├── .gitattributes ├── .github └── workflows │ ├── python-publish.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── SECURITY.md ├── _config.yml ├── doc ├── Algorithm.rst ├── Background.rst ├── COMMAND_MODE.rst ├── Installation.rst ├── Makefile ├── README.txt ├── Settings.rst ├── Symmetry_representation.rst ├── Usage.rst ├── conf.py ├── files │ └── all.cif ├── index.rst ├── make.bat ├── modules.rst ├── pyxtal.XRD.rst ├── pyxtal.block_crystal.rst ├── pyxtal.constants.rst ├── pyxtal.crystal.rst ├── pyxtal.database.cifs.rst ├── pyxtal.database.collection.rst ├── pyxtal.database.element.rst ├── pyxtal.database.rst ├── pyxtal.db.rst ├── pyxtal.descriptor.rst ├── pyxtal.elasticity.rst ├── pyxtal.interface.LJ.rst ├── pyxtal.interface.ase_opt.rst ├── pyxtal.interface.charmm.rst ├── pyxtal.interface.dftb.rst ├── pyxtal.interface.gulp.rst ├── pyxtal.interface.lammpslib.rst ├── pyxtal.interface.rst ├── pyxtal.interface.vasp.rst ├── pyxtal.io.rst ├── pyxtal.lattice.rst ├── pyxtal.lego.SO3.rst ├── pyxtal.lego.basinhopping.rst ├── pyxtal.lego.builder.rst ├── pyxtal.lego.rst ├── pyxtal.molecular_crystal.rst ├── pyxtal.molecule.rst ├── pyxtal.msg.rst ├── pyxtal.operations.rst ├── pyxtal.optimize.DFS.rst ├── pyxtal.optimize.QRS.rst ├── pyxtal.optimize.WFS.rst ├── pyxtal.optimize.base.rst ├── pyxtal.optimize.benchmark.rst ├── pyxtal.optimize.common.rst ├── pyxtal.optimize.rst ├── pyxtal.plane.rst ├── pyxtal.potentials.LJ_cluster.rst ├── pyxtal.potentials.rst ├── pyxtal.representation.rst ├── pyxtal.rst ├── pyxtal.supergroup.rst ├── pyxtal.symmetry.rst ├── pyxtal.tolerance.rst ├── pyxtal.util.rst ├── pyxtal.version.rst ├── pyxtal.viz.rst ├── pyxtal.wyckoff_site.rst ├── pyxtal.wyckoff_split.rst └── requirements.txt ├── examples ├── README.md ├── example_00_LJ_simple.py ├── example_01_3D_VASP.py ├── example_02_LJ_cluster.py ├── example_03_LJ_optalg.py ├── example_04_LJ_38.py ├── example_05_LJ_4D.py ├── example_06_C_2D_lammps.py ├── example_07_3D_ICE_lammps.py ├── test_installation.py └── tutorials_notebook │ ├── 01_atomic_crystals.ipynb │ ├── 02_molecular_crystals.ipynb │ ├── 03_pxrd.ipynb │ ├── 04_box.ipynb │ ├── 05-crystal-packing.ipynb │ ├── ABAVUW.cif │ ├── aspirin.cif │ └── lt_quartz.cif ├── flask ├── .flaskenv ├── README.md ├── app │ ├── __init__.py │ ├── errors.py │ ├── forms.py │ ├── routes.py │ ├── static │ │ ├── css │ │ │ └── custom.css │ │ ├── img │ │ │ ├── brand.png │ │ │ ├── favicon.ico │ │ │ ├── grid.jpg │ │ │ └── logo.png │ │ └── jsmol.js │ └── templates │ │ ├── 404.html │ │ ├── 500.html │ │ ├── _formhelpers.html │ │ ├── base.html │ │ ├── comparison.html │ │ ├── index.html │ │ ├── individual.html │ │ └── scratch.html ├── config.py ├── instance │ └── uploads │ │ ├── C1-POSCAR │ │ ├── NaCl-POSCAR │ │ ├── NaCl.cif │ │ ├── R3c-POSCAR │ │ └── fail_test.txt ├── requirements.txt └── vxrd.py ├── images ├── 1000px_logomark.png ├── 1000px_logomark_black-01.png ├── 1000px_logomark_white-01.png ├── 1500px_type2.png ├── 1500px_type2_black-01.png ├── 1500px_type2_white-01.png ├── 1920px_type 1_black-01.png ├── 1920px_type1.png ├── 1920px_type1_gray.png ├── 1920px_type1_white-01.png ├── 256px_type1.png ├── 512px_type1.png ├── Bucky.png ├── C60-x.png ├── C60.png ├── C8-diamond.png ├── Flowchart.png ├── Logo license.txt ├── MoS2.png ├── PaperSnowflake.png ├── Pmmm.png ├── ROY.png ├── affine_matrix.png ├── cubic_F.png ├── cubic_I.png ├── cubic_P.png ├── equivalent_lattices.png ├── fractional.png ├── fractional_coordinates.png ├── hexagon.png ├── hexagonal.png ├── matrix4x4.png ├── merge.png ├── monoclinic_C.png ├── monoclinic_P.png ├── orthorhombic_C.png ├── orthorhombic_F.png ├── orthorhombic_I.png ├── orthorhombic_P.png ├── rhombohedral.png ├── skew.png ├── tetragonal_I.png ├── tetragonal_P.png ├── triangle.png ├── triclinic.png ├── unit_cell1.png ├── unit_cell2.png ├── unit_cell3.png ├── unit_cell4.png ├── water.gif └── water_symmetry_1.gif ├── pyproject.toml ├── pyxtal ├── XRD.py ├── XRD_indexer.py ├── __init__.py ├── block_crystal.py ├── constants.py ├── crystal.py ├── database │ ├── HM_Full.csv │ ├── __init__.py │ ├── atomic_scattering_params.json │ ├── bonds.json │ ├── bug.json │ ├── cifs │ │ ├── 0-G62.cif │ │ ├── 1-G59.cif │ │ ├── 191.vasp │ │ ├── 2-G71.cif │ │ ├── 3-G139.cif │ │ ├── 4-G225.cif │ │ ├── ACBNZA01.cif │ │ ├── AXOSOW01.cif │ │ ├── Al2SiO5_mp-4753_symmetrized.cif │ │ ├── BTO-Amm2.cif │ │ ├── BTO.cif │ │ ├── FAU.cif │ │ ├── Fd3.cif │ │ ├── Fd3.vasp │ │ ├── Fd3m.cif │ │ ├── GUMMUW.cif │ │ ├── GeF2.cif │ │ ├── HAHCOI.cif │ │ ├── I41amd.vasp │ │ ├── I4_132.cif │ │ ├── JAPWIH.cif │ │ ├── JVASP-119184.cif │ │ ├── JVASP-119739.cif │ │ ├── JVASP-141590.cif │ │ ├── JVASP-25063.cif │ │ ├── JVASP-28565.cif │ │ ├── JVASP-28634.cif │ │ ├── JVASP-36885.cif │ │ ├── JVASP-37583.cif │ │ ├── JVASP-42300.cif │ │ ├── JVASP-43424.cif │ │ ├── JVASP-45907.cif │ │ ├── JVASP-47532.cif │ │ ├── JVASP-50935.cif │ │ ├── JVASP-59313.cif │ │ ├── JVASP-62168.cif │ │ ├── JVASP-85365.cif │ │ ├── JVASP-86205.cif │ │ ├── JVASP-97915.cif │ │ ├── JVASP-98225.cif │ │ ├── LAGNAL.cif │ │ ├── LUFHAW.cif │ │ ├── LiCs.cif │ │ ├── MERQIM.cif │ │ ├── MPWO.cif │ │ ├── NaCl.cif │ │ ├── NaSb3F10.cif │ │ ├── NbO2.cif │ │ ├── NiS-Cm.cif │ │ ├── P3_112.cif │ │ ├── P4_332.cif │ │ ├── P4nmm.vasp │ │ ├── P6_422.cif │ │ ├── PAHYON01.cif │ │ ├── PPO.cif │ │ ├── PVO.cif │ │ ├── Pm3.cif │ │ ├── Pmmn.vasp │ │ ├── Pn3.vasp │ │ ├── Pn3m.vasp │ │ ├── R-3.cif │ │ ├── R-3c.cif │ │ ├── R32.cif │ │ ├── TMPPIO03.cif │ │ ├── WEXBOS.cif │ │ ├── YICMOP.cif │ │ ├── __init__.py │ │ ├── anthracene.cif │ │ ├── aspirin-c.cif │ │ ├── aspirin.cif │ │ ├── benzene.cif │ │ ├── bug.vasp │ │ ├── c_bug.vasp │ │ ├── c_bug2.vasp │ │ ├── coumarin.cif │ │ ├── dist_6_0.cif │ │ ├── dist_6_1.cif │ │ ├── gdh.cif │ │ ├── ht_KNbBO.cif │ │ ├── ht_cristobalite.cif │ │ ├── ht_quartz.cif │ │ ├── ice.cif │ │ ├── lt_KNbBO.cif │ │ ├── lt_cristobalite.cif │ │ ├── lt_quartz.cif │ │ ├── naphthalene.cif │ │ ├── resorcinol.cif │ │ ├── sim-0.vasp │ │ ├── sim-1.vasp │ │ └── xxvi.cif │ ├── clusters.json │ ├── collection.py │ ├── element.py │ ├── k_subgroup.json │ ├── layer.csv │ ├── layer_generators.csv │ ├── layer_symmetry.csv │ ├── mech.db │ ├── molecules.json │ ├── packing-analysis │ │ ├── ACETYL02.cif │ │ ├── ADAMAN08.cif │ │ ├── CONGRS.cif │ │ ├── DNNAPH.cif │ │ ├── HCCYHB.cif │ │ ├── HCLBNZ.cif │ │ ├── HXMTAM.cif │ │ ├── PNDMAM10.cif │ │ └── ZZZWOU01.cif │ ├── point.csv │ ├── point_generators.csv │ ├── point_symmetry.csv │ ├── rod.csv │ ├── rod_generators.csv │ ├── rod_symmetry.csv │ ├── symbols.json │ ├── t_subgroup.json │ ├── test.cif │ ├── test.db │ ├── wyckoff_generators.csv │ ├── wyckoff_list.csv │ ├── wyckoff_sets.json │ └── wyckoff_symmetry.csv ├── db.py ├── descriptor.py ├── elasticity.py ├── interface │ ├── Installation.md │ ├── LATTE_templates │ │ ├── MDcontroller │ │ ├── TBparam │ │ │ ├── bondints.nonortho │ │ │ ├── control.in │ │ │ ├── control.in.bak │ │ │ ├── electrons.dat │ │ │ ├── ppots.nonortho │ │ │ └── ppotsplusD.nonortho │ │ ├── alpha_match.cif │ │ ├── bl │ │ │ └── inputblock.dat │ │ ├── latte_calc.py │ │ └── test.py │ ├── LJ.py │ ├── __init__.py │ ├── ase_opt.py │ ├── ase_opt2.py │ ├── charmm.py │ ├── dftb.py │ ├── gulp.py │ ├── lammpslib.py │ ├── latte_calculator.py │ └── vasp.py ├── io.py ├── lattice.py ├── lego │ ├── SO3.py │ ├── __init__.py │ ├── basinhopping.py │ ├── builder.py │ └── util.py ├── miscellaneous │ ├── 2datomic.py │ ├── 2dmolecular.py │ ├── LJ_bug.py │ ├── Random_vasp_ase.py │ ├── bug_2_components.py │ ├── bug_spglib.py │ ├── bugs │ │ ├── bug.py │ │ └── bug.vasp │ ├── c60.py │ ├── check_cluster_distances.py │ ├── check_rotation.py │ ├── check_wyckoff_generators.py │ ├── cifs │ │ ├── A2=a.cif │ │ ├── A2=m.cif │ │ ├── Aa.cif │ │ ├── Aba2.cif │ │ ├── Abmm.cif │ │ ├── Acam.cif │ │ ├── Acmm-1.cif │ │ ├── Acmm.cif │ │ ├── Ama2.cif │ │ ├── Amam.cif │ │ ├── Amm2.cif │ │ ├── Amma.cif │ │ ├── B2=b.cif │ │ ├── B2_1=d.cif │ │ ├── Bb2_1m.cif │ │ ├── Bbmm.cif │ │ ├── Bmab.cif │ │ ├── Bmmb.cif │ │ ├── C-1.cif │ │ ├── C-42b.cif │ │ ├── C2.cif │ │ ├── C222.cif │ │ ├── C222_1.cif │ │ ├── C2=c.cif │ │ ├── C2=m.cif │ │ ├── Cc.cif │ │ ├── Ccca.cif │ │ ├── Cccm.cif │ │ ├── Ccm2_1.cif │ │ ├── Ccmb.cif │ │ ├── Ccmm.cif │ │ ├── Cm.cif │ │ ├── Cmc2_1.cif │ │ ├── Cmca.cif │ │ ├── Cmcm.cif │ │ ├── Cmm2.cif │ │ ├── Cmma.cif │ │ ├── Cmmm.cif │ │ ├── F-43m.cif │ │ ├── F1.cif │ │ ├── F2.cif │ │ ├── Fd-3m.cif │ │ ├── Fd.cif │ │ ├── Fdd2.cif │ │ ├── Fddd.cif │ │ ├── Fm-3m.cif │ │ ├── Fm3m.cif │ │ ├── Fmmm.cif │ │ ├── I-4.cif │ │ ├── I-42d.cif │ │ ├── I-42m.cif │ │ ├── I-43m.cif │ │ ├── I-4c2.cif │ │ ├── I-4m2.cif │ │ ├── I2=a.cif │ │ ├── I2=b.cif │ │ ├── I2=c.cif │ │ ├── I2=m.cif │ │ ├── I2_12_12_1.cif │ │ ├── I2_13.cif │ │ ├── I2_1=a-3.cif │ │ ├── I2cm.cif │ │ ├── I2mb.cif │ │ ├── I4=m.cif │ │ ├── I4=mcm.cif │ │ ├── I4=mmm.cif │ │ ├── I4_122.cif │ │ ├── I4_1=a.cif │ │ ├── I4_1=amd.cif │ │ ├── Ia-3d.cif │ │ ├── Ia3.cif │ │ ├── Ia3d.cif │ │ ├── Iba2.cif │ │ ├── Ibam.cif │ │ ├── Im-3m.cif │ │ ├── Im.cif │ │ ├── Im2m.cif │ │ ├── Im3.cif │ │ ├── Ima2.cif │ │ ├── Imam.cif │ │ ├── Imm2.cif │ │ ├── Imma.cif │ │ ├── Immm.cif │ │ ├── P-3.cif │ │ ├── P-31c.cif │ │ ├── P-31m.cif │ │ ├── P-3c1.cif │ │ ├── P-3m1.cif │ │ ├── P-4.cif │ │ ├── P-42_1c.cif │ │ ├── P-42_1m.cif │ │ ├── P-42c.cif │ │ ├── P-42m.cif │ │ ├── P-43m.cif │ │ ├── P-43n.cif │ │ ├── P-4b2.cif │ │ ├── P-4m2.cif │ │ ├── P-4n2.cif │ │ ├── P-6.cif │ │ ├── P-62c.cif │ │ ├── P-62m.cif │ │ ├── P-6c2.cif │ │ ├── P-6m2.cif │ │ ├── P23.cif │ │ ├── P2=a.cif │ │ ├── P2=b.cif │ │ ├── P2=c.cif │ │ ├── P2=m.cif │ │ ├── P2_1.cif │ │ ├── P2_122_1.cif │ │ ├── P2_12_12.cif │ │ ├── P2_12_12_1.cif │ │ ├── P2_13.cif │ │ ├── P2_1ca.cif │ │ ├── P2_1cn.cif │ │ ├── P2_1nm.cif │ │ ├── P312.cif │ │ ├── P31c.cif │ │ ├── P31m.cif │ │ ├── P321.cif │ │ ├── P3_121.cif │ │ ├── P3_221.cif │ │ ├── P4.cif │ │ ├── P42_12.cif │ │ ├── P4=mbm.cif │ │ ├── P4=mmm.cif │ │ ├── P4=mnc.cif │ │ ├── P4=n.cif │ │ ├── P4=ncc.cif │ │ ├── P4=nmm.cif │ │ ├── P4=nnc.cif │ │ ├── P4_122.cif │ │ ├── P4_132.cif │ │ ├── P4_232.cif │ │ ├── P4_2=m.cif │ │ ├── P4_2=mbc.cif │ │ ├── P4_2=mnm.cif │ │ ├── P4_2=n.cif │ │ ├── P4_2=ncm.cif │ │ ├── P4_2=nmc.cif │ │ ├── P4_2=nnm.cif │ │ ├── P4_2nm.cif │ │ ├── P4_322.cif │ │ ├── P4_32_12.cif │ │ ├── P4bm.cif │ │ ├── P4mm.cif │ │ ├── P622.cif │ │ ├── P6=mcc.cif │ │ ├── P6=mmm.cif │ │ ├── P6_222.cif │ │ ├── P6_3.cif │ │ ├── P6_322.cif │ │ ├── P6_3=m.cif │ │ ├── P6_3=mcm.cif │ │ ├── P6_3=mmc.cif │ │ ├── P6_3cm.cif │ │ ├── P6_3mc.cif │ │ ├── Pa3.cif │ │ ├── Pbam.cif │ │ ├── Pban.cif │ │ ├── Pbc2_1.cif │ │ ├── Pbca.cif │ │ ├── Pbcm.cif │ │ ├── Pbcn.cif │ │ ├── Pbma.cif │ │ ├── Pbmn.cif │ │ ├── Pbn2_1.cif │ │ ├── Pbnm.cif │ │ ├── Pbnn.cif │ │ ├── Pca2_1.cif │ │ ├── Pcab.cif │ │ ├── Pcam.cif │ │ ├── Pcca.cif │ │ ├── Pccn.cif │ │ ├── Pcmb.cif │ │ ├── Pcmn.cif │ │ ├── Pcnb.cif │ │ ├── Pm.cif │ │ ├── Pm3m.cif │ │ ├── Pm3n.cif │ │ ├── Pma2.cif │ │ ├── Pmab.cif │ │ ├── Pman.cif │ │ ├── Pmc2_1.cif │ │ ├── Pmcn.cif │ │ ├── Pmm2.cif │ │ ├── Pmma.cif │ │ ├── Pmmm.cif │ │ ├── Pmmn.cif │ │ ├── Pmn2_1.cif │ │ ├── Pmna.cif │ │ ├── Pmnb.cif │ │ ├── Pmnm.cif │ │ ├── Pmnn.cif │ │ ├── Pn2_1m.cif │ │ ├── Pn3m.cif │ │ ├── Pna2_1.cif │ │ ├── Pnam.cif │ │ ├── Pnca.cif │ │ ├── Pncn.cif │ │ ├── Pnm2_1.cif │ │ ├── Pnma.cif │ │ ├── Pnmn.cif │ │ ├── Pnn2.cif │ │ ├── Pnna.cif │ │ ├── R-3m.cif │ │ ├── R3.cif │ │ ├── R3c.cif │ │ └── R3m.cif │ ├── compatibility.py │ ├── create_generators.py │ ├── debug_charmm.py │ ├── distance_bug.py │ ├── extra_test.py │ ├── from_ase_molecule.py │ ├── generate_mol_symm.py │ ├── generate_site_symm.py │ ├── get_lj_cluster.py │ ├── get_molecule_from_pubchem.py │ ├── grid.py │ ├── gulp_c.py │ ├── heavy_check.py │ ├── mol.py │ ├── regen_wyckoffs_list.py │ ├── search_csd_from_pubchem.py │ ├── speed.py │ ├── subgroup_data.py │ ├── test.py │ ├── test_1d_rep.py │ ├── test_3D_molecule.py │ ├── test_CSD.py │ ├── test_all.py │ ├── test_atom_mole.py │ ├── test_db.py │ ├── test_euclidean.py │ ├── test_generators.py │ ├── test_get_csd.py │ ├── test_matrix.py │ ├── test_read.py │ ├── test_site_symm.py │ ├── test_smile.py │ ├── test_spgs.py │ ├── test_subgroup.py │ ├── test_subgroup2.py │ ├── test_supergroup.py │ ├── test_symmetry_rep.py │ ├── test_torsion.py │ ├── test_wp.py │ ├── test_wyckoff_check.py │ ├── test_xrd.py │ ├── web_scalping_script │ │ ├── README.md │ │ ├── pubchem_import.py │ │ └── requirements.txt │ ├── xrd.py │ └── xrd_comp.py ├── molecular_crystal.py ├── molecule.py ├── msg.py ├── operations.py ├── optimize │ ├── DFS.py │ ├── QRS.py │ ├── WFS.py │ ├── __init__.py │ ├── base.py │ ├── benchmark.py │ └── common.py ├── plane.py ├── potentials │ ├── CuAg.eam.alloy │ ├── LJ_cluster.py │ ├── Si.tersoff │ ├── SiCGe.tersoff │ └── __init__.py ├── reciprocal.py ├── representation.py ├── supergroup.py ├── symmetry.py ├── symmetry_sampler.py ├── tolerance.py ├── util.py ├── version.py ├── viz.py ├── wyckoff_site.py └── wyckoff_split.py ├── requirements.txt ├── scripts ├── match.py ├── pyxtal_csp_match.py ├── pyxtal_csp_plot.py ├── pyxtal_csp_rank.py ├── pyxtal_main.py ├── pyxtal_symmetry.py └── rank.py ├── setup.cfg ├── setup.py └── tests ├── test_SO3.py ├── test_all.py ├── test_crystal.py ├── test_ff.py ├── test_group.py ├── test_jl.py ├── test_lattice.py ├── test_lego.py ├── test_mem.py ├── test_molecule.py ├── test_oc_relax.py ├── test_site_symm.py ├── test_supergroup.py ├── test_symmetry.py ├── test_wyckoff.py └── test_xrd.py /.gitattributes: -------------------------------------------------------------------------------- 1 | doc/* linguist-documentation 2 | -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- 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