dpdata package

Subpackages

• dpdata.abacus package
  • Submodules
  • dpdata.abacus.md module
    • get_coord_dump_freq()
    • get_coords_from_dump()
    • get_energy()
    • get_frame()
    • get_path_out()
  • dpdata.abacus.relax module
    • get_coords_from_log()
    • get_frame()
    • get_log_file()
  • dpdata.abacus.scf module
    • CheckFile()
    • get_block()
    • get_cell()
    • get_coords()
    • get_energy()
    • get_force()
    • get_frame()
    • get_frame_from_stru()
    • get_geometry_in()
    • get_nele_from_stru()
    • get_path_out()
    • get_stress()
    • make_unlabeled_stru()
• dpdata.amber package
  • Submodules
  • dpdata.amber.mask module
    • load_param_file()
    • pick_by_amber_mask()
  • dpdata.amber.md module
    • read_amber_traj()
  • dpdata.amber.sqm module
    • make_sqm_in()
    • parse_sqm_out()
• dpdata.cp2k package
  • Submodules
  • dpdata.cp2k.cell module
    • cell_to_low_triangle()
  • dpdata.cp2k.output module
    • Cp2kSystems
      • Cp2kSystems.get_log_block_generator()
      • Cp2kSystems.get_xyz_block_generator()
      • Cp2kSystems.handle_single_log_frame()
      • Cp2kSystems.handle_single_xyz_frame()
    • get_frames()
• dpdata.deepmd package
  • Submodules
  • dpdata.deepmd.comp module
    • dump()
    • to_system_data()
  • dpdata.deepmd.hdf5 module
    • dump()
    • to_system_data()
  • dpdata.deepmd.mixed module
    • dump()
    • formula()
    • load_type()
    • mix_system()
    • split_system()
    • to_system_data()
  • dpdata.deepmd.raw module
    • dump()
    • load_type()
    • to_system_data()
• dpdata.fhi_aims package
  • Submodules
  • dpdata.fhi_aims.output module
    • analyze_block()
    • get_fhi_aims_block()
    • get_frames()
    • get_info()
• dpdata.gaussian package
  • Submodules
  • dpdata.gaussian.gjf module
    • detect_multiplicity()
    • make_gaussian_input()
  • dpdata.gaussian.log module
    • to_system_data()
• dpdata.gromacs package
  • Submodules
  • dpdata.gromacs.gro module
    • file_to_system_data()
    • from_system_data()
• dpdata.lammps package
  • Submodules
  • dpdata.lammps.dump module
    • UnwrapWarning
    • box2dumpbox()
    • dumpbox2box()
    • get_atype()
    • get_coordtype_and_scalefactor()
    • get_dumpbox()
    • get_natoms()
    • get_natoms_vec()
    • get_natomtypes()
    • load_file()
    • safe_get_posi()
    • split_traj()
    • system_data()
  • dpdata.lammps.lmp module
    • box2lmpbox()
    • from_system_data()
    • get_atoms()
    • get_atype()
    • get_lmpbox()
    • get_natoms()
    • get_natoms_vec()
    • get_natomtypes()
    • get_posi()
    • lmpbox2box()
    • system_data()
    • to_system_data()
• dpdata package
  • Subpackages
    • dpdata.abacus package
      • Submodules
      • dpdata.abacus.md module
      • dpdata.abacus.relax module
      • dpdata.abacus.scf module
    • dpdata.amber package
      • Submodules
      • dpdata.amber.mask module
      • dpdata.amber.md module
      • dpdata.amber.sqm module
    • dpdata.cp2k package
      • Submodules
      • dpdata.cp2k.cell module
      • dpdata.cp2k.output module
    • dpdata.deepmd package
      • Submodules
      • dpdata.deepmd.comp module
      • dpdata.deepmd.hdf5 module
      • dpdata.deepmd.mixed module
      • dpdata.deepmd.raw module
    • dpdata.fhi_aims package
      • Submodules
      • dpdata.fhi_aims.output module
    • dpdata.gaussian package
      • Submodules
      • dpdata.gaussian.gjf module
      • dpdata.gaussian.log module
    • dpdata.gromacs package
