PyXtal

PyXtal (pronounced pie-crystal) is an open source Python library for the ab-initio generation of random crystal structures. It has the following features:

• Generation of atomic structures for a given symmetry and stoichiometry (0-3D)

• Generation of molecular crystals (1-3D) with the support of special Wyckoff positions

• Internal support of cif file and many other formats via pymatgen or ASE

• Easy access to symmetry information (e.g., Wyckoff, site symmetry and international symbols)

• X-ray diffraction analysis and its online application

• Structural manipulation via symmetry relation (both subgroup and supergroup)

• Geometry optimization from built-in and external optimization methods

The current version is 1.1.4 at GitHub. It is available for use under the MIT license. Expect updates upon request by Qiang Zhu's group at the University of North Carolina at Charlotte.

PyXtal is an open source project. You are welcome to contribute it directly via the GitHub platform or send your comments and suggestions to the developer.

A basic tutorial is provided below for common functions. Additionally, documentation and source code are provided for individual modules.

For an experienced Python user who are familiar with Jupyter notebook, you are also encouraged to check out the following examples

• Atomic crystal

• Molecular crystal

• XRD

Tutorial

• Installation and Setup
  • Dependencies
  • Installation
• Run PyXtal executables
  • PyXtal_symmetry utility
  • PyXtal_main utility
• PyXtal as a library
  • Available Tools in PyXtal
  • Crystal structure generation
  • Crystal structure Post Analysis
  • Subgroup/supergroup manipulation
  • Advanced examples in random structure generation
  • 1D Representation
  • Database
  • Space Group and Site Symmetry
• Symmetry Representation
  • Space Group Symmetry
  • Space Group Symmetry’s Digital Representation
  • Wyckoff Site Symmetry
  • Site Symmetry’s Digital Representation
  • Complete list of Wyckoff Site Symmetry Table
  • References
• Background and Theory
  • Crystals and Structures
  • Periodicity, Lattices, and Unit Cells
  • Symmetry Operations
  • Groups
  • Symmetry Groups
  • Wyckoff Positions
  • Molecular Wyckoff Positions
  • Crystal File Formats
• How PyXtal Works
  • Overview
  • User Input
  • Checking Compatibility
  • Lattice Generation
  • Generation of Wyckoff Positions
  • Checking Inter-atomic Distances
  • Merging and Checking Wyckoff Positions
  • Finding Valid Molecular Orientations
• Group Settings
  • Space Group
  • Layer Group
  • Rod Group
  • Point Group

