Index

A

ackland_jones_analysis() (in module mdapy.main) AcklandJonesAnalysis (class in mdapy.ackland_jones_analysis) atom_colored_by_atom_type() (mdapy.visualize.Visualize method) atom_colored_by_structure_type() (mdapy.visualize.Visualize method) atom_distance() (mdapy.system.System method) atomic_entropy() (in module mdapy.main)

atomic_numbers (in module mdapy.tool_function) atomic_temperature() (in module mdapy.main) AtomicEntropy (class in mdapy.entropy) AtomicTemperature (class in mdapy.temperature) atoms_colored_by() (mdapy.system.System method) (mdapy.visualize.Visualize method)

B

BasePotential (class in mdapy.potential) boundary (mdapy.system.System property) box (mdapy.system.System property) box2axis() (in module mdapy.main) box2lines() (in module mdapy.main) (mdapy.visualize.Visualize method)

build_lattice() (in module mdapy.main) build_neighbor() (mdapy.system.System method) build_polycrystal() (in module mdapy.main) BuildSystem (class in mdapy.load_save_data)

C

cal_ackland_jones_analysis() (mdapy.system.System method) cal_atomic_entropy() (mdapy.system.System method) cal_atomic_temperature() (mdapy.system.System method) cal_centro_symmetry_parameter() (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_energy_force_virial() (mdapy.system.System method) cal_identify_SFs_TBs() (mdapy.system.System method) cal_lindemann_parameter() (mdapy.system.MultiSystem method) cal_mean_squared_displacement() (mdapy.system.MultiSystem method) cal_pair_distribution() (mdapy.system.System method) cal_phono_dispersion() (mdapy.system.System method) cal_polyhedral_template_matching() (mdapy.system.System method) cal_species_number() (mdapy.system.System method) cal_steinhardt_bond_orientation() (mdapy.system.System method) cal_void_distribution() (mdapy.system.System method) cal_voronoi_volume() (mdapy.system.System method) cal_warren_cowley_parameter() (mdapy.system.System method) calculate_chunk_check() (mdapy.pigz.PigzFile method) callback() (in module mdapy.main) cavity_radius() (mdapy.create_polycrystalline.Cell method) Cell (class in mdapy.create_polycrystalline) cell_opt() (mdapy.system.System method) centro_symmetry_parameter() (in module mdapy.main) CentroSymmetryParameter (class in mdapy.centro_symmetry_parameter) change_filename() (mdapy.system.System method) clean_up() (mdapy.pigz.PigzFile method) close() (mdapy.visualize.Visualize method) cluster_analysis() (in module mdapy.main) ClusterAnalysis (class in mdapy.cluser_analysis) cm2inch() (in module mdapy.plotset) common_neighbor_analysis() (in module mdapy.main)

common_neighbor_parameter() (in module mdapy.main) 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.centro_symmetry_parameter.CentroSymmetryParameter method) (mdapy.cluser_analysis.ClusterAnalysis method) (mdapy.common_neighbor_analysis.CommonNeighborAnalysis method) (mdapy.common_neighbor_parameter.CommonNeighborParameter method) (mdapy.create_polycrystalline.CreatePolycrystalline method) (mdapy.create_polycrystalline.DeleteOverlap method) (mdapy.entropy.AtomicEntropy method) (mdapy.identify_SFs_TBs.IdentifySFTBinFCC method) (mdapy.lattice_maker.LatticeMaker method) (mdapy.lindemann_parameter.LindemannParameter method) (mdapy.mean_squared_displacement.MeanSquaredDisplacement method) (mdapy.neighbor.Neighbor method) (mdapy.pair_distribution.PairDistribution method) (mdapy.perturb_model.PerturbModel method) (mdapy.polyhedral_template_matching.PolyhedralTemplateMatching method) (mdapy.potential.BasePotential method) (mdapy.potential.EAM method) (mdapy.potential.EAMCalculator method) (mdapy.potential.LammpsPotential method) (mdapy.potential.NEP method) (mdapy.replicate.Replicate method) (mdapy.spatial_binning.SpatialBinning method) (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation method) (mdapy.temperature.AtomicTemperature method) (mdapy.void_distribution.VoidDistribution method) (mdapy.voronoi_analysis.VoronoiAnalysis method) (mdapy.warren_cowley_parameter.WarrenCowleyParameter method) Container (class in mdapy.create_polycrystalline) CreatePolycrystalline (class in mdapy.create_polycrystalline)

D

data (mdapy.system.System property) DeleteOverlap (class in mdapy.create_polycrystalline) DFT2NEPXYZ (class in mdapy.dft2nepxyz)

display() (mdapy.system.System method) (mdapy.visualize.Visualize method) distance_list (mdapy.system.System property)

