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Develop (#324)
* 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. * Mineral name. * Add atoms update. * Add atoms update. * Update proto pytest. * Update atoms, old prototype back. * Update atoms, old prototype back. * Describe out. * Fix surface layers. * Make c surface an option. * Lint fix. * Verbose false. * Parse outcar. * Outputs fix. * Update OUTCAR parser. * Update OUTCAR parser. * Update OUTCAR parser. * Update atoms describer. * Update atoms describer. * Fix motif and composition. * Rotate. * Add additionals DBs. * PyTest fix. * DB update. * 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]>
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‎jarvis/__init__.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
"""Version number."""
22

3-
__version__ = "2024.4.30"
3+
__version__ = "2024.5.10"
44

55
import os
66

‎jarvis/core/atoms.py

Lines changed: 133 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323
from sklearn.metrics import mean_absolute_error
2424
import zipfile
2525
import json
26+
from math import cos, pi, sin
2627

2728
amu_gm = 1.66054e-24
2829
ang_cm = 1e-8
@@ -867,6 +868,128 @@ def get_neighbors_cutoffs(self, max_cut=10, r=5, bond_tol=0.15):
867868
pass
868869
return rcut1, rcut2, neighbors
869870

871+
def rotate_pos(self, phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0)):
872+
"""Rotate atom sites via Euler angles (in degrees).
873+
874+
See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.
875+
Adapted from
876+
https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate
877+
center :
878+
The point to rotate about. A sequence of length 3 with the
879+
coordinates.
880+
phi :
881+
The 1st rotation angle around the z axis.
882+
theta :
883+
Rotation around the x axis.
884+
psi :
885+
2nd rotation around the z axis.
886+
887+
"""
888+
phi *= pi / 180
889+
theta *= pi / 180
890+
psi *= pi / 180
891+
892+
rcoords = self.cart_coords - center
893+
D = np.array(
894+
(
895+
(cos(phi), sin(phi), 0.0),
896+
(-sin(phi), cos(phi), 0.0),
897+
(0.0, 0.0, 1.0),
898+
)
899+
)
900+
# Second Euler rotation about x:
901+
C = np.array(
902+
(
903+
(1.0, 0.0, 0.0),
904+
(0.0, cos(theta), sin(theta)),
905+
(0.0, -sin(theta), cos(theta)),
906+
)
907+
)
908+
# Third Euler rotation, 2nd rotation about z:
909+
B = np.array(
910+
(
911+
(cos(psi), sin(psi), 0.0),
912+
(-sin(psi), cos(psi), 0.0),
913+
(0.0, 0.0, 1.0),
914+
)
915+
)
916+
# Total Euler rotation
917+
A = np.dot(B, np.dot(C, D))
918+
# Do the rotation
919+
rcoords = np.dot(A, np.transpose(rcoords))
920+
positions = np.transpose(rcoords) + center
921+
922+
return Atoms(
923+
lattice_mat=self.lattice_mat,
924+
elements=self.elements,
925+
coords=positions,
926+
cartesian=True,
927+
props=self.props,
928+
)
929+
930+
def rotate_cell(self, phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0)):
931+
"""Rotate atom cell via Euler angles (in degrees).
932+
933+
See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.
934+
Adapted from
935+
https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate
936+
center :
937+
The point to rotate about. A sequence of length 3 with the
938+
coordinates.
939+
phi :
940+
The 1st rotation angle around the z axis.
941+
theta :
942+
Rotation around the x axis.
943+
psi :
944+
2nd rotation around the z axis.
945+
946+
"""
947+
phi *= pi / 180
948+
theta *= pi / 180
949+
psi *= pi / 180
950+
951+
# First move the molecule to the origin In contrast to MATLAB,
952+
# numpy broadcasts the smaller array to the larger row-wise,
953+
# so there is no need to play with the Kronecker product.
954+
# rcoords = atoms.cart_coords - center
955+
# First Euler rotation about z in matrix form
956+
D = np.array(
957+
(
958+
(cos(phi), sin(phi), 0.0),
959+
(-sin(phi), cos(phi), 0.0),
960+
(0.0, 0.0, 1.0),
961+
)
962+
)
963+
# Second Euler rotation about x:
964+
C = np.array(
965+
(
966+
(1.0, 0.0, 0.0),
967+
(0.0, cos(theta), sin(theta)),
968+
(0.0, -sin(theta), cos(theta)),
969+
)
970+
)
971+
# Third Euler rotation, 2nd rotation about z:
972+
B = np.array(
973+
(
974+
(cos(psi), sin(psi), 0.0),
975+
(-sin(psi), cos(psi), 0.0),
976+
(0.0, 0.0, 1.0),
977+
)
978+
)
979+
# Total Euler rotation
980+
A = np.dot(B, np.dot(C, D))
981+
# Do the rotation
982+
r_lattice_mat = np.dot(A, self.lattice_mat)
983+
# Move back to the roactation point
984+
# positions = np.transpose(rcoords) + center
985+
return Atoms(
986+
lattice_mat=r_lattice_mat,
987+
elements=self.elements,
988+
coords=self.frac_coords,
989+
cartesian=False,
990+
props=self.props,
991+
)
992+
870993
def atomwise_angle_and_radial_distribution(
871994
self, r=5, bond_tol=0.15, c_size=10, verbose=False
872995
):
@@ -1335,6 +1458,7 @@ def hook(model, input, output):
13351458
def get_mineral_prototype_name(
13361459
self, prim=True, include_c_over_a=False, digits=3
13371460
):
1461+
"""Get mineral_prototype_name."""
13381462
from jarvis.analysis.structure.spacegroup import Spacegroup3D
13391463