      • Submodules
      • dpdata.gromacs.gro module
    • dpdata.lammps package
      • Submodules
      • dpdata.lammps.dump module
      • dpdata.lammps.lmp module
    • dpdata.plugins package
      • Submodules
      • dpdata.plugins.3dmol module
      • dpdata.plugins.abacus module
      • dpdata.plugins.amber module
      • dpdata.plugins.ase module
      • dpdata.plugins.cp2k module
      • dpdata.plugins.deepmd module
      • dpdata.plugins.dftbplus module
      • dpdata.plugins.fhi_aims module
      • dpdata.plugins.gaussian module
      • dpdata.plugins.gromacs module
      • dpdata.plugins.lammps module
      • dpdata.plugins.list module
      • dpdata.plugins.pwmat module
      • dpdata.plugins.pymatgen module
      • dpdata.plugins.qe module
      • dpdata.plugins.rdkit module
      • dpdata.plugins.siesta module
      • dpdata.plugins.vasp module
      • dpdata.plugins.xyz module
    • dpdata.pwmat package
      • Submodules
      • dpdata.pwmat.atomconfig module
      • dpdata.pwmat.movement module
    • dpdata.pymatgen package
      • Submodules
      • dpdata.pymatgen.molecule module
    • dpdata.qe package
      • Submodules
      • dpdata.qe.scf module
      • dpdata.qe.traj module
    • dpdata.rdkit package
      • Submodules
      • dpdata.rdkit.sanitize module
      • dpdata.rdkit.utils module
    • dpdata.siesta package
      • Submodules
      • dpdata.siesta.aiMD_output module
      • dpdata.siesta.output module
    • dpdata.vasp package
      • Submodules
      • dpdata.vasp.outcar module
      • dpdata.vasp.poscar module
      • dpdata.vasp.xml module
    • dpdata.xyz package
      • Submodules
      • dpdata.xyz.quip_gap_xyz module
      • dpdata.xyz.xyz module
  • Submodules
  • dpdata.ase_calculator module
  • dpdata.bond_order_system module
  • dpdata.cli module
    • convert()
    • dpdata_cli()
    • dpdata_parser()
  • dpdata.driver module
    • Driver
      • Driver.ase_calculator
      • Driver.get_driver()
      • Driver.get_drivers()
      • Driver.label()
      • Driver.register()
    • HybridDriver
      • HybridDriver.label()
    • Minimizer
      • Minimizer.get_minimizer()
      • Minimizer.get_minimizers()
      • Minimizer.minimize()
      • Minimizer.register()
  • dpdata.format module
    • Format
      • Format.MultiMode
      • Format.MultiModes
      • Format.from_bond_order_system()
      • Format.from_labeled_system()
      • Format.from_multi_systems()
      • Format.from_system()
      • Format.get_formats()
      • Format.get_from_methods()
      • Format.get_to_methods()
      • Format.mix_system()
      • Format.post()
      • Format.register()
      • Format.register_from()
      • Format.register_to()
      • Format.to_bond_order_system()
      • Format.to_labeled_system()
      • Format.to_multi_systems()
      • Format.to_system()
  • dpdata.periodic_table module
    • Element
      • Element.X
      • Element.Z
      • Element.calculated_radius
      • Element.from_Z()
      • Element.mass
      • Element.name
      • Element.radius
  • dpdata.plugin module
    • Plugin
      • Plugin.get_plugin()
      • Plugin.register()
  • dpdata.stat module
    • Errors
      • Errors.SYSTEM_TYPE
      • Errors.e_errors
      • Errors.f_errors
    • ErrorsBase
      • ErrorsBase.SYSTEM_TYPE
      • ErrorsBase.e_errors
      • ErrorsBase.e_mae
      • ErrorsBase.e_rmse
      • ErrorsBase.f_errors
      • ErrorsBase.f_mae
      • ErrorsBase.f_rmse
    • MultiErrors
      • MultiErrors.SYSTEM_TYPE
      • MultiErrors.e_errors
