Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ _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) apply_deformation_to_cell() (in module mdapy.elastic) apply_deformation_to_positions() (in module mdapy.elastic) 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 backend (mdapy.render.TachyonRender property) 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) bond_table (mdapy.bond_stiffness.BondStiffness attribute) BondAnalysis (class in mdapy.bond_analysis) BondStiffness (class in mdapy.bond_stiffness) born_stable_cubic() (mdapy.md_elastic.MDElasticResult method) boundary (mdapy.box.Box property) Box (class in mdapy.box) box (mdapy.ackland_jones_analysis.AcklandJonesAnalysis 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 property) (mdapy.visualize.View attribute) (mdapy.voronoi.Voronoi attribute) build_bond() (in module mdapy.build_bond) 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_chill_plus() (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 property) calculate() (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE method) CalculatorMP (class in mdapy.calculator) CameraParams (class in mdapy.render) cavity_radius (mdapy.voronoi.Cell attribute) Cell (class in mdapy.voronoi) CentroSymmetryParameter (class in mdapy.centro_symmetry_parameter) cfg2xyz() (in module mdapy.potential_tool) channel_info (mdapy.sqs.SQS attribute) check_small_box() (mdapy.box.Box method) chemical_symbols (in module mdapy.data) ChillPlus (class in mdapy.chill_plus) cij_voigt (mdapy.md_elastic.MDElasticResult attribute) close() (mdapy.lammps_runner.LammpsRunner method) (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.bond_stiffness.BondStiffness method) (mdapy.centro_symmetry_parameter.CentroSymmetryParameter method) (mdapy.chill_plus.ChillPlus method) (mdapy.cluster_analysis.ClusterAnalysis method) (mdapy.common_neighbor_analysis.CommonNeighborAnalysis method) (mdapy.common_neighbor_parameter.CommonNeighborParameter method) (mdapy.create_polycrystal.CreatePolycrystal 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.sqs.SQS 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) Container (class in mdapy.voronoi) correlations (mdapy.sqs.SQS attribute) create_bonds() (mdapy.system.System method) CreatePolycrystal (class in mdapy.create_polycrystal) csp (mdapy.centro_symmetry_parameter.CentroSymmetryParameter attribute) cubic_average() (mdapy.md_elastic.MDElasticResult method) 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 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) deformations (mdapy.elastic.DeformedStructureSet attribute) deformed_systems (mdapy.elastic.DeformedStructureSet attribute) DeformedStructureSet (class in mdapy.elastic) delete_color_bar() (mdapy.visualize.View method) delete_overlap() (mdapy.system.System 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) E EAM (class in mdapy.eam) EAMAverage (class in mdapy.eam) EAMGenerator (class in mdapy.eam) ElasticTensor (class in mdapy.elastic) ele2type (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) ele_unique (mdapy.angular_distribution_function.AngularDistributionFunction attribute) elements (mdapy.radial_distribution_function.RadialDistributionFunction attribute) ensemble (mdapy.md_elastic.MDElasticResult attribute) entropy (mdapy.structure_entropy.StructureEntropy attribute) entropy_ave (mdapy.structure_entropy.StructureEntropy attribute) evaluate() (mdapy.spline.Spline method) F 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) 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_independent_strains() (mdapy.elastic.ElasticTensor class method) from_ovito() (mdapy.load_save.BuildSystem static method) G g_partial (mdapy.radial_distribution_function.RadialDistributionFunction attribute) g_total (mdapy.radial_distribution_function.RadialDistributionFunction attribute) generate_perturbed_structures() (mdapy.bond_stiffness.BondStiffness method) generate_velocity() (in module mdapy.tool_function) get_average_sfe_fcc_hea() (in module mdapy.potential_tool) get_bec() (mdapy.nep.NEP method) (mdapy.nep4ase.NEP4ASE 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_elastic_constant() (in module mdapy.elastic) get_electron_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_electron_radial_distribution_function() (mdapy.structure_factor.StructureFactor