Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y _ _data (mdapy.voronoi.Container attribute) _enlarge_box (mdapy.knn.NearestNeighbor attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.voronoi.Voronoi attribute) _enlarge_data (mdapy.knn.NearestNeighbor attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.voronoi.Voronoi attribute) A AcklandJonesAnalysis (class in mdapy.ackland_jones_analysis) affine (mdapy.atomic_strain.AtomicStrain attribute) aja (mdapy.ackland_jones_analysis.AcklandJonesAnalysis attribute) align_to_lammps_box() (mdapy.box.Box method) AngularDistributionFunction (class in mdapy.angular_distribution_function) append() (mdapy.trajectory.XYZTrajectory method) atomic_masses (in module mdapy.data) atomic_numbers (in module mdapy.data) AtomicStrain (class in mdapy.atomic_strain) AtomicTemperature (class in mdapy.atomic_temperature) atoms (mdapy.visualize.View attribute) average_by_neighbor() (in module mdapy.tool_function) (mdapy.system.System method) B bin_volume (mdapy.spatial_binning.SpatialBinning attribute) bond_angle_distribution (mdapy.angular_distribution_function.AngularDistributionFunction attribute) (mdapy.bond_analysis.BondAnalysis attribute) bond_length_distribution (mdapy.bond_analysis.BondAnalysis attribute) BondAnalysis (class in mdapy.bond_analysis) boundary (mdapy.box.Box attribute) (mdapy.box.Box property) Box (class in mdapy.box) box (mdapy.ackland_jones_analysis.AcklandJonesAnalysis attribute) (mdapy.box.Box attribute) (mdapy.box.Box property) (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.create_polycrystal.CreatePolycrystal attribute) (mdapy.identify_diamond_structure.IdentifyDiamondStructure attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) (mdapy.visualize.View attribute) (mdapy.voronoi.Voronoi attribute) build_crystal() (in module mdapy.build_lattice) build_hea() (in module mdapy.build_lattice) build_hea_fromsystem() (in module mdapy.build_lattice) build_nearest_neighbor() (mdapy.system.System method) build_neighbor() (mdapy.system.System method) build_partial_dislocation_fcc() (in module mdapy.build_lattice) build_voronoi_neighbor() (mdapy.system.System method) BuildSystem (class in mdapy.load_save) C cal_ackland_jones_analysis() (mdapy.system.System method) cal_angular_distribution_function() (mdapy.system.System method) cal_atomic_temperature() (mdapy.system.System method) cal_bond_analysis() (mdapy.system.System method) cal_centro_symmetry_parameter() (mdapy.system.System method) cal_chemical_species() (mdapy.system.System method) cal_cluster_analysis() (mdapy.system.System method) cal_common_neighbor_analysis() (mdapy.system.System method) cal_common_neighbor_parameter() (mdapy.system.System method) cal_esf (mdapy.identify_fcc_planar_faults.IdentifyFccPlanarFaults attribute) cal_identify_diamond_structure() (mdapy.system.System method) cal_polyhedral_template_matching() (mdapy.system.System method) cal_radial_distribution_function() (mdapy.system.System method) cal_steinhardt_bond_orientation() (mdapy.system.System method) cal_structure_entropy() (mdapy.system.System method) cal_structure_factor() (mdapy.system.System method) cal_voronoi_volume() (mdapy.system.System method) cal_warren_cowley_parameter() (mdapy.system.System method) calc (mdapy.nep.NEP attribute) (mdapy.nep4ase.NEP4ASE attribute) (mdapy.system.System attribute) calculate() (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) CalculatorMP (class in mdapy.calculator) cavity_radius (mdapy.voronoi.Cell attribute) Cell (class in mdapy.voronoi) CentroSymmetryParameter (class in mdapy.centro_symmetry_parameter) cfg2xyz() (in module mdapy.potential_tool) check_small_box() (mdapy.box.Box method) chemical_symbols (in module mdapy.data) Cij (mdapy.elastic.ElasticConstant attribute) close() (mdapy.visualize.View method) cluster_number (mdapy.cluster_analysis.ClusterAnalysis attribute) ClusterAnalysis (class in mdapy.cluster_analysis) cnp (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) colored_by() (mdapy.visualize.View method) colored_by_element() (mdapy.visualize.View method) colored_by_type() (mdapy.visualize.View method) CommonNeighborAnalysis (class in mdapy.common_neighbor_analysis) CommonNeighborParameter (class in mdapy.common_neighbor_parameter) compress_file() (in module mdapy.pigz) compute() (mdapy.ackland_jones_analysis.AcklandJonesAnalysis method) (mdapy.angular_distribution_function.AngularDistributionFunction