13401464
spg = Spacegroup3D(self)
@@ -1524,9 +1648,9 @@ def describe(
15241648
list(set(spg._dataset["wyckoffs"]))
15251649
)
15261650
struct_info["natoms_primitive"] = spg.primitive_atoms.num_atoms
1527-
struct_info[
1528-
"natoms_conventional"
1529-
] = spg.conventional_standard_structure.num_atoms
1651+
struct_info["natoms_conventional"] = (
1652+
spg.conventional_standard_structure.num_atoms
1653+
)
15301654
info["chemical_info"] = chem_info
15311655
info["structure_info"] = struct_info
15321656
line = "The number of atoms are: " + str(
@@ -2276,18 +2400,18 @@ def to_optimade(
22762400
info_at["cartesian_site_positions"] = atoms.cart_coords[order].tolist()
22772401
info_at["nperiodic_dimensions"] = 3
22782402
# info_at["species"] = atoms.elements
2279-
info_at[
2280-
"species"
2281-
] = self.get_optimade_species() # dict(atoms.composition.to_dict())
2403+
info_at["species"] = (
2404+
self.get_optimade_species()
2405+
) # dict(atoms.composition.to_dict())
22822406
info_at["elements_ratios"] = list(
22832407
atoms.composition.atomic_fraction.values()
22842408
)
22852409
info_at["structure_features"] = []
22862410
info_at["last_modified"] = str(now)
22872411
# info_at["more_data_available"] = True
2288-
info_at[
2289-
"chemical_formula_descriptive"
2290-
] = atoms.composition.reduced_formula
2412+
info_at["chemical_formula_descriptive"] = (
2413+
atoms.composition.reduced_formula
2414+
)
22912415
info_at["dimension_types"] = [1, 1, 1]
22922416
info["attributes"] = info_at
22932417
return info

‎jarvis/core/composition.py

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -156,10 +156,14 @@ def formula(self):
156156
form = ""
157157
for specie, count in self._content.items():
158158
if float(count).is_integer():
159-
form = form + str(specie) + str(int(count))
159+
# form = form + str(specie) + str(int(count))
160+
if count == 1:
161+
form = form + specie
162+
else:
163+
form = form + specie + str(int(count))
160164
else:
161165
form = form + str(specie) + str(count)
162-
return form.replace("1", "")
166+
return form # .replace("1", "")
163167

164168
@property
165169
def atomic_fraction(self):