      • MultiErrors.f_errors
    • mae()
    • rmse()
  • dpdata.system module
    • Axis
      • Axis.NATOMS
      • Axis.NBONDS
      • Axis.NFRAMES
      • Axis.NTYPES
    • DataError
    • DataType
      • DataType.check()
      • DataType.real_shape()
    • LabeledSystem
      • LabeledSystem.DTYPES
      • LabeledSystem.affine_map_fv()
      • LabeledSystem.correction()
      • LabeledSystem.from_3dmol()
      • LabeledSystem.from_abacus_lcao_md()
      • LabeledSystem.from_abacus_lcao_relax()
      • LabeledSystem.from_abacus_lcao_scf()
      • LabeledSystem.from_abacus_md()
      • LabeledSystem.from_abacus_pw_md()
      • LabeledSystem.from_abacus_pw_relax()
      • LabeledSystem.from_abacus_pw_scf()
      • LabeledSystem.from_abacus_relax()
      • LabeledSystem.from_abacus_scf()
      • LabeledSystem.from_abacus_stru()
      • LabeledSystem.from_amber_md()
      • LabeledSystem.from_ase_structure()
      • LabeledSystem.from_atomconfig()
      • LabeledSystem.from_contcar()
      • LabeledSystem.from_cp2k_aimd_output()
      • LabeledSystem.from_cp2k_output()
      • LabeledSystem.from_deepmd()
      • LabeledSystem.from_deepmd_comp()
      • LabeledSystem.from_deepmd_hdf5()
      • LabeledSystem.from_deepmd_npy()
      • LabeledSystem.from_deepmd_npy_mixed()
      • LabeledSystem.from_deepmd_raw()
      • LabeledSystem.from_dump()
      • LabeledSystem.from_fhi_aims_md()
      • LabeledSystem.from_fhi_aims_output()
      • LabeledSystem.from_fhi_aims_scf()
      • LabeledSystem.from_finalconfig()
      • LabeledSystem.from_fmt_obj()
      • LabeledSystem.from_gaussian_gjf()
      • LabeledSystem.from_gaussian_log()
      • LabeledSystem.from_gaussian_md()
      • LabeledSystem.from_gro()
      • LabeledSystem.from_gromacs_gro()
      • LabeledSystem.from_lammps_dump()
      • LabeledSystem.from_lammps_lmp()
      • LabeledSystem.from_list()
      • LabeledSystem.from_lmp()
      • LabeledSystem.from_mlmd()
      • LabeledSystem.from_mol()
      • LabeledSystem.from_mol_file()
      • LabeledSystem.from_movement()
      • LabeledSystem.from_outcar()
      • LabeledSystem.from_poscar()
      • LabeledSystem.from_pwmat_atomconfig()
      • LabeledSystem.from_pwmat_finalconfig()
      • LabeledSystem.from_pwmat_mlmd()
      • LabeledSystem.from_pwmat_movement()
      • LabeledSystem.from_pwmat_output()
      • LabeledSystem.from_pymatgen_computedstructureentry()
      • LabeledSystem.from_pymatgen_molecule()
      • LabeledSystem.from_pymatgen_structure()
      • LabeledSystem.from_qe_cp_traj()
      • LabeledSystem.from_qe_pw_scf()
      • LabeledSystem.from_quip_gap_xyz()
      • LabeledSystem.from_quip_gap_xyz_file()
      • LabeledSystem.from_sdf()
      • LabeledSystem.from_sdf_file()
      • LabeledSystem.from_siesta_aiMD_output()
      • LabeledSystem.from_siesta_aimd_output()
      • LabeledSystem.from_siesta_output()
      • LabeledSystem.from_sqm_in()
      • LabeledSystem.from_sqm_out()
      • LabeledSystem.from_stru()
      • LabeledSystem.from_vasp_contcar()
      • LabeledSystem.from_vasp_outcar()
      • LabeledSystem.from_vasp_poscar()
      • LabeledSystem.from_vasp_string()
      • LabeledSystem.from_vasp_xml()
      • LabeledSystem.from_xml()
      • LabeledSystem.from_xyz()
      • LabeledSystem.has_virial()
      • LabeledSystem.post_funcs
      • LabeledSystem.remove_outlier()
      • LabeledSystem.rot_frame_lower_triangular()
      • LabeledSystem.to_3dmol()
      • LabeledSystem.to_abacus_lcao_md()
      • LabeledSystem.to_abacus_lcao_relax()