method) (mdapy.atomic_strain.AtomicStrain method) (mdapy.atomic_temperature.AtomicTemperature method) (mdapy.bond_analysis.BondAnalysis method) (mdapy.centro_symmetry_parameter.CentroSymmetryParameter method) (mdapy.cluster_analysis.ClusterAnalysis method) (mdapy.common_neighbor_analysis.CommonNeighborAnalysis method) (mdapy.common_neighbor_parameter.CommonNeighborParameter method) (mdapy.create_polycrystal.CreatePolycrystal method) (mdapy.elastic.ElasticConstant method) (mdapy.identify_diamond_structure.IdentifyDiamondStructure method) (mdapy.identify_fcc_planar_faults.IdentifyFccPlanarFaults method) (mdapy.knn.NearestNeighbor method) (mdapy.lindemann_parameter.LindemannParameter method) (mdapy.mean_squared_displacement.MeanSquaredDisplacement method) (mdapy.neighbor.Neighbor method) (mdapy.polyhedral_template_matching.PolyhedralTemplateMatching method) (mdapy.radial_distribution_function.RadialDistributionFunction method) (mdapy.spatial_binning.SpatialBinning method) (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation method) (mdapy.structure_entropy.StructureEntropy method) (mdapy.structure_factor.StructureFactor method) (mdapy.void_analysis.VoidAnalysis method) (mdapy.warren_cowley_parameter.WarrenCowleyParameter method) (mdapy.wigner_seitz_defect.WignerSeitzAnalysis method) con (mdapy.create_polycrystal.CreatePolycrystal attribute) concatenate() (mdapy.trajectory.XYZTrajectory method) Container (class in mdapy.voronoi) CreatePolycrystal (class in mdapy.create_polycrystal) csp (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) D data (mdapy.ackland_jones_analysis.AcklandJonesAnalysis attribute) (mdapy.atomic_temperature.AtomicTemperature attribute) (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.identify_diamond_structure.IdentifyDiamondStructure attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) (mdapy.system.System property) (mdapy.voronoi.Voronoi attribute) (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) DEFAULT_NR (mdapy.eam.EAMGenerator attribute) DEFAULT_NRHO (mdapy.eam.EAMGenerator attribute) DEFAULT_RST (mdapy.eam.EAMGenerator attribute) delete_color_bar() (mdapy.visualize.View method) derivative() (mdapy.spline.Spline method) display() (mdapy.visualize.View method) distance_list (mdapy.ackland_jones_analysis.AcklandJonesAnalysis attribute) (mdapy.atomic_temperature.AtomicTemperature attribute) (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) distances_py (mdapy.knn.NearestNeighbor attribute) dr (mdapy.eam.EAM attribute) drho (mdapy.eam.EAM attribute) E EAM (class in mdapy.eam) EAMAverage (class in mdapy.eam) EAMGenerator (class in mdapy.eam) ElasticConstant (class in mdapy.elastic) ele2type (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) ele_unique (mdapy.angular_distribution_function.AngularDistributionFunction attribute) elements_list (mdapy.eam.EAM attribute) entropy (mdapy.structure_entropy.StructureEntropy attribute) entropy_ave (mdapy.structure_entropy.StructureEntropy attribute) evaluate() (mdapy.spline.Spline method) extend() (mdapy.trajectory.XYZTrajectory method) F F_rho (mdapy.eam.EAM attribute) face_areas (mdapy.voronoi.Cell attribute) face_vertices (mdapy.voronoi.Cell attribute) factor (mdapy.atomic_temperature.AtomicTemperature attribute) fault_types (mdapy.identify_fcc_planar_faults.IdentifyFccPlanarFaults attribute) filename (mdapy.eam.EAM attribute) FIRE (class in mdapy.minimizer) fit_transform() (mdapy.potential_tool.PCA method) fps_sample() (in module mdapy.potential_tool) from_array() (mdapy.load_save.BuildSystem static method) from_ase() (mdapy.load_save.BuildSystem static method) from_data() (mdapy.load_save.BuildSystem static method) from_file() (mdapy.load_save.BuildSystem class method) from_ovito() (mdapy.load_save.BuildSystem static method) G g (mdapy.radial_distribution_function.RadialDistributionFunction attribute) g_total (mdapy.radial_distribution_function.RadialDistributionFunction attribute) generate_deformations() (mdapy.elastic.ElasticConstant method) generate_velocity() (in module mdapy.tool_function) get_atoms_count() (mdapy.trajectory.XYZTrajectory method) get_average_sfe_fcc_hea() (in module mdapy.potential_tool) get_bec() (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) get_cart_deformed_cell() (mdapy.elastic.ElasticConstant method) get_cell_info() (mdapy.voronoi.Voronoi