method) get_electron_reduced_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_electron_structure_factor() (mdapy.structure_factor.StructureFactor 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_neutron_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_neutron_radial_distribution_function() (mdapy.structure_factor.StructureFactor method) get_neutron_reduced_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_neutron_structure_factor() (mdapy.structure_factor.StructureFactor method) get_num_threads() (in module mdapy.parallel) get_positions() (mdapy.system.System method) get_sfe_fcc() (in module mdapy.potential_tool) get_stress() (mdapy.calculator.CalculatorMP method) (mdapy.eam.EAM method) (mdapy.lammps_potential.LammpsPotential method) (mdapy.nep.NEP method) (mdapy.system.System method) get_system() (mdapy.lammps_runner.LammpsRunner 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) get_xray_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_xray_radial_distribution_function() (mdapy.structure_factor.StructureFactor method) get_xray_reduced_pair_distribution_function() (mdapy.structure_factor.StructureFactor method) get_xray_structure_factor() (mdapy.structure_factor.StructureFactor method) global_info (mdapy.system.System property) H 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) indices_py (mdapy.knn.NearestNeighbor attribute) init_plot() (mdapy.visualize.View method) inverse_box (mdapy.box.Box property) is_general_box() (mdapy.box.Box method) is_gpu_available() (in module mdapy.render) is_sqs() (mdapy.sqs.SQS method) K k (mdapy.structure_factor.StructureFactor attribute) L label (mdapy.visualize.View attribute) LammpsPotential (class in mdapy.lammps_potential) LammpsRunner (class in mdapy.lammps_runner) 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) load_image() (in module mdapy.render) 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.bond_stiffness module mdapy.box module mdapy.build_bond module mdapy.build_lattice module mdapy.calculator module mdapy.centro_symmetry_parameter module mdapy.chill_plus 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.lammps_runner module mdapy.lindemann_parameter module mdapy.load_save module mdapy.md_elastic module mdapy.mean_squared_displacement module mdapy.minimizer module mdapy.neighbor module mdapy.nep module mdapy.nep4ase module mdapy.orthogonal_cell module mdapy.parallel module mdapy.pigz module mdapy.plotset module mdapy.polyhedral_template_matching module mdapy.potential_tool module mdapy.radial_distribution_function module mdapy.render module mdapy.spatial_binning module mdapy.spline module mdapy.sqs 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.unwrap_trajectory module mdapy.visualize module mdapy.void_analysis module mdapy.voronoi module mdapy.warren_cowley_parameter module mdapy.wigner_seitz_defect module MDElastic (class in mdapy.md_elastic) MDElasticResult (class in mdapy.md_elastic) MeanSquaredDisplacement (class in mdapy.mean_squared_displacement) minimize() (mdapy.lammps_runner.LammpsRunner method) minimize_box() (mdapy.lammps_runner.LammpsRunner method) 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.bond_stiffness mdapy.box mdapy.build_bond mdapy.build_lattice mdapy.calculator mdapy.centro_symmetry_parameter mdapy.chill_plus 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.lammps_runner mdapy.lindemann_parameter mdapy.load_save mdapy.md_elastic mdapy.mean_squared_displacement mdapy.minimizer mdapy.neighbor mdapy.nep mdapy.nep4ase mdapy.orthogonal_cell mdapy.parallel mdapy.pigz mdapy.plotset mdapy.polyhedral_template_matching mdapy.potential_tool mdapy.radial_distribution_function mdapy.render mdapy.spatial_binning mdapy.spline mdapy.sqs mdapy.steinhardt_bond_orientation mdapy.structure_entropy mdapy.structure_factor mdapy.system mdapy.tool_function mdapy.trajectory mdapy.unwrap_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 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) NEP (class in mdapy.nep) NEP4ASE (class in mdapy.nep4ase) neutron_form_factor (in module mdapy.data) Ntype (mdapy.radial_distribution_function.RadialDistributionFunction attribute) (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) O objective (mdapy.sqs.SQS attribute) origin (mdapy.box.Box property) orthogonal_cell() (in module