt * Update databases. * Add eigs. * Add eigs. * Add eigs. * Fix STM test. * Delete .travis.yml * Update README. * Add python docs. * GA * Update action_build.yml * Atoms class update with props. * Atoms class update with props. * Delete .readthedocs.yaml * Update README.md * QEjob fix. * Chang poscar write. * Add check_polar update, locpot update. * Locpot pytest. * X locpot. * Lint. --------- Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: Ramya Gurunathan <[email protected]> * Update tutorials.md --------- Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: Ramya Gurunathan <[email protected]> * Qsiqskit dversion and CFID chemical feature doc issue. * Update dev-requirements.txt * Update dev-requirements.txt * Update dev-requirements.txt * Update inputs.py * Update figshare.py * Update figshare.py * chore: update .gitignore to add pycharm .idea * improvements: clone method and remove multiple sites, including in place * tests: attempt adding tests for the new functionality not sure how to run these - some documentation would be good to have in README.md * Flake8 fix. * Add pydantic. * wien2k fix. * Comment out qiskit related tests. * Fix OneHotEncoder. * Check conda * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update action_build.yml * Update docs. * Update index.md * Update index.md * Minor lint fix. * Update deploy_nist_pages.yml * fix: lint * Fix bug in the PR. --------- Co-authored-by: knc6 <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: Ramya Gurunathan <[email protected]> Co-authored-by: Sangjoon Bob Lee <[email protected]> * Version update. * QE PSP url updae. * Remove mkdocs hard dependency. * Update lammps. * Lint fix. * Adding restapi. * Update super.py. * Add describer. * Add describer. * Add describer. * Update describe. * Lint fix. --------- Co-authored-by: Timur Bazhirov <[email protected]> Co-authored-by: wines1 <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: Saurav Maheshkar <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: Ramya Gurunathan <[email protected]> Co-authored-by: Sangjoon Bob Lee <[email protected]>
usnistgov · Apr 14, 2024 · 4ec2bf5 · 4ec2bf5
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diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,6 +1,6 @@
 """Version number."""
 
-__version__ = "2024.3.30"
+__version__ = "2024.4.10"
 
 import os
 

diff --git a/jarvis/core/atoms.py b/jarvis/core/atoms.py
@@ -19,6 +19,7 @@
 import random
 import string
 import datetime
+from collections import defaultdict
 
 amu_gm = 1.66054e-24
 ang_cm = 1e-8
@@ -1224,6 +1225,157 @@ def lattice_points_in_supercell(self, supercell_matrix):
         assert len(tvects) == round(abs(np.linalg.det(supercell_matrix)))
         return tvects
 