method) get_charges() (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) get_descriptor() (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) get_energies() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.system.System method) get_energy() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.system.System method) get_eos() (in module mdapy.potential_tool) get_force() (mdapy.system.System method) get_forces() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.minimizer.FIRE method) (mdapy.nep.NEP method) get_latentspace() (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) get_neighbor() (mdapy.voronoi.Voronoi method) get_positions() (mdapy.system.System method) get_pressure() (mdapy.elastic.ElasticConstant static method) get_sfe_fcc() (in module mdapy.potential_tool) get_strain() (mdapy.elastic.ElasticConstant static method) get_stress() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.system.System method) get_thickness() (mdapy.box.Box method) get_velocities() (mdapy.system.System method) get_virials() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) (mdapy.system.System method) get_volume() (mdapy.voronoi.Voronoi method) global_info (mdapy.system.System attribute) (mdapy.system.System property) H header (mdapy.eam.EAM attribute) hide_object_by_group_name() (mdapy.visualize.View method) I IdentifyDiamondStructure (class in mdapy.identify_diamond_structure) IdentifyFccPlanarFaults (class in mdapy.identify_fcc_planar_faults) implemented_properties (mdapy.nep4ase.NEP4ASE attribute), [1] indices_py (mdapy.knn.NearestNeighbor attribute) init_plot() (mdapy.visualize.View method) insert() (mdapy.trajectory.XYZTrajectory method) inverse_box (mdapy.box.Box attribute) (mdapy.box.Box property) K k (mdapy.structure_factor.StructureFactor attribute) L label (mdapy.visualize.View attribute) LammpsPotential (class in mdapy.lammps_potential) lindemann_atom (mdapy.lindemann_parameter.LindemannParameter attribute) lindemann_frame (mdapy.lindemann_parameter.LindemannParameter attribute) lindemann_trj (mdapy.lindemann_parameter.LindemannParameter attribute) LindemannParameter (class in mdapy.lindemann_parameter) M max_neigh (mdapy.atomic_strain.AtomicStrain attribute) (mdapy.neighbor.Neighbor attribute) max_rc (mdapy.cluster_analysis.ClusterAnalysis attribute) mdapy.ackland_jones_analysis module mdapy.angular_distribution_function module mdapy.atomic_strain module mdapy.atomic_temperature module mdapy.bond_analysis module mdapy.box module mdapy.build_lattice module mdapy.calculator module mdapy.centro_symmetry_parameter module mdapy.cluster_analysis module mdapy.common_neighbor_analysis module mdapy.common_neighbor_parameter module mdapy.create_polycrystal module mdapy.data module mdapy.eam module mdapy.elastic module mdapy.identify_diamond_structure module mdapy.identify_fcc_planar_faults module mdapy.knn module mdapy.lammps_potential module mdapy.lindemann_parameter module mdapy.load_save module mdapy.mean_squared_displacement module mdapy.minimizer module mdapy.neighbor module mdapy.nep module mdapy.nep4ase module mdapy.pigz module mdapy.plotset module mdapy.polyhedral_template_matching module mdapy.potential_tool module mdapy.radial_distribution_function module mdapy.spatial_binning module mdapy.spline module mdapy.steinhardt_bond_orientation module mdapy.structure_entropy module mdapy.structure_factor module mdapy.system module mdapy.tool_function module mdapy.trajectory module mdapy.visualize module mdapy.void_analysis module mdapy.voronoi module mdapy.warren_cowley_parameter module mdapy.wigner_seitz_defect module MeanSquaredDisplacement (class in mdapy.mean_squared_displacement) mode (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) module mdapy.ackland_jones_analysis mdapy.angular_distribution_function mdapy.atomic_strain mdapy.atomic_temperature mdapy.bond_analysis mdapy.box mdapy.build_lattice mdapy.calculator mdapy.centro_symmetry_parameter mdapy.cluster_analysis mdapy.common_neighbor_analysis mdapy.common_neighbor_parameter mdapy.create_polycrystal mdapy.data mdapy.eam mdapy.elastic mdapy.identify_diamond_structure mdapy.identify_fcc_planar_faults mdapy.knn mdapy.lammps_potential mdapy.lindemann_parameter mdapy.load_save mdapy.mean_squared_displacement mdapy.minimizer mdapy.neighbor mdapy.nep mdapy.nep4ase mdapy.pigz mdapy.plotset mdapy.polyhedral_template_matching mdapy.potential_tool mdapy.radial_distribution_function mdapy.spatial_binning mdapy.spline mdapy.steinhardt_bond_orientation mdapy.structure_entropy mdapy.structure_factor