E

EAM (class in mdapy.potential) EAMAverage (class in mdapy.eam_average)

EAMCalculator (class in mdapy.potential) EAMGenerate (class in mdapy.eam_generate)

F

face_areas() (mdapy.create_polycrystalline.Cell method) face_vertices() (mdapy.create_polycrystalline.Cell method) filename (mdapy.system.System property) filter_by_type() (in module mdapy.cluser_analysis)

fmt (mdapy.system.System property) fps_sample() (mdapy.potential.NEP method) fromarray() (mdapy.load_save_data.BuildSystem static method) fromdata() (mdapy.load_save_data.BuildSystem static method) fromfile() (mdapy.load_save_data.BuildSystem class method)

G

get_descriptors() (mdapy.potential.NEP method) get_size_of_cluster() (mdapy.cluser_analysis.ClusterAnalysis method)

getformat() (mdapy.load_save_data.BuildSystem static method) global_info (mdapy.system.System property)

I

identify_SFs_TBs() (in module mdapy.main) identify_species() (in module mdapy.main) IdentifySFTBinFCC (class in mdapy.identify_SFs_TBs) identifySolidLiquid() (mdapy.steinhardt_bond_orientation.SteinhardtBondOrientation method)

init() (in module mdapy) init_color() (mdapy.visualize.Visualize method) init_global_parameters() (in module mdapy.main) init_plot() (mdapy.visualize.Visualize method)

K

kdtree (class in mdapy.nearest_neighbor)

L

LabeledSystem (class in mdapy.dft2nepxyz) LammpsPotential (class in mdapy.potential) LatticeMaker (class in mdapy.lattice_maker)

LindemannParameter (class in mdapy.lindemann_parameter) load_file_gui() (in module mdapy.main) loadfile() (in module mdapy.main)

M

main() (in module mdapy.main) mdapy module mdapy.ackland_jones_analysis module mdapy.centro_symmetry_parameter module mdapy.cluser_analysis module mdapy.common_neighbor_analysis module mdapy.common_neighbor_parameter module mdapy.create_polycrystalline module mdapy.dft2nepxyz module mdapy.eam_average module mdapy.eam_generate module mdapy.entropy module mdapy.identify_SFs_TBs module mdapy.lattice_maker module mdapy.lindemann_parameter module mdapy.load_save_data module mdapy.main module mdapy.mean_squared_displacement module mdapy.nearest_neighbor module mdapy.neighbor module mdapy.pair_distribution module mdapy.perturb_model module mdapy.pigz module mdapy.plotset module mdapy.polyhedral_template_matching module mdapy.potential module mdapy.replicate module mdapy.spatial_binning module

mdapy.steinhardt_bond_orientation module mdapy.system module mdapy.temperature module mdapy.tool_function module mdapy.visualize module mdapy.void_distribution module mdapy.voronoi_analysis module mdapy.warren_cowley_parameter module MeanSquaredDisplacement (class in mdapy.mean_squared_displacement) module mdapy mdapy.ackland_jones_analysis mdapy.centro_symmetry_parameter mdapy.cluser_analysis mdapy.common_neighbor_analysis mdapy.common_neighbor_parameter mdapy.create_polycrystalline mdapy.dft2nepxyz mdapy.eam_average mdapy.eam_generate mdapy.entropy mdapy.identify_SFs_TBs mdapy.lattice_maker mdapy.lindemann_parameter mdapy.load_save_data mdapy.main mdapy.mean_squared_displacement mdapy.nearest_neighbor mdapy.neighbor mdapy.pair_distribution mdapy.perturb_model mdapy.pigz mdapy.plotset mdapy.polyhedral_template_matching mdapy.potential mdapy.replicate mdapy.spatial_binning mdapy.steinhardt_bond_orientation mdapy.system mdapy.temperature mdapy.tool_function mdapy.visualize mdapy.void_distribution mdapy.voronoi_analysis mdapy.warren_cowley_parameter MultiSystem (class in mdapy.system)

N

N (mdapy.lattice_maker.LatticeMaker property) (mdapy.replicate.Replicate property) (mdapy.system.System property)

NearestNeighbor (class in mdapy.nearest_neighbor) Neighbor (class in mdapy.neighbor) neighbor_number (mdapy.system.System property) NEP (class in mdapy.potential)