+    def describe(
+        self,
+        xrd_peaks=5,
+        xrd_round=1,
+        cutoff=4,
+        take_n_bonds=2,
+        include_spg=True,
+    ):
+        """Describe for NLP applications."""
+        from jarvis.analysis.diffraction.xrd import XRD
+
+        if include_spg:
+            from jarvis.analysis.structure.spacegroup import Spacegroup3D
+
+            spg = Spacegroup3D(self)
+        theta, d_hkls, intens = XRD().simulate(atoms=self)
+        #     x = atoms.atomwise_angle_and_radial_distribution()
+        #     bond_distances = {}
+        #     for i, j in x[-1]["different_bond"].items():
+        #         bond_distances[i.replace("_", "-")] = ", ".join(
+        #             map(str, (sorted(list(set([round(jj, 2) for jj in j])))))
+        #         )
+        dists = defaultdict(list)
+        elements = self.elements
+        for i in self.get_all_neighbors(r=cutoff):
+            for j in i:
+                key = "-".join(sorted([elements[j[0]], elements[j[1]]]))
+                dists[key].append(j[2])
+        bond_distances = {}
+        for i, j in dists.items():
+            dist = sorted(set([round(k, 2) for k in j]))
+            if len(dist) >= take_n_bonds:
+                dist = dist[0:take_n_bonds]
+            bond_distances[i] = ", ".join(map(str, dist))
+        fracs = {}
+        for i, j in (self.composition.atomic_fraction).items():
+            fracs[i] = round(j, 3)
+        info = {}
+        chem_info = {
+            "atomic_formula": self.composition.reduced_formula,
+            "prototype": self.composition.prototype,
+            "molecular_weight": round(self.composition.weight / 2, 2),
+            "atomic_fraction": (fracs),
+            "atomic_X": ", ".join(
+                map(str, [Specie(s).X for s in self.uniq_species])
+            ),
+            "atomic_Z": ", ".join(
+                map(str, [Specie(s).Z for s in self.uniq_species])
+            ),
+        }
+        struct_info = {
+            "lattice_parameters": ", ".join(
+                map(str, [round(j, 2) for j in self.lattice.abc])
+            ),
+            "lattice_angles": ", ".join(
+                map(str, [round(j, 2) for j in self.lattice.angles])
+            ),
+            # "spg_number": spg.space_group_number,
+            # "spg_symbol": spg.space_group_symbol,
+            "top_k_xrd_peaks": ", ".join(
+                map(
+                    str,
+                    sorted(list(set([round(i, xrd_round) for i in theta])))[
+                        0:xrd_peaks
+                    ],
+                )
+            ),
+            "density": round(self.density, 3),
+            # "crystal_system": spg.crystal_system,
+            # "point_group": spg.point_group_symbol,
+            # "wyckoff": ", ".join(list(set(spg._dataset["wyckoffs"]))),
+            "bond_distances": bond_distances,
+        }
+        if include_spg:
+            struct_info["spg_number"] = spg.space_group_number
+            struct_info["spg_symbol"] = spg.space_group_symbol
+            struct_info["crystal_system"] = spg.crystal_system
+            struct_info["point_group"] = spg.point_group_symbol
+            struct_info["wyckoff"] = ", ".join(
+                list(set(spg._dataset["wyckoffs"]))
+            )
+            struct_info["natoms_primitive"] = spg.primitive_atoms.num_atoms
+            struct_info[
+                "natoms_conventional"
+            ] = spg.conventional_standard_structure.num_atoms
+        info["chemical_info"] = chem_info
+        info["structure_info"] = struct_info
+        line = "The number of atoms are: " + str(
+            self.num_atoms
+        )  # +"., The elements are: "+",".join(atoms.elements)+". "
+        for i, j in info.items():
+            if not isinstance(j, dict):
+                line += "The " + i + " is " + j + ". "
+            else:
+                # print("i",i)
+                # print("j",j)
+                for ii, jj in j.items():
+                    tmp = ""
+                    if isinstance(jj, dict):
+                        for iii, jjj in jj.items():
+                            tmp += iii + ": " + str(jjj) + " "
+                    else:
+                        tmp = jj
+                    line += "The " + ii + " is " + str(tmp) + ". "
+        line1 = line
+        # print('bond_distances', struct_info['bond_distances'])
+        tmp = ""
+        p = struct_info["bond_distances"]
+        for ii, (kk, vv) in enumerate(p.items()):
+            if ii == len(p) - 1:
+                punc = " Å."
+            else:
+                punc = " Å; "
+            tmp += kk + ": " + vv + punc
+        line2 = (
+            chem_info["atomic_formula"]
+            + " crystallizes in the "
+            + struct_info["crystal_system"]
+            + " "
+            + str(struct_info["spg_symbol"])
