PyXtal Logo
  • Installation and Setup
    • Dependencies
    • Installation
  • Run PyXtal executables
    • PyXtal_symmetry utility
    • PyXtal_main utility
      • A quick example of C60
      • 3D crystals
      • 2D and 1D crystals
      • Molecular crystals occupying general Wyckoff positions
      • Molecular crystals occupying special Wyckoff positions
      • How to define the molecules?
  • PyXtal as a library
    • Available Tools in PyXtal
      • pyxtal.symmetry.Group
      • pyxtal.symmetry.Wyckoff_position
      • pyxtal.molecule.pyxtal_molecule
      • pyxtal.lattice.Lattice
      • pyxtal.tolerance.Tol_matrix
    • Crystal structure generation
      • Loading the existing structures
      • Random 3D Atomic Crystals
      • Random 3D molecular crystals
      • Random sub-periodic crystals
    • Crystal structure Post Analysis
    • Subgroup/supergroup manipulation
      • Generating subgroup and supergroup xtals
      • Chemical Substitution
    • Advanced examples in random structure generation
      • Constraints on lattice and sites
      • Random molecular crystal without calling pyxtal_molecule
      • Random molecular crystal with constraints on torsion
      • Symmetry Compatibility in Molecular Crystals
    • 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
      • Point Groups
      • Space 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
  • 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_neighboring_dists()
      • pyxtal.get_neighboring_molecules()
      • pyxtal.get_num_torsions()
      • pyxtal.get_orientation_energy()
      • 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.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.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
        • create_index()
        • gaussian()
        • get_all_intensity()
        • get_all_intensity_par()
        • get_intensity()
        • lorentzian()
        • mod_pseudo_voigt()
        • pseudo_voigt()
        • pxrd_refine()
        • similarity_calculate()
      • pyxtal.block_crystal module
        • block_crystal()
      • pyxtal.constants module
      • 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()
        • get_all_polar_space_groups()
        • get_close_packed_groups()
        • get_generators()
        • 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()
        • 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()
        • extract_ase_db()
        • find_dir()
        • generate_wp_lib()
        • get_pmg_dist()
        • get_similar_cids_from_pubchem()
        • get_struc_from__parser()
        • get_symmetrized_pmg()
        • 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
PyXtal
  • pyxtal package
  • pyxtal.lego package
  • View page source

pyxtal.lego package

Submodules

  • pyxtal.lego.builder module
    • RandomDispBounds
    • builder
      • builder.generate_xtal()
      • builder.generate_xtals_from_wp_libs()
      • builder.get_input_from_letters()
      • builder.get_input_from_ref_xtal()
      • builder.get_similarity()
      • builder.get_wp_libs_from_spglist()
      • builder.get_wp_libs_from_xtals()
      • builder.import_structures()
      • builder.optimize_reps()
      • builder.optimize_reps_mproc()
      • builder.optimize_reps_serial()
      • builder.optimize_xtal()
      • builder.optimize_xtals()
      • builder.optimize_xtals_mproc()
      • builder.optimize_xtals_serial()
      • builder.print_memory_usage()
      • builder.process_xtal()
      • builder.process_xtals()
      • builder.set_criteria()
      • builder.set_descriptor_calculator()
      • builder.set_reference_enviroments()
    • generate_wp_lib_par()
    • generate_xtal()
    • generate_xtal_par()
    • minimize_from_x()
    • minimize_from_x_par()
  • pyxtal.lego.SO3 module
    • Cosine()
    • GaussChebyshevQuadrature()
    • SO3
      • SO3.alpha
      • SO3.build_neighbor_list()
      • SO3.calculate()
      • SO3.clear_memory()
      • SO3.compute_dpdr()
      • SO3.compute_dpdr_5d()
      • SO3.compute_p()
      • SO3.cutoff_function
      • SO3.init_atoms()
      • SO3.lmax
      • SO3.load_from_dict()
      • SO3.nmax
      • SO3.rcut
      • SO3.save_dict()
    • W()
    • compute_cs()
    • compute_dcs()
    • g()
    • phi()
  • pyxtal.lego.basinhopping module
    • basinhopping()
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