‎jarvis/core/element_names.json

Lines changed: 120 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,120 @@
1+
{
2+
"H": "Hydrogen",
3+
"He": "Helium",
4+
"Li": "Lithium",
5+
"Be": "Beryllium",
6+
"B": "Boron",
7+
"C": "Carbon",
8+
"N": "Nitrogen",
9+
"O": "Oxygen",
10+
"F": "Fluorine",
11+
"Ne": "Neon",
12+
"Na": "Sodium",
13+
"Mg": "Magnesium",
14+
"Al": "Aluminum",
15+
"Si": "Silicon",
16+
"P": "Phosphorus",
17+
"S": "Sulfur",
18+
"Cl": "Chlorine",
19+
"Ar": "Argon",
20+
"K": "Potassium",
21+
"Ca": "Calcium",
22+
"Sc": "Scandium",
23+
"Ti": "Titanium",
24+
"V": "Vanadium",
25+
"Cr": "Chromium",
26+
"Mn": "Manganese",
27+
"Fe": "Iron",
28+
"Co": "Cobalt",
29+
"Ni": "Nickel",
30+
"Cu": "Copper",
31+
"Zn": "Zinc",
32+
"Ga": "Gallium",
33+
"Ge": "Germanium",
34+
"As": "Arsenic",
35+
"Se": "Selenium",
36+
"Br": "Bromine",
37+
"Kr": "Krypton",
38+
"Rb": "Rubidium",
39+
"Sr": "Strontium",
40+
"Y": "Yttrium",
41+
"Zr": "Zirconium",
42+
"Nb": "Niobium",
43+
"Mo": "Molybdenum",
44+
"Tc": "Technetium",
45+
"Ru": "Ruthenium",
46+
"Rh": "Rhodium",
47+
"Pd": "Palladium",
48+
"Ag": "Silver",
49+
"Cd": "Cadmium",
50+
"In": "Indium",
51+
"Sn": "Tin",
52+
"Sb": "Antimony",
53+
"Te": "Tellurium",
54+
"I": "Iodine",
55+
"Xe": "Xenon",
56+
"Cs": "Cesium",
57+
"Ba": "Barium",
58+
"La": "Lanthanum",
59+
"Ce": "Cerium",
60+
"Pr": "Praseodymium",
61+
"Nd": "Neodymium",
62+
"Pm": "Promethium",
63+
"Sm": "Samarium",
64+
"Eu": "Europium",
65+
"Gd": "Gadolinium",
66+
"Tb": "Terbium",
67+
"Dy": "Dysprosium",
68+
"Ho": "Holmium",
69+
"Er": "Erbium",
70+
"Tm": "Thulium",
71+
"Yb": "Ytterbium",
72+
"Lu": "Lutetium",
73+
"Hf": "Hafnium",
74+
"Ta": "Tantalum",
75+
"W": "Tungsten",
76+
"Re": "Rhenium",
77+
"Os": "Osmium",
78+
"Ir": "Iridium",
79+
"Pt": "Platinum",
80+
"Au": "Gold",
81+
"Hg": "Mercury",
82+
"Tl": "Thallium",
83+
"Pb": "Lead",
84+
"Bi": "Bismuth",
85+
"Po": "Polonium",
86+
"At": "Astatine",
87+
"Rn": "Radon",
88+
"Fr": "Francium",
89+
"Ra": "Radium",
90+
"Ac": "Actinium",
91+
"Th": "Thorium",
92+
"Pa": "Protactinium",
93+
"U": "Uranium",
94+
"Np": "Neptunium",
95+
"Pu": "Plutonium",
96+
"Am": "Americium",
97+
"Cm": "Curium",
98+
"Bk": "Berkelium",
99+
"Cf": "Californium",
100+
"Es": "Einsteinium",
101+
"Fm": "Fermium",
102+
"Md": "Mendelevium",
103+
"No": "Nobelium",
104+
"Lr": "Lawrencium",
105+
"Rf": "Rutherfordium",
106+
"Db": "Dubnium",
107+
"Sg": "Seaborgium",
108+
"Bh": "Bohrium",
109+
"Hs": "Hassium",
110+
"Mt": "Meitnerium",
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"Ds": "Darmstadtium",
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"Rg": "Roentgenium",
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"Cn": "Copernicium",
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"Nh": "Nihonium",
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"Fl": "Flerovium",
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"Mc": "Moscovium",
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"Lv": "Livermorium",
118+
"Ts": "Tennessine",
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"Og": "Oganesson"
120+
}

‎jarvis/core/specie.py

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,14 @@
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el_chrg_json.close()
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cgcnn_feature_json = os.path.join(os.path.dirname(__file__), "atom_init.json")
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31+
element_full_name = os.path.join(
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os.path.dirname(__file__), "element_names.json"
33+
)
34+
35+
36+
def get_element_full_names():
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return loadjson(element_full_name)
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3139

3240
def get_descrp_arr_name(elm="Al"):
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"""

‎jarvis/db/figshare.py

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -421,6 +421,27 @@ def get_db_info():
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"Obtaining m3gnet_mpf dataset 168917...",
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"https://github.com/materialsvirtuallab/m3gnet",
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],
424+
# https://doi.org/10.6084/m9.figshare.23267852
425+
"m3gnet_mpf_1.5mil": [
426+
"https://figshare.com/ndownloader/files/47281519",
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"id_prop.json",
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"Obtaining m3gnet_mpf dataset 1.5mil...",
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"https://github.com/materialsvirtuallab/m3gnet",
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],
431+
# https://doi.org/10.6084/m9.figshare.23531523
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"mxene275": [
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"https://figshare.com/ndownloader/files/41266233",
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"mxene275.json",
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"Obtaining mxene dataset 275...",
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"https://cmr.fysik.dtu.dk/c2db/c2db.html",
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],
438+
# https://doi.org/10.6084/m9.figshare.26117998
439+
"cccbdb": [
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"https://figshare.com/ndownloader/files/47283808",
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"cccbdb.json",
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"Obtaining CCCBDB dataset 1333...",
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"https://cccbdb.nist.gov/",
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],
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# https://doi.org/10.6084/m9.figshare.13154159
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"raw_files": [
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"https://ndownloader.figshare.com/files/25295732",

‎jarvis/tests/testfiles/core/test_atoms.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -132,6 +132,8 @@ def test_basic_atoms():
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rem = (Si.make_supercell([2, 2, 2]).remove_site_by_index(site=0)).num_atoms
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prim = Si.get_primitive_atoms
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print(prim.cart_coords)
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#print(prim.get_pos())
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#print(prim.get_cell())
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conv = Si.get_conventional_atoms
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spgn = Si.get_spacegroup
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comp = compare_atoms(atoms1=prim, atoms2=conv)

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