      • LabeledSystem.to_abacus_lcao_scf()
      • LabeledSystem.to_abacus_md()
      • LabeledSystem.to_abacus_pw_md()
      • LabeledSystem.to_abacus_pw_relax()
      • LabeledSystem.to_abacus_pw_scf()
      • LabeledSystem.to_abacus_relax()
      • LabeledSystem.to_abacus_scf()
      • LabeledSystem.to_abacus_stru()
      • LabeledSystem.to_amber_md()
      • LabeledSystem.to_ase_structure()
      • LabeledSystem.to_atomconfig()
      • LabeledSystem.to_contcar()
      • LabeledSystem.to_cp2k_aimd_output()
      • LabeledSystem.to_cp2k_output()
      • LabeledSystem.to_deepmd()
      • LabeledSystem.to_deepmd_comp()
      • LabeledSystem.to_deepmd_hdf5()
      • LabeledSystem.to_deepmd_npy()
      • LabeledSystem.to_deepmd_npy_mixed()
      • LabeledSystem.to_deepmd_raw()
      • LabeledSystem.to_dump()
      • LabeledSystem.to_fhi_aims_md()
      • LabeledSystem.to_fhi_aims_output()
      • LabeledSystem.to_fhi_aims_scf()
      • LabeledSystem.to_finalconfig()
      • LabeledSystem.to_fmt_obj()
      • LabeledSystem.to_gaussian_gjf()
      • LabeledSystem.to_gaussian_log()
      • LabeledSystem.to_gaussian_md()
      • LabeledSystem.to_gro()
      • LabeledSystem.to_gromacs_gro()
      • LabeledSystem.to_lammps_dump()
      • LabeledSystem.to_lammps_lmp()
      • LabeledSystem.to_list()
      • LabeledSystem.to_lmp()
      • LabeledSystem.to_mlmd()
      • LabeledSystem.to_mol()
      • LabeledSystem.to_mol_file()
      • LabeledSystem.to_movement()
      • LabeledSystem.to_outcar()
      • LabeledSystem.to_poscar()
      • LabeledSystem.to_pwmat_atomconfig()
      • LabeledSystem.to_pwmat_finalconfig()
      • LabeledSystem.to_pwmat_mlmd()
      • LabeledSystem.to_pwmat_movement()
      • LabeledSystem.to_pwmat_output()
      • LabeledSystem.to_pymatgen_ComputedStructureEntry()
      • LabeledSystem.to_pymatgen_computedstructureentry()
      • LabeledSystem.to_pymatgen_molecule()
      • LabeledSystem.to_pymatgen_structure()
      • LabeledSystem.to_qe_cp_traj()
      • LabeledSystem.to_qe_pw_scf()
      • LabeledSystem.to_quip_gap_xyz()
      • LabeledSystem.to_quip_gap_xyz_file()
      • LabeledSystem.to_sdf()
      • LabeledSystem.to_sdf_file()
      • LabeledSystem.to_siesta_aimd_output()
      • LabeledSystem.to_siesta_output()
      • LabeledSystem.to_sqm_in()
      • LabeledSystem.to_sqm_out()
      • LabeledSystem.to_stru()
      • LabeledSystem.to_vasp_contcar()
      • LabeledSystem.to_vasp_outcar()
      • LabeledSystem.to_vasp_poscar()
      • LabeledSystem.to_vasp_string()
      • LabeledSystem.to_vasp_xml()
      • LabeledSystem.to_xml()
      • LabeledSystem.to_xyz()
    • MultiSystems
      • MultiSystems.append()
      • MultiSystems.check_atom_names()
      • MultiSystems.correction()
      • MultiSystems.from_3dmol()
      • MultiSystems.from_abacus_lcao_md()
      • MultiSystems.from_abacus_lcao_relax()
      • MultiSystems.from_abacus_lcao_scf()
      • MultiSystems.from_abacus_md()
      • MultiSystems.from_abacus_pw_md()
      • MultiSystems.from_abacus_pw_relax()
      • MultiSystems.from_abacus_pw_scf()
      • MultiSystems.from_abacus_relax()
      • MultiSystems.from_abacus_scf()
      • MultiSystems.from_abacus_stru()
      • MultiSystems.from_amber_md()
      • MultiSystems.from_ase_structure()
      • MultiSystems.from_atomconfig()
      • MultiSystems.from_contcar()
      • MultiSystems.from_cp2k_aimd_output()
      • MultiSystems.from_cp2k_output()
      • MultiSystems.from_deepmd()
      • MultiSystems.from_deepmd_comp()