Indices and tables

• Index

• Module Index

• Search Page

Modules

• pyxtal package
  • print_logo()
  • pyxtal
    • pyxtal.apply_perturbation()
    • pyxtal.are_valid_numIons()
    • pyxtal.build()
    • pyxtal.check_H_coordination()
    • pyxtal.check_distance()
    • pyxtal.check_mapping()
    • pyxtal.check_short_distances()
    • pyxtal.check_short_distances_by_dict()
    • pyxtal.check_validity()
    • pyxtal.copy()
    • pyxtal.cut_lattice()
    • pyxtal.find_matched_lattice()
    • pyxtal.from_1d_rep()
    • pyxtal.from_CSD()
    • pyxtal.from_json()
    • pyxtal.from_prototype()
    • pyxtal.from_random()
    • pyxtal.from_seed()
    • pyxtal.from_spg_wps_rep()
    • pyxtal.from_tabular_representation()
    • pyxtal.get_1D_comp()
    • pyxtal.get_1D_representation()
    • pyxtal.get_1d_rep_x()
    • pyxtal.get_Pearson_Symbol()
    • pyxtal.get_XRD()
    • pyxtal.get_alternatives()
    • pyxtal.get_bounds()
    • pyxtal.get_density()
    • pyxtal.get_dimensionality()
    • pyxtal.get_disps_optim()
    • pyxtal.get_disps_sets()
    • pyxtal.get_disps_single()
    • pyxtal.get_dof()
    • pyxtal.get_forcefield()
    • pyxtal.get_free_axis()
    • pyxtal.get_init_translations()
    • pyxtal.get_intermolecular_energy()
    • pyxtal.get_min_values()
    • pyxtal.get_neighboring_dists()
    • pyxtal.get_neighboring_molecules()
    • pyxtal.get_num_torsions()
    • pyxtal.get_orientation_energy()
    • pyxtal.get_reduced_composition()
    • pyxtal.get_rep_bounds_from_spg_wps_cell()
    • pyxtal.get_rms_dist()
    • pyxtal.get_separations()
    • pyxtal.get_site_labels()
    • pyxtal.get_spherical_images()
    • pyxtal.get_std_representation()
    • pyxtal.get_structure_factor()
    • pyxtal.get_tabular_representation()
    • pyxtal.get_tabular_representations()
    • pyxtal.get_transition()
    • pyxtal.get_transition_by_path()
    • pyxtal.get_xtal_string()
    • pyxtal.get_zprime()
    • pyxtal.has_special_site()
    • pyxtal.is_duplicate()
    • pyxtal.load_dict()
    • pyxtal.make_transitions()
    • pyxtal.optimize_lattice()
    • pyxtal.optimize_lattice_and_rotation()
    • pyxtal.optimize_orientation_by_energy()
    • pyxtal.remove_species()
    • pyxtal.remove_water()
    • pyxtal.resort()
    • pyxtal.resort_species()
    • pyxtal.resymmetrize()
    • pyxtal.save_dict()
    • pyxtal.set_cutoff()
    • pyxtal.set_site_coordination()
    • pyxtal.show()
    • pyxtal.show_mol_cluster()
    • pyxtal.sort_sites_by_mult()
    • pyxtal.sort_sites_by_numIons()
    • pyxtal.subgroup()
    • pyxtal.subgroup_by_path()
    • pyxtal.subgroup_once()
    • pyxtal.substitute()
    • pyxtal.substitute_1_2()
    • pyxtal.substitute_linear()
    • pyxtal.substitute_molecules()
    • pyxtal.supergroup()
    • pyxtal.supergroups()
    • pyxtal.to_ase()
    • pyxtal.to_atomic_xtal()
    • pyxtal.to_file()
    • pyxtal.to_json()
    • pyxtal.to_molecular_xtal()
    • pyxtal.to_pymatgen()
    • pyxtal.to_pyxtal_center()
    • pyxtal.to_standard_setting()
    • pyxtal.to_subgroup()
    • pyxtal.to_subgroup_zp2()
    • pyxtal.transform()
    • pyxtal.translate()
    • pyxtal.update_from_1d_rep()
    • pyxtal.update_wyckoffs()
  • Subpackages
    • pyxtal.database package
      • Subpackages
      • Submodules
    • pyxtal.interface package
      • Submodules
    • pyxtal.lego package
      • Submodules
    • pyxtal.optimize package
      • Submodules
    • pyxtal.potentials package
      • Submodules
  • Submodules
    • pyxtal.XRD module
      • Profile
      • Similarity
      • XRD
      • add_peak()
      • axial_div()
      • axial_div_bak()
      • check_pxrd_match()
      • create_index()
      • gaussian()
      • gaussian_integrated()
      • get_all_intensity()
      • get_all_intensity_par()
      • get_intensity()
      • get_para_from_pxrd()
      • is_multiple()
      • lorentzian()
      • map_intensity()
      • mod_pseudo_voigt()
      • pseudo_voigt()
      • pxrd_refine()
      • similarity_calculate()
    • pyxtal.block_crystal module
      • block_crystal()
    • pyxtal.constants module
      • get_additional_asu_conditions()
      • logo
    • pyxtal.crystal module
      • random_crystal
    • pyxtal.db module
      • call_opt_single()
      • database
      • database_topology
      • dftb_opt_single()
      • gulp_opt_single()
      • mace_opt_single()
      • make_db_from_CSD()
      • make_entry_from_CSD()
      • make_entry_from_CSD_web()
      • make_entry_from_pyxtal()
      • opt_single()
      • process_xtal()
      • setup_worker_logger()
      • vasp_opt_single()
    • pyxtal.descriptor module
      • cart2sph()
      • correlation()
      • correlation_go()
      • correlation_opt()
      • expand_sph()
      • fibonacci_sphere()
      • get_alignment()
      • orientation_order
      • sph2cart()
      • spherical_image
      • xyz2sph()
    • pyxtal.elasticity module
      • CubicElasticModuli
      • Voigt_6_to_full_3x3_strain()
      • Voigt_6_to_full_3x3_stress()
      • Voigt_6x6_to_cubic()
      • Voigt_6x6_to_full_3x3x3x3()