+            + " spacegroup, "
+            + struct_info["point_group"]
+            + " pointgroup with a prototype of "
+            + str(chem_info["prototype"])
+            # " and a molecular weight of " +
+            # str(chem_info['molecular_weight']) +
+            + ". The atomic fractions are: "
+            + str(chem_info["atomic_fraction"])
+            .replace("{", "")
+            .replace("}", "")
+            + " with electronegaticities as "
+            + str(chem_info["atomic_X"])
+            + " and atomic numbers as "
+            + str(chem_info["atomic_Z"])
+            + ". The bond distances are: "
+            + str(tmp)
+            + "The lattice lengths are: "
+            + struct_info["lattice_parameters"]
+            + " Å, and the lattice angles are: "
+            + struct_info["lattice_angles"]
+            + "º with some of the top XRD peaks at "
+            + struct_info["top_k_xrd_peaks"]
+            + "º with "
+            + "Wyckoff symbols "
+            + struct_info["wyckoff"]
+            + "."
+        )
+        info["desc_1"] = line1
+        info["desc_2"] = line2
+        return info
+
     def make_supercell_matrix(self, scaling_matrix):
         """
         Adapted from Pymatgen.
@@ -1279,49 +1431,52 @@ def make_supercell(self, dim=[2, 2, 2]):
         if dim.shape == (3, 3):
             dim = np.array([int(np.linalg.norm(v)) for v in dim])
         return self.make_supercell_matrix(dim)
-        # coords = self.frac_coords
-        # all_symbs = self.elements  # [i.symbol for i in s.species]
-        # nat = len(coords)
-
-        # new_nat = nat * dim[0] * dim[1] * dim[2]
-        # new_coords = np.zeros((new_nat, 3))
-        # new_symbs = []  # np.chararray((new_nat))
-        # props = []  # self.props
-
-        # ct = 0
-        # for i in range(nat):
-        #    for j in range(dim[0]):
-        #        for k in range(dim[1]):
-        #            for m in range(dim[2]):
-        #                props.append(self.props[i])
-        #                new_coords[ct][0] = (coords[i][0] + j) / float(dim[0])
-        #                new_coords[ct][1] = (coords[i][1] + k) / float(dim[1])
-        #                new_coords[ct][2] = (coords[i][2] + m) / float(dim[2])
-        #                new_symbs.append(all_symbs[i])
-        #                ct = ct + 1
-
-        # nat = new_nat
-
-        # nat = len(coords)  # int(s.composition.num_atoms)
-        # lat = np.zeros((3, 3))
-        # box = self.lattice_mat
-        # lat[0][0] = dim[0] * box[0][0]
-        # lat[0][1] = dim[0] * box[0][1]
-        # lat[0][2] = dim[0] * box[0][2]
-        # lat[1][0] = dim[1] * box[1][0]
-        # lat[1][1] = dim[1] * box[1][1]
-        # lat[1][2] = dim[1] * box[1][2]
-        # lat[2][0] = dim[2] * box[2][0]
-        # lat[2][1] = dim[2] * box[2][1]
-        # lat[2][2] = dim[2] * box[2][2]
-        # super_cell = Atoms(
-        #    lattice_mat=lat,
-        #    coords=new_coords,
-        #    elements=new_symbs,
-        #    props=props,
-        #    cartesian=False,
-        # )
-        # return super_cell
+
+    def make_supercell_old(self, dim=[2, 2, 2]):
+        """Make supercell of dimension dim using for loop."""
+        coords = self.frac_coords
+        all_symbs = self.elements  # [i.symbol for i in s.species]
+        nat = len(coords)
+
+        new_nat = nat * dim[0] * dim[1] * dim[2]
+        new_coords = np.zeros((new_nat, 3))
+        new_symbs = []  # np.chararray((new_nat))
+        props = []  # self.props
+
+        ct = 0
+        for i in range(nat):
+            for j in range(dim[0]):
+                for k in range(dim[1]):
+                    for m in range(dim[2]):
+                        props.append(self.props[i])
+                        new_coords[ct][0] = (coords[i][0] + j) / float(dim[0])
+                        new_coords[ct][1] = (coords[i][1] + k) / float(dim[1])
+                        new_coords[ct][2] = (coords[i][2] + m) / float(dim[2])
+                        new_symbs.append(all_symbs[i])
+                        ct = ct + 1
+
+        nat = new_nat
+
+        nat = len(coords)  # int(s.composition.num_atoms)
+        lat = np.zeros((3, 3))
+        box = self.lattice_mat
+        lat[0][0] = dim[0] * box[0][0]
+        lat[0][1] = dim[0] * box[0][1]
+        lat[0][2] = dim[0] * box[0][2]
+        lat[1][0] = dim[1] * box[1][0]
+        lat[1][1] = dim[1] * box[1][1]
+        lat[1][2] = dim[1] * box[1][2]
+        lat[2][0] = dim[2] * box[2][0]
+        lat[2][1] = dim[2] * box[2][1]
+        lat[2][2] = dim[2] * box[2][2]
+        super_cell = Atoms(
+            lattice_mat=lat,
+            coords=new_coords,
+            elements=new_symbs,
+            props=props,
+            cartesian=False,
+        )
+        return super_cell
 