      • MultiSystems.from_deepmd_hdf5()
      • MultiSystems.from_deepmd_npy()
      • MultiSystems.from_deepmd_npy_mixed()
      • MultiSystems.from_deepmd_raw()
      • MultiSystems.from_dir()
      • MultiSystems.from_dump()
      • MultiSystems.from_fhi_aims_md()
      • MultiSystems.from_fhi_aims_output()
      • MultiSystems.from_fhi_aims_scf()
      • MultiSystems.from_file()
      • MultiSystems.from_finalconfig()
      • MultiSystems.from_fmt_obj()
      • MultiSystems.from_gaussian_gjf()
      • MultiSystems.from_gaussian_log()
      • MultiSystems.from_gaussian_md()
      • MultiSystems.from_gro()
      • MultiSystems.from_gromacs_gro()
      • MultiSystems.from_lammps_dump()
      • MultiSystems.from_lammps_lmp()
      • MultiSystems.from_list()
      • MultiSystems.from_lmp()
      • MultiSystems.from_mlmd()
      • MultiSystems.from_mol()
      • MultiSystems.from_mol_file()
      • MultiSystems.from_movement()
      • MultiSystems.from_outcar()
      • MultiSystems.from_poscar()
      • MultiSystems.from_pwmat_atomconfig()
      • MultiSystems.from_pwmat_finalconfig()
      • MultiSystems.from_pwmat_mlmd()
      • MultiSystems.from_pwmat_movement()
      • MultiSystems.from_pwmat_output()
      • MultiSystems.from_pymatgen_computedstructureentry()
      • MultiSystems.from_pymatgen_molecule()
      • MultiSystems.from_pymatgen_structure()
      • MultiSystems.from_qe_cp_traj()
      • MultiSystems.from_qe_pw_scf()
      • MultiSystems.from_quip_gap_xyz()
      • MultiSystems.from_quip_gap_xyz_file()
      • MultiSystems.from_sdf()
      • MultiSystems.from_sdf_file()
      • MultiSystems.from_siesta_aiMD_output()
      • MultiSystems.from_siesta_aimd_output()
      • MultiSystems.from_siesta_output()
      • MultiSystems.from_sqm_in()
      • MultiSystems.from_sqm_out()
      • MultiSystems.from_stru()
      • MultiSystems.from_vasp_contcar()
      • MultiSystems.from_vasp_outcar()
      • MultiSystems.from_vasp_poscar()
      • MultiSystems.from_vasp_string()
      • MultiSystems.from_vasp_xml()
      • MultiSystems.from_xml()
      • MultiSystems.from_xyz()
      • MultiSystems.get_nframes()
      • MultiSystems.load_systems_from_file()
      • MultiSystems.minimize()
      • MultiSystems.pick_atom_idx()
      • MultiSystems.predict()
      • MultiSystems.to()
      • MultiSystems.to_3dmol()
      • MultiSystems.to_abacus_lcao_md()
      • MultiSystems.to_abacus_lcao_relax()
      • MultiSystems.to_abacus_lcao_scf()
      • MultiSystems.to_abacus_md()
      • MultiSystems.to_abacus_pw_md()
      • MultiSystems.to_abacus_pw_relax()
      • MultiSystems.to_abacus_pw_scf()
      • MultiSystems.to_abacus_relax()
      • MultiSystems.to_abacus_scf()
      • MultiSystems.to_abacus_stru()
      • MultiSystems.to_amber_md()
      • MultiSystems.to_ase_structure()
      • MultiSystems.to_atomconfig()
      • MultiSystems.to_contcar()
      • MultiSystems.to_cp2k_aimd_output()
      • MultiSystems.to_cp2k_output()
      • MultiSystems.to_deepmd()
      • MultiSystems.to_deepmd_comp()
      • MultiSystems.to_deepmd_hdf5()
      • MultiSystems.to_deepmd_npy()
      • MultiSystems.to_deepmd_npy_mixed()
      • MultiSystems.to_deepmd_raw()
      • MultiSystems.to_dump()
      • MultiSystems.to_fhi_aims_md()
      • MultiSystems.to_fhi_aims_output()
      • MultiSystems.to_fhi_aims_scf()
      • MultiSystems.to_finalconfig()
      • MultiSystems.to_fmt_obj()
      • MultiSystems.to_gaussian_gjf()
      • MultiSystems.to_gaussian_log()
      • MultiSystems.to_gaussian_md()