      • cubic_to_Voigt_6x6()
      • elastic_moduli()
      • elastic_properties()
      • fit_elastic_constants()
      • full_3x3_to_Voigt_6_index()
      • full_3x3_to_Voigt_6_strain()
      • full_3x3_to_Voigt_6_stress()
      • full_3x3x3x3_to_Voigt_6x6()
      • generate_strained_configs()
      • invariants()
      • measure_triclinic_elastic_constants()
      • poisson_ratio()
      • rotate_cubic_elastic_constants()
      • rotate_elastic_constants()
      • youngs_modulus()
    • pyxtal.io module
      • get_cif_str_for_pyxtal()
      • in_merged_coords()
      • read_cif()
      • search_molecules_in_crystal()
      • structure_from_ext
      • write_cif()
    • pyxtal.lattice module
      • Lattice
      • gaussian_random_variable()
      • generate_cellpara()
      • generate_cellpara_0D()
      • generate_cellpara_1D()
      • generate_cellpara_2D()
      • matrix2para()
      • para2matrix()
      • random_shear_matrix()
      • random_vector()
    • pyxtal.molecular_crystal module
      • molecular_crystal
    • pyxtal.molecule module
      • Box
      • Orientation
      • compare_mol_connectivity()
      • find_rotor_from_smile()
      • generate_molecules()
      • get_inertia_tensor()
      • has_non_aromatic_ring()
      • is_compatible_symmetry()
      • make_graph()
      • pyxtal_molecule
      • reoriented_molecule()
    • pyxtal.msg module
      • AtomTypeError
      • CSDError
      • Comp_CompatibilityError
      • ConformerError
      • Error
      • ReadSeedError
      • Symm_CompatibilityError
      • VolumeError
      • printx()
    • pyxtal.operations module
      • OperationAnalyzer
      • aa2matrix()
      • angle()
      • apply_ops()
      • apply_ops_diagonal()
      • are_equal()
      • check_distance()
      • check_images()
      • create_matrix()
      • distance()
      • distance_matrix()
      • distance_matrix_no_PBC()
      • filtered_coords()
      • filtered_coords_euclidean()
      • find_ids()
      • get_best_match()
      • get_inverse()
      • get_inverse_ops()
      • is_orthogonal()
      • rotate_vector()
      • verify_distances()
    • pyxtal.plane module
      • get_dspacing()
      • has_reduction()
      • plane
      • planes
      • reduced_hkl()
      • structure_factor()
    • pyxtal.representation module
      • representation
      • representation_atom
    • pyxtal.supergroup module
      • find_mapping()
      • find_mapping_per_element()
      • find_xyz()
      • new_path()
      • new_structure()
      • search_G1()
      • search_G2()
      • supergroup
      • supergroups
      • write_poscars()
    • pyxtal.symmetry module
      • Group
      • Hall
      • SymmetryData
      • Wyckoff_position
      • abc2matrix()
      • are_equivalent_ops()
      • check_symmetry_and_dim()
      • check_wyckoff_position()
      • choose_wyckoff()
      • choose_wyckoff_mol()
      • find_axis_order()
      • generate_possible_hkls()
      • get_all_polar_space_groups()
      • get_bravais_lattice()
      • get_canonical_hkl()
      • get_canonical_hkl_series()
      • get_close_packed_groups()
      • get_generators()
      • get_lattice_type()
      • get_pbc_and_lattice()
      • get_point_group()
      • get_symbol_and_number()
      • get_symmetry_directions()
      • get_symmetry_from_ops()
      • get_wyckoff_symmetry()
      • get_wyckoffs()
      • identity_ops()
      • index_from_letter()
      • is_hkl_allowed()
      • is_hkl_allowed_by_bravais()
      • jk_from_i()
      • letter_from_index()
      • op_transform()
      • op_translation()
      • organized_wyckoffs()
      • para2ferro()
      • rf()
      • search_cloest_wp()
      • site_symm()
      • site_symmetry
      • swap_xyz_ops()
      • swap_xyz_string()
      • symmetry_element_from_axis()
      • transform_ops()
      • trim_ops()
    • pyxtal.tolerance module
      • Tol_matrix
    • pyxtal.util module
      • Kgrid()
      • ase2pymatgen()
      • check_upper_bounds()
      • extract_ase_db()
      • find_dir()
      • generate_wp_lib()
      • get_pmg_dist()
      • get_similar_cids_from_pubchem()
      • get_struc_from__parser()
      • get_symmetrized_pmg()
      • get_wyc_from_comp()
      • good_lattice()
      • listToString()
      • new_struc()
      • new_struc_wo_energy()
      • parse_cif()
      • prettify()
      • process_csd_cif()
      • pymatgen2ase()
      • reset_lammps_cell()
      • search_csd_code_by_pubchem()
      • search_csd_entries_by_code()
      • sort_by_dimer()
      • split_list_by_ratio()
      • symmetrize()
      • symmetrize_cell()
    • pyxtal.version module
    • pyxtal.viz module
      • addBox()
      • addlines()
      • display_atomic()
      • display_cluster()
      • display_crystals()
      • display_mol_crystals()
      • display_molecular()
      • display_molecular_site()
      • display_molecule()
      • display_molecules()
    • pyxtal.wyckoff_site module
      • atom_site
      • mol_site
    • pyxtal.wyckoff_split module
      • in_lists()
      • wyckoff_split