mdapy

• mdapy package
  • Submodules
  • mdapy.ackland_jones_analysis module
    • AcklandJonesAnalysis
      • AcklandJonesAnalysis.compute()
  • mdapy.atomic_strain module
    • AtomicStrain
      • AtomicStrain.compute()
  • mdapy.box module
    • init_box()
  • mdapy.cell_opt module
  • mdapy.centro_symmetry_parameter module
    • CentroSymmetryParameter
      • CentroSymmetryParameter.compute()
  • mdapy.cluser_analysis module
    • ClusterAnalysis
      • ClusterAnalysis.compute()
      • ClusterAnalysis.get_size_of_cluster()
    • filter_by_type()
  • mdapy.common_neighbor_analysis module
    • CommonNeighborAnalysis
      • CommonNeighborAnalysis.compute()
  • mdapy.common_neighbor_parameter module
    • CommonNeighborParameter
      • CommonNeighborParameter.compute()
  • mdapy.create_polycrystalline module
    • Cell
      • Cell.cavity_radius()
      • Cell.face_areas()
      • Cell.face_vertices()
      • Cell.vertices()
      • Cell.volume()
    • Container
    • CreatePolycrystalline
      • CreatePolycrystalline.compute()
    • DeleteOverlap
      • DeleteOverlap.compute()
  • mdapy.dft2nepxyz module
    • DFT2NEPXYZ
    • LabeledSystem
      • LabeledSystem.get_data()
  • mdapy.eam_average module
    • EAMAverage
  • mdapy.eam_generate module
    • EAMGenerate
  • mdapy.entropy module
    • AtomicEntropy
      • AtomicEntropy.compute()
  • mdapy.identify_SFs_TBs module
    • IdentifySFTBinFCC
      • IdentifySFTBinFCC.compute()
  • mdapy.identify_diamond_structure module
    • IdentifyDiamondStructure
      • IdentifyDiamondStructure.compute()
  • mdapy.lattice_maker module
    • LatticeMaker
      • LatticeMaker.N
      • LatticeMaker.compute()
      • LatticeMaker.vol
      • LatticeMaker.write_POSCAR()
      • LatticeMaker.write_cif()
      • LatticeMaker.write_data()
      • LatticeMaker.write_dump()
      • LatticeMaker.write_xyz()
  • mdapy.lindemann_parameter module
    • LindemannParameter
      • LindemannParameter.compute()
      • LindemannParameter.plot()
  • mdapy.load_save_data module
    • BuildSystem
      • BuildSystem.fromarray()
      • BuildSystem.fromdata()
      • BuildSystem.fromfile()
      • BuildSystem.getformat()
      • BuildSystem.read_POSCAR()
      • BuildSystem.read_cif()
      • BuildSystem.read_data()
      • BuildSystem.read_dump()
      • BuildSystem.read_xyz()
    • SaveFile
      • SaveFile.write_POSCAR()
      • SaveFile.write_cif()
      • SaveFile.write_cp2k()
      • SaveFile.write_data()
      • SaveFile.write_dump()
      • SaveFile.write_xyz()
  • mdapy.main module
    • ackland_jones_analysis()
    • atomic_entropy()
    • atomic_temperature()
    • box2axis()
    • box2lines()
    • build_lattice()
    • build_polycrystal()
    • callback()
    • centro_symmetry_parameter()
    • cluster_analysis()
    • common_neighbor_analysis()
    • common_neighbor_parameter()
    • identify_SFs_TBs()
    • identify_species()
    • init_global_parameters()
    • load_file_gui()
    • loadfile()
    • main()
    • polyhedral_template_matching()
    • radiul_distribution_function()
    • replicate()
    • save_file_POSCAR()
    • save_file_cif()
    • save_file_data()
    • save_file_dump()
    • save_file_gui()
    • save_file_xyz()
    • show_system_info()
    • spatial_binning()
    • steinhardt_bond_orientation()
    • void_analysis()
    • voronoi_analysis()
    • warren_cowley_parameter()
    • whether_init_file()
  • mdapy.mean_squared_displacement module
    • MeanSquaredDisplacement
      • MeanSquaredDisplacement.compute()
      • MeanSquaredDisplacement.plot()
  • mdapy.minimizer module
    • Minimizer
      • Minimizer.compute()
  • mdapy.nearest_neighbor module
    • NearestNeighbor
      • NearestNeighbor.query_nearest_neighbors()
    • kdtree
      • kdtree.query_nearest_neighbors()
  • mdapy.neighbor module
    • Neighbor
      • Neighbor.compute()
      • Neighbor.sort_verlet_by_distance()
  • mdapy.orthogonal_box module
    • OrthogonalBox
      • OrthogonalBox.compute()
  • mdapy.pair_distribution module
    • PairDistribution
      • PairDistribution.compute()
      • PairDistribution.plot()
      • PairDistribution.plot_partial()
  • mdapy.perturb_model module
    • PerturbModel
      • PerturbModel.compute()
  • mdapy.phonon module
  • mdapy.pigz module
    • PigzFile
      • PigzFile.calculate_chunk_check()
      • PigzFile.clean_up()