     def get_lll_reduced_structure(self):
         """Get LLL algorithm based reduced structure."""
@@ -1882,18 +2037,18 @@ def to_optimade(
         info_at["cartesian_site_positions"] = atoms.cart_coords[order].tolist()
         info_at["nperiodic_dimensions"] = 3
         # info_at["species"] = atoms.elements
-        info_at["species"] = (
-            self.get_optimade_species()
-        )  # dict(atoms.composition.to_dict())
+        info_at[
+            "species"
+        ] = self.get_optimade_species()  # dict(atoms.composition.to_dict())
         info_at["elements_ratios"] = list(
             atoms.composition.atomic_fraction.values()
         )
         info_at["structure_features"] = []
         info_at["last_modified"] = str(now)
         # info_at["more_data_available"] = True
-        info_at["chemical_formula_descriptive"] = (
-            atoms.composition.reduced_formula
-        )
+        info_at[
+            "chemical_formula_descriptive"
+        ] = atoms.composition.reduced_formula
         info_at["dimension_types"] = [1, 1, 1]
         info["attributes"] = info_at
         return info

diff --git a/jarvis/core/graphs.py b/jarvis/core/graphs.py
@@ -49,7 +49,8 @@ def nearest_neighbor_edges(
     cutoff=8,
     max_neighbors=12,
     id=None,
-    use_canonize=False,
+    use_canonize=True,
+    # use_canonize=False,
 ):
     """Construct k-NN edge list."""
     # returns List[List[Tuple[site, distance, index, image]]]
@@ -200,7 +201,8 @@ def atom_dgl_multigraph(
         max_attempts=3,
         id: Optional[str] = None,
         compute_line_graph: bool = True,
-        use_canonize: bool = False,
+        use_canonize: bool = True,
+        # use_canonize: bool = False,
     ):
         """Obtain a DGLGraph for Atoms object."""
         if neighbor_strategy == "k-nearest":

diff --git a/jarvis/tasks/qe/super.py b/jarvis/tasks/qe/super.py
@@ -218,7 +218,8 @@ def runjob(self):
                 "outdir": "'./'",
                 "tstress": ".true.",
                 "tprnfor": ".true.",
-                "disk_io": "'nowf'",
+                "disk_io": "'low'",
+                # "disk_io": "'nowf'",
                 "pseudo_dir": None,
                 "verbosity": "'high'",
                 "nstep": 100,

diff --git a/jarvis/tests/testfiles/core/test_atoms.py b/jarvis/tests/testfiles/core/test_atoms.py
@@ -118,6 +118,8 @@ def test_basic_atoms():
     den_0d = round(vac_pad.get_effective_molecule().density, 2)
     den_lll_red = round(Si.get_lll_reduced_structure().density, 2)
     strng = Si.get_string()
+    scell_nat_old = Si.make_supercell_old([2, 2, 2]).num_atoms
+    descr = Si.describe()
     scell_nat = Si.make_supercell([2, 2, 2]).num_atoms
     scell_nat2 = Si.make_supercell_matrix(
         [[2, 0, 0], [0, 2, 0], [0, 0, 2]]

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2024.3.30",
+    version="2024.4.10",
     long_description=long_d,
     install_requires=[
         "numpy>=1.20.1",