      • MultiSystems.to_gro()
      • MultiSystems.to_gromacs_gro()
      • MultiSystems.to_lammps_dump()
      • MultiSystems.to_lammps_lmp()
      • MultiSystems.to_list()
      • MultiSystems.to_lmp()
      • MultiSystems.to_mlmd()
      • MultiSystems.to_mol()
      • MultiSystems.to_mol_file()
      • MultiSystems.to_movement()
      • MultiSystems.to_outcar()
      • MultiSystems.to_poscar()
      • MultiSystems.to_pwmat_atomconfig()
      • MultiSystems.to_pwmat_finalconfig()
      • MultiSystems.to_pwmat_mlmd()
      • MultiSystems.to_pwmat_movement()
      • MultiSystems.to_pwmat_output()
      • MultiSystems.to_pymatgen_ComputedStructureEntry()
      • MultiSystems.to_pymatgen_computedstructureentry()
      • MultiSystems.to_pymatgen_molecule()
      • MultiSystems.to_pymatgen_structure()
      • MultiSystems.to_qe_cp_traj()
      • MultiSystems.to_qe_pw_scf()
      • MultiSystems.to_quip_gap_xyz()
      • MultiSystems.to_quip_gap_xyz_file()
      • MultiSystems.to_sdf()
      • MultiSystems.to_sdf_file()
      • MultiSystems.to_siesta_aimd_output()
      • MultiSystems.to_siesta_output()
      • MultiSystems.to_sqm_in()
      • MultiSystems.to_sqm_out()
      • MultiSystems.to_stru()
      • MultiSystems.to_vasp_contcar()
      • MultiSystems.to_vasp_outcar()
      • MultiSystems.to_vasp_poscar()
      • MultiSystems.to_vasp_string()
      • MultiSystems.to_vasp_xml()
      • MultiSystems.to_xml()
      • MultiSystems.to_xyz()
    • System
      • System.DTYPES
      • System.add_atom_names()
      • System.affine_map()
      • System.append()
      • System.apply_pbc()
      • System.apply_type_map()
      • System.as_dict()
      • System.check_data()
      • System.check_type_map()
      • System.convert_to_mixed_type()
      • System.copy()
      • System.dump()
      • System.extend()
      • System.formula
      • System.from_3dmol()
      • System.from_abacus_lcao_md()
      • System.from_abacus_lcao_relax()
      • System.from_abacus_lcao_scf()
      • System.from_abacus_md()
      • System.from_abacus_pw_md()
      • System.from_abacus_pw_relax()
      • System.from_abacus_pw_scf()
      • System.from_abacus_relax()
      • System.from_abacus_scf()
      • System.from_abacus_stru()
      • System.from_amber_md()
      • System.from_ase_structure()
      • System.from_atomconfig()
      • System.from_contcar()
      • System.from_cp2k_aimd_output()
      • System.from_cp2k_output()
      • System.from_deepmd()
      • System.from_deepmd_comp()
      • System.from_deepmd_hdf5()
      • System.from_deepmd_npy()
      • System.from_deepmd_npy_mixed()
      • System.from_deepmd_raw()
      • System.from_dump()
      • System.from_fhi_aims_md()
      • System.from_fhi_aims_output()
      • System.from_fhi_aims_scf()
      • System.from_finalconfig()
      • System.from_fmt()
      • System.from_fmt_obj()
      • System.from_gaussian_gjf()
      • System.from_gaussian_log()
      • System.from_gaussian_md()
      • System.from_gro()
      • System.from_gromacs_gro()
      • System.from_lammps_dump()
      • System.from_lammps_lmp()
      • System.from_list()
      • System.from_lmp()
      • System.from_mlmd()
      • System.from_mol()
      • System.from_mol_file()
      • System.from_movement()
      • System.from_outcar()
      • System.from_poscar()
      • System.from_pwmat_atomconfig()
      • System.from_pwmat_finalconfig()
      • System.from_pwmat_mlmd()
      • System.from_pwmat_movement()
      • System.from_pwmat_output()
      • System.from_pymatgen_computedstructureentry()
      • System.from_pymatgen_molecule()
      • System.from_pymatgen_structure()
      • System.from_qe_cp_traj()
      • System.from_qe_pw_scf()
      • System.from_quip_gap_xyz()
      • System.from_quip_gap_xyz_file()
      • System.from_sdf()
      • System.from_sdf_file()
      • System.from_siesta_aiMD_output()
      • System.from_siesta_aimd_output()
      • System.from_siesta_output()
      • System.from_sqm_in()
      • System.from_sqm_out()
      • System.from_stru()
      • System.from_vasp_contcar()
      • System.from_vasp_outcar()
      • System.from_vasp_poscar()
      • System.from_vasp_string()
      • System.from_vasp_xml()
      • System.from_xml()
      • System.from_xyz()
      • System.get_atom_names()
      • System.get_atom_numbs()
      • System.get_atom_types()
      • System.get_natoms()
      • System.get_nframes()
      • System.get_ntypes()
      • System.load()
      • System.map_atom_types()
      • System.minimize()
      • System.nopbc
      • System.perturb()
      • System.pick_atom_idx()
      • System.pick_by_amber_mask()
      • System.post_funcs
      • System.predict()
      • System.remove_atom_names()
      • System.remove_pbc()
      • System.replace()
      • System.replicate()
      • System.rot_frame_lower_triangular()
      • System.rot_lower_triangular()
      • System.shuffle()
      • System.sort_atom_names()
      • System.sort_atom_types()
      • System.sub_system()
      • System.to()
      • System.to_3dmol()
      • System.to_abacus_lcao_md()
      • System.to_abacus_lcao_relax()
      • System.to_abacus_lcao_scf()
      • System.to_abacus_md()
      • System.to_abacus_pw_md()
      • System.to_abacus_pw_relax()
      • System.to_abacus_pw_scf()
      • System.to_abacus_relax()
      • System.to_abacus_scf()
      • System.to_abacus_stru()
      • System.to_amber_md()
      • System.to_ase_structure()
      • System.to_atomconfig()
      • System.to_contcar()
      • System.to_cp2k_aimd_output()
      • System.to_cp2k_output()
      • System.to_deepmd()
      • System.to_deepmd_comp()
      • System.to_deepmd_hdf5()
      • System.to_deepmd_npy()
      • System.to_deepmd_npy_mixed()
      • System.to_deepmd_raw()
      • System.to_dump()
      • System.to_fhi_aims_md()
      • System.to_fhi_aims_output()
      • System.to_fhi_aims_scf()
      • System.to_finalconfig()
      • System.to_fmt_obj()
      • System.to_gaussian_gjf()
      • System.to_gaussian_log()
      • System.to_gaussian_md()
      • System.to_gro()
      • System.to_gromacs_gro()
      • System.to_lammps_dump()
      • System.to_lammps_lmp()
      • System.to_list()
      • System.to_lmp()
      • System.to_mlmd()
      • System.to_mol()
      • System.to_mol_file()
      • System.to_movement()
      • System.to_outcar()
      • System.to_poscar()
      • System.to_pwmat_atomconfig()
      • System.to_pwmat_finalconfig()
      • System.to_pwmat_mlmd()
      • System.to_pwmat_movement()
      • System.to_pwmat_output()
      • System.to_pymatgen_ComputedStructureEntry()
      • System.to_pymatgen_computedstructureentry()
      • System.to_pymatgen_molecule()
      • System.to_pymatgen_structure()
      • System.to_qe_cp_traj()
      • System.to_qe_pw_scf()
      • System.to_quip_gap_xyz()
      • System.to_quip_gap_xyz_file()
      • System.to_sdf()
      • System.to_sdf_file()
      • System.to_siesta_aimd_output()
      • System.to_siesta_output()
      • System.to_sqm_in()
      • System.to_sqm_out()
      • System.to_stru()
      • System.to_vasp_contcar()
      • System.to_vasp_outcar()
      • System.to_vasp_poscar()
      • System.to_vasp_string()
      • System.to_vasp_xml()
      • System.to_xml()
      • System.to_xyz()
      • System.uniq_formula
    • add_format_methods()
    • get_atom_perturb_vector()
    • get_cell_perturb_matrix()
    • get_cls_name()
    • load_format()
  • dpdata.unit module
    • Conversion
      • Conversion.set_value()
      • Conversion.value()
    • EnergyConversion
    • ForceConversion
    • LengthConversion
    • PressureConversion
    • check_unit()
  • dpdata.utils module
    • add_atom_names()
    • elements_index_map()
    • remove_pbc()
    • sort_atom_names()
    • uniq_atom_names()
• dpdata.plugins package
  • Submodules
  • dpdata.plugins.3dmol module
    • Py3DMolFormat
      • Py3DMolFormat.to_system()
  • dpdata.plugins.abacus module
    • AbacusMDFormat
      • AbacusMDFormat.from_labeled_system()
    • AbacusRelaxFormat
      • AbacusRelaxFormat.from_labeled_system()
    • AbacusSCFFormat
      • AbacusSCFFormat.from_labeled_system()
    • AbacusSTRUFormat
      • AbacusSTRUFormat.from_system()
      • AbacusSTRUFormat.to_system()
  • dpdata.plugins.amber module
    • AmberMDFormat
      • AmberMDFormat.from_labeled_system()
      • AmberMDFormat.from_system()
    • SQMDriver
      • SQMDriver.label()
    • SQMINFormat
      • SQMINFormat.to_system()
    • SQMMinimizer
      • SQMMinimizer.minimize()
    • SQMOutFormat
      • SQMOutFormat.from_labeled_system()
      • SQMOutFormat.from_system()
  • dpdata.plugins.ase module
    • ASEDriver
      • ASEDriver.label()
    • ASEMinimizer
      • ASEMinimizer.minimize()
    • ASEStructureFormat
      • ASEStructureFormat.from_labeled_system()
      • ASEStructureFormat.from_multi_systems()
      • ASEStructureFormat.from_system()
      • ASEStructureFormat.to_labeled_system()
      • ASEStructureFormat.to_system()
  • dpdata.plugins.cp2k module
    • CP2KAIMDOutputFormat
      • CP2KAIMDOutputFormat.from_labeled_system()
    • CP2KOutputFormat
      • CP2KOutputFormat.from_labeled_system()
  • dpdata.plugins.deepmd module
    • DPDriver
      • DPDriver.label()
    • DeePMDCompFormat
      • DeePMDCompFormat.MultiMode
      • DeePMDCompFormat.from_labeled_system()
      • DeePMDCompFormat.from_system()
      • DeePMDCompFormat.to_system()
    • DeePMDHDF5Format
      • DeePMDHDF5Format.from_labeled_system()
      • DeePMDHDF5Format.from_multi_systems()
      • DeePMDHDF5Format.from_system()
      • DeePMDHDF5Format.to_multi_systems()
      • DeePMDHDF5Format.to_system()
    • DeePMDMixedFormat
      • DeePMDMixedFormat.MultiMode
      • DeePMDMixedFormat.from_labeled_system_mix()
      • DeePMDMixedFormat.from_multi_systems()
      • DeePMDMixedFormat.from_system_mix()
      • DeePMDMixedFormat.mix_system()
      • DeePMDMixedFormat.to_system()
    • DeePMDRawFormat
      • DeePMDRawFormat.MultiMode
      • DeePMDRawFormat.from_labeled_system()
      • DeePMDRawFormat.from_system()
      • DeePMDRawFormat.to_system()
  • dpdata.plugins.dftbplus module
  • dpdata.plugins.fhi_aims module
    • FhiMDFormat
      • FhiMDFormat.from_labeled_system()
    • FhiSCFFormat
      • FhiSCFFormat.from_labeled_system()
  • dpdata.plugins.gaussian module
    • GaussiaGJFFormat
      • GaussiaGJFFormat.to_system()
    • GaussianDriver
      • GaussianDriver.label()
    • GaussianLogFormat
      • GaussianLogFormat.from_labeled_system()
    • GaussianMDFormat
      • GaussianMDFormat.from_labeled_