mdapy.system mdapy.tool_function mdapy.trajectory mdapy.visualize mdapy.void_analysis mdapy.voronoi mdapy.warren_cowley_parameter mdapy.wigner_seitz_defect msd (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) N N (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.radial_distribution_function.RadialDistributionFunction attribute) (mdapy.system.System attribute) (mdapy.system.System property) nbin (mdapy.bond_analysis.BondAnalysis attribute) nbond (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation attribute) NearestNeighbor (class in mdapy.knn) Neighbor (class in mdapy.neighbor) neighbor_number (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) Nelements (mdapy.eam.EAM attribute) NEP (class in mdapy.nep) NEP4ASE (class in mdapy.nep4ase) nr (mdapy.eam.EAM attribute) nrho (mdapy.eam.EAM attribute) Ntype (mdapy.radial_distribution_function.RadialDistributionFunction attribute) (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) O origin (mdapy.box.Box attribute) (mdapy.box.Box property) outcar2xyz() (in module mdapy.potential_tool) outcars2xyz() (in module mdapy.potential_tool) output (mdapy.polyhedral_template_matching.PolyhedralTemplateMatching attribute) P pair_list (mdapy.angular_distribution_function.AngularDistributionFunction attribute) particle_msd (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) particleClusters (mdapy.cluster_analysis.ClusterAnalysis attribute) pattern (mdapy.common_neighbor_analysis.CommonNeighborAnalysis attribute) (mdapy.identify_diamond_structure.IdentifyDiamondStructure attribute) pbc() (mdapy.box.Box method) PCA (class in mdapy.potential_tool) phi_r (mdapy.eam.EAM attribute) plot (mdapy.visualize.View attribute) plot() (mdapy.eam.EAM method) (mdapy.lindemann_parameter.LindemannParameter method) (mdapy.mean_squared_displacement.MeanSquaredDisplacement method) (mdapy.radial_distribution_function.RadialDistributionFunction method) (mdapy.structure_factor.StructureFactor method) (mdapy.warren_cowley_parameter.WarrenCowleyParameter method) plot_bond_angle_distribution() (mdapy.angular_distribution_function.AngularDistributionFunction method) (mdapy.bond_analysis.BondAnalysis method) plot_bond_length_distribution() (mdapy.bond_analysis.BondAnalysis method) plot_nep_train() (in module mdapy.potential_tool) plot_partial() (mdapy.radial_distribution_function.RadialDistributionFunction method) (mdapy.structure_factor.StructureFactor method) PolyhedralTemplateMatching (class in mdapy.polyhedral_template_matching) pop() (mdapy.trajectory.XYZTrajectory method) pos (mdapy.voronoi.Cell attribute) pos_list (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) print_Cij() (mdapy.elastic.ElasticConstant method) ptm_indices (mdapy.identify_fcc_planar_faults.IdentifyFccPlanarFaults attribute) (mdapy.polyhedral_template_matching.PolyhedralTemplateMatching attribute) Q qlm_i (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation attribute) qlm_r (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation attribute) qnarray (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation attribute) R r (mdapy.eam.EAM attribute) (mdapy.radial_distribution_function.RadialDistributionFunction attribute) r_angle (mdapy.angular_distribution_function.AngularDistributionFunction attribute) (mdapy.bond_analysis.BondAnalysis attribute) r_length (mdapy.bond_analysis.BondAnalysis attribute) RadialDistributionFunction (class in mdapy.radial_distribution_function) randomseed (mdapy.create_polycrystal.CreatePolycrystal attribute) rc (mdapy.atomic_strain.AtomicStrain attribute) (mdapy.atomic_temperature.AtomicTemperature attribute) (mdapy.bond_analysis.BondAnalysis attribute) (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.eam.EAM attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) (mdapy.void_analysis.VoidAnalysis attribute) rc_list (mdapy.angular_distribution_function.AngularDistributionFunction attribute) read_data() (mdapy.load_save.BuildSystem static method) read_dump() (mdapy.load_save.BuildSystem static method) read_mp() (mdapy.load_save.BuildSystem static method) read_OUTCAR() (in module mdapy.potential_tool) read_poscar() (mdapy.load_save.BuildSystem static method) read_thermo() (in module mdapy.potential_tool) read_xyz() (mdapy.load_save.BuildSystem static method) ref (mdapy.atomic_strain.AtomicStrain attribute) relax_struc() (mdapy.elastic.ElasticConstant static method) remove() (mdapy.trajectory.XYZTrajectory