P

PairDistribution (class in mdapy.pair_distribution) PerturbModel (class in mdapy.perturb_model) PigzFile (class in mdapy.pigz) plot() (mdapy.lindemann_parameter.LindemannParameter method) (mdapy.mean_squared_displacement.MeanSquaredDisplacement method) (mdapy.pair_distribution.PairDistribution method) (mdapy.potential.EAM method) (mdapy.spatial_binning.SpatialBinning method) (mdapy.warren_cowley_parameter.WarrenCowleyParameter method)

plot_embded_rho() (mdapy.potential.EAM method) plot_partial() (mdapy.pair_distribution.PairDistribution method) plot_phi_r() (mdapy.potential.EAM method) plot_rho_r() (mdapy.potential.EAM method) pltset() (in module mdapy.plotset) pltset_old() (in module mdapy.plotset) polyhedral_template_matching() (in module mdapy.main) PolyhedralTemplateMatching (class in mdapy.polyhedral_template_matching) pos (mdapy.system.System property) process_compression_target() (mdapy.pigz.PigzFile method)

Q

query_nearest_neighbors() (mdapy.nearest_neighbor.kdtree method) (mdapy.nearest_neighbor.NearestNeighbor method)

R

radiul_distribution_function() (in module mdapy.main) rc (mdapy.system.System property) read_cif() (mdapy.load_save_data.BuildSystem static method) read_data() (mdapy.load_save_data.BuildSystem static method) read_dump() (mdapy.load_save_data.BuildSystem static method) read_POSCAR() (mdapy.load_save_data.BuildSystem static method)

read_xyz() (mdapy.load_save_data.BuildSystem static method) Replicate (class in mdapy.replicate) replicate() (in module mdapy.main) (mdapy.system.System method) rgb_structure_type (mdapy.visualize.Visualize attribute) rgb_type (mdapy.visualize.Visualize attribute) rho (mdapy.system.System property)

S

save_file_cif() (in module mdapy.main) save_file_data() (in module mdapy.main) save_file_dump() (in module mdapy.main) save_file_gui() (in module mdapy.main) save_file_POSCAR() (in module mdapy.main) save_file_xyz() (in module mdapy.main) SaveFile (class in mdapy.load_save_data) select() (mdapy.system.System method) set_figure() (in module mdapy.plotset)

show_system_info() (in module mdapy.main) sort_verlet_by_distance() (mdapy.neighbor.Neighbor method) spatial_binning() (in module mdapy.main) (mdapy.system.System method) SpatialBinning (class in mdapy.spatial_binning) split_dump() (in module mdapy.tool_function) split_xyz() (in module mdapy.tool_function) steinhardt_bond_orientation() (in module mdapy.main) SteinhardtBondOrientation (class in mdapy.steinhardt_bond_orientation) System (class in mdapy.system)

T

timer() (in module mdapy.tool_function)

to_lammps_box() (mdapy.potential.LammpsPotential method)

U

update_data() (mdapy.system.System method)

update_pos() (mdapy.system.System method) update_vel() (mdapy.system.System method)

V

value2color() (in module mdapy.visualize) vel (mdapy.system.System property) verlet_list (mdapy.system.System property) vertices() (mdapy.create_polycrystalline.Cell method) Visualize (class in mdapy.visualize) void_analysis() (in module mdapy.main)

VoidDistribution (class in mdapy.void_distribution) vol (mdapy.lattice_maker.LatticeMaker property) (mdapy.system.System property) volume() (mdapy.create_polycrystalline.Cell method) voronoi_analysis() (in module mdapy.main) VoronoiAnalysis (class in mdapy.voronoi_analysis)

W

warren_cowley_parameter() (in module mdapy.main) WarrenCowleyParameter (class in mdapy.warren_cowley_parameter) whether_init_file() (in module mdapy.main) wrap_pos() (mdapy.system.System method) write_cif() (mdapy.lattice_maker.LatticeMaker method) (mdapy.load_save_data.SaveFile static method) (mdapy.replicate.Replicate method) (mdapy.system.System method) write_cp2k() (mdapy.load_save_data.SaveFile static method) (mdapy.system.System method) write_data() (mdapy.lattice_maker.LatticeMaker method) (mdapy.load_save_data.SaveFile static method) (mdapy.replicate.Replicate method) (mdapy.system.System method)

write_dump() (mdapy.lattice_maker.LatticeMaker method) (mdapy.load_save_data.SaveFile static method) (mdapy.replicate.Replicate method) (mdapy.system.System method) write_dumps() (mdapy.system.MultiSystem method) write_eam_alloy() (mdapy.potential.EAM method) write_file_trailer() (mdapy.pigz.PigzFile method) write_POSCAR() (mdapy.lattice_maker.LatticeMaker method) (mdapy.load_save_data.SaveFile static method) (mdapy.replicate.Replicate method) (mdapy.system.System method) write_xyz() (mdapy.lattice_maker.LatticeMaker method) (mdapy.load_save_data.SaveFile static method) (mdapy.replicate.Replicate method) (mdapy.system.System method)