      • PigzFile.process_compression_target()
      • PigzFile.write_file_trailer()
    • compress_file()
  • mdapy.plotset module
    • cm2inch()
    • pltset()
    • pltset_old()
    • set_figure()
  • mdapy.polyhedral_template_matching module
    • PolyhedralTemplateMatching
      • PolyhedralTemplateMatching.compute()
  • mdapy.potential module
    • BasePotential
      • BasePotential.compute()
    • EAM
      • EAM.compute()
      • EAM.plot()
      • EAM.plot_embded_rho()
      • EAM.plot_phi_r()
      • EAM.plot_rho_r()
      • EAM.write_eam_alloy()
    • EAMCalculator
      • EAMCalculator.compute()
    • LammpsPotential
      • LammpsPotential.compute()
      • LammpsPotential.to_lammps_box()
    • NEP
      • NEP.compute()
      • NEP.fps_sample()
      • NEP.get_descriptors()
  • mdapy.replicate module
    • Replicate
      • Replicate.N
      • Replicate.compute()
      • Replicate.write_POSCAR()
      • Replicate.write_cif()
      • Replicate.write_data()
      • Replicate.write_dump()
      • Replicate.write_xyz()
  • mdapy.spatial_binning module
    • SpatialBinning
      • SpatialBinning.compute()
      • SpatialBinning.plot()
  • mdapy.steinhardt_bond_orientation module
    • SteinhardtBondOrientation
      • SteinhardtBondOrientation.compute()
      • SteinhardtBondOrientation.identifySolidLiquid()
  • mdapy.system module
    • MultiSystem
      • MultiSystem.cal_lindemann_parameter()
      • MultiSystem.cal_mean_squared_displacement()
      • MultiSystem.write_dumps()
    • System
      • System.N
      • System.atom_distance()
      • System.atoms_colored_by()
      • System.boundary
      • System.box
      • System.build_neighbor()
      • System.cal_ackland_jones_analysis()
      • System.cal_atomic_entropy()
      • System.cal_atomic_strain()
      • System.cal_atomic_temperature()
      • System.cal_centro_symmetry_parameter()
      • System.cal_cluster_analysis()
      • System.cal_common_neighbor_analysis()
      • System.cal_common_neighbor_parameter()
      • System.cal_energy_force_virial()
      • System.cal_identify_SFs_TBs()
      • System.cal_identify_diamond_structure()
      • System.cal_pair_distribution()
      • System.cal_phono_dispersion()
      • System.cal_polyhedral_template_matching()
      • System.cal_species_number()
      • System.cal_steinhardt_bond_orientation()
      • System.cal_void_distribution()
      • System.cal_voronoi_volume()
      • System.cal_warren_cowley_parameter()
      • System.cell_opt()
      • System.change_filename()
      • System.data
      • System.display()
      • System.distance_list
      • System.filename
      • System.fmt
      • System.global_info
      • System.minimize()
      • System.neighbor_number
      • System.orthogonal_box()
      • System.pos
      • System.rc
      • System.replicate()
      • System.rho
      • System.select()
      • System.spatial_binning()
      • System.update_data()
      • System.update_pos()
      • System.update_vel()
      • System.vel
      • System.verlet_list
      • System.vol
      • System.wrap_pos()
      • System.write_POSCAR()
      • System.write_cif()
      • System.write_cp2k()
      • System.write_data()
      • System.write_dump()
      • System.write_xyz()
  • mdapy.temperature module
    • AtomicTemperature
      • AtomicTemperature.compute()
  • mdapy.tool_function module
    • atomic_numbers
    • run_cmd()
    • split_dump()
    • split_xyz()
    • timer()
  • mdapy.visualize module
    • Visualize
      • Visualize.atom_colored_by()
      • Visualize.atom_colored_by_atom_type()
      • Visualize.atom_colored_by_atom_type_name()
      • Visualize.atom_colored_by_structure_type()
      • Visualize.box2lines()
      • Visualize.close()
      • Visualize.delete_color_bar()
      • Visualize.display()
      • Visualize.hide_object_by_group_name()
      • Visualize.init_color()
      • Visualize.init_plot()
      • Visualize.init_radius()
      • Visualize.show_object_by_group_name()
    • value2color()
  • mdapy.void_distribution module
    • VoidDistribution
      • VoidDistribution.compute()
  • mdapy.voronoi_analysis module
    • VoronoiAnalysis
      • VoronoiAnalysis.compute()
  • mdapy.warren_cowley_parameter module
    • WarrenCowleyParameter
      • WarrenCowleyParameter.compute()
      • WarrenCowleyParameter.plot()
  • Module contents
    • init()