mdapy.orthogonal_cell) 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) parse_dump_frame() (mdapy.load_save.BuildSystem static method) parse_log() (mdapy.md_elastic.MDElastic static method) particle_msd (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) particleClusters (mdapy.cluster_analysis.ClusterAnalysis attribute) pattern (mdapy.chill_plus.ChillPlus attribute) (mdapy.common_neighbor_analysis.CommonNeighborAnalysis attribute) (mdapy.identify_diamond_structure.IdentifyDiamondStructure attribute) pbc() (mdapy.box.Box method) PCA (class in mdapy.potential_tool) plot (mdapy.visualize.View attribute) plot() (mdapy.bond_stiffness.BondStiffness method) (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) pos (mdapy.voronoi.Cell attribute) pos_list (mdapy.mean_squared_displacement.MeanSquaredDisplacement attribute) preset_camera() (in module mdapy.render) PRESET_VIEWS (in module mdapy.render) print() (mdapy.elastic.ElasticTensor method) (mdapy.md_elastic.MDElasticResult method) print_vrh() (mdapy.elastic.ElasticTensor 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.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.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) render() (mdapy.render.TachyonRender method) render_system() (mdapy.render.TachyonRender method) repeat (mdapy.atomic_strain.AtomicStrain attribute) replicate() (in module mdapy.tool_function) (mdapy.system.System method) results (mdapy.calculator.CalculatorMP attribute) (mdapy.nep.NEP attribute) (mdapy.nep4ase.NEP4ASE attribute) rmse() (in module mdapy.potential_tool) run() (mdapy.md_elastic.MDElastic method) (mdapy.minimizer.FIRE method) run_gpumd() (in module mdapy.potential_tool) run_md() (mdapy.lammps_runner.LammpsRunner method) S save() (mdapy.trajectory.Trajectory method) (mdapy.trajectory.XYZTrajectory method) save_figure() (in module mdapy.plotset) save_image() (in module mdapy.render) SaveSystem (class in mdapy.load_save) scan_parallel() (mdapy.md_elastic.MDElastic static method) second_derivative() (mdapy.spline.Spline method) 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) shells (mdapy.bond_stiffness.BondStiffness attribute) silence() (in module mdapy.lammps_potential) Sk (mdapy.structure_factor.StructureFactor attribute) Sk_partial (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) SQS (class in mdapy.sqs) SteinhardtBondOrientation (class in mdapy.steinhardt_bond_orientation) strain_from_deformation() (in module mdapy.elastic) strain_to_voigt() (in module mdapy.elastic) stress_ref (mdapy.md_elastic.MDElasticResult attribute) stress_to_voigt() (in module mdapy.elastic) 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.sqs.SQS attribute) (mdapy.visualize.View attribute) (mdapy.void_analysis.VoidAnalysis attribute) T T (mdapy.atomic_temperature.AtomicTemperature attribute) T_actual (mdapy.md_elastic.MDElasticResult attribute) TachyonRender (class in mdapy.render) temperature (mdapy.md_elastic.MDElasticResult attribute) thermal_expansion() (mdapy.md_elastic.MDElastic static method) 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) Trajectory (class in mdapy.trajectory) triclinic (mdapy.box.Box property) type_list (mdapy.warren_cowley_parameter.WarrenCowleyParameter attribute) U unitcell (mdapy.create_polycrystal.CreatePolycrystal attribute) unwrap() (mdapy.trajectory.Trajectory method) unwrap_trajectory() (in module mdapy.unwrap_trajectory) update_box() (mdapy.system.System method) update_data() (mdapy.system.System method) update_data_box() (mdapy.minimizer.FIRE method) V V_eq (mdapy.md_elastic.MDElasticResult attribute) 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) voigt (mdapy.elastic.ElasticTensor attribute) vol (mdapy.radial_distribution_function.RadialDistributionFunction attribute) volume (mdapy.box.Box property) (mdapy.voronoi.Cell attribute) Voronoi (class in mdapy.voronoi) vrh() (mdapy.elastic.ElasticTensor method) (mdapy.md_elastic.MDElasticResult method) 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_dump_frame_to() (mdapy.load_save.SaveSystem static 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_slspring() (mdapy.bond_stiffness.BondStiffness method) write_xyz() (mdapy.load_save.SaveSystem static method) (mdapy.system.System method) X xray_form_factor (in module mdapy.data) XYZTrajectory (class in mdapy.trajectory)