method) repeat (mdapy.atomic_strain.AtomicStrain attribute) replicate() (in module mdapy.tool_function) (mdapy.system.System method) results (mdapy.calculator.CalculatorMP attribute), [1] (mdapy.eam.EAM attribute) (mdapy.nep.NEP attribute) (mdapy.nep4ase.NEP4ASE attribute) rho (mdapy.eam.EAM attribute) rho_r (mdapy.eam.EAM attribute) rmse() (in module mdapy.potential_tool) run() (mdapy.minimizer.FIRE method) run_gpumd() (in module mdapy.potential_tool) S save() (mdapy.trajectory.XYZTrajectory method) save_figure() (in module mdapy.plotset) SaveSystem (class in mdapy.load_save) seed_number (mdapy.create_polycrystal.CreatePolycrystal attribute) seed_position (mdapy.create_polycrystal.CreatePolycrystal attribute) set_boundary() (mdapy.box.Box method) set_box() (mdapy.box.Box method) set_element() (mdapy.system.System method) set_figure() (in module mdapy.plotset) set_nep() (mdapy.nep4ase.NEP4ASE method) set_origin() (mdapy.box.Box method) set_pka() (mdapy.system.System method) set_type_by_element() (mdapy.system.System method) setAtoms() (mdapy.nep.NEP method) Sk (mdapy.structure_factor.StructureFactor attribute) Sk_partial (mdapy.structure_factor.StructureFactor attribute) Sk_partial_xray (mdapy.structure_factor.StructureFactor attribute) Sk_xray (mdapy.structure_factor.StructureFactor attribute) solidliquid (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation attribute) sort_neighbor() (in module mdapy.tool_function) SpatialBinning (class in mdapy.spatial_binning) Spline (class in mdapy.spline) split_xyz() (in module mdapy.tool_function) SteinhardtBondOrientation (class in mdapy.steinhardt_bond_orientation) structure_types (mdapy.identify_fcc_planar_faults.IdentifyFccPlanarFaults attribute) StructureEntropy (class in mdapy.structure_entropy) StructureFactor (class in mdapy.structure_factor) SUPPORTED_ELEMENTS (mdapy.eam.EAMGenerator attribute) System (class in mdapy.system) system (mdapy.elastic.ElasticConstant attribute) (mdapy.visualize.View attribute) (mdapy.void_analysis.VoidAnalysis attribute) T T (mdapy.atomic_temperature.AtomicTemperature attribute) theta_list (mdapy.create_polycrystal.CreatePolycrystal attribute) to_ase() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) to_ovito() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) triclinic (mdapy.box.Box attribute) (mdapy.box.Box property) triclinic_deform() (mdapy.elastic.ElasticConstant static method) type_list (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) U unitcell (mdapy.create_polycrystal.CreatePolycrystal attribute) update_box() (mdapy.system.System method) update_data() (mdapy.system.System method) update_data_box() (mdapy.minimizer.FIRE method) V vdw_radii (in module mdapy.data) verlet_list (mdapy.ackland_jones_analysis.AcklandJonesAnalysis attribute) (mdapy.atomic_temperature.AtomicTemperature attribute) (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) (mdapy.common_neighbor_parameter.CommonNeighborParameter attribute) (mdapy.identify_diamond_structure.IdentifyDiamondStructure attribute) (mdapy.neighbor.Neighbor attribute) (mdapy.system.System attribute) (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) vertices (mdapy.voronoi.Cell attribute) View (class in mdapy.visualize) void_number (mdapy.void_analysis.VoidAnalysis attribute) void_system (mdapy.void_analysis.VoidAnalysis attribute) void_volume (mdapy.void_analysis.VoidAnalysis attribute) VoidAnalysis (class in mdapy.void_analysis) vol (mdapy.radial_distribution_function.RadialDistributionFunction attribute) volume (mdapy.box.Box attribute) (mdapy.box.Box property) (mdapy.voronoi.Cell attribute) Voronoi (class in mdapy.voronoi) W WarrenCowleyParameter (class in mdapy.warren_cowley_parameter) WCP (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) WignerSeitzAnalysis (class in mdapy.wigner_seitz_defect) wrap_pos() (in module mdapy.tool_function) (mdapy.system.System method) write_data() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) write_dump() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) write_eam_alloy() (mdapy.eam.EAM method) write_mp() (mdapy.load_save.SaveSystem method) (mdapy.system.System method) write_poscar() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) write_xyz() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) X x (mdapy.spline.Spline attribute) xray_form_factor (in module mdapy.data) XYZTrajectory (class in mdapy.trajectory) Y y (mdapy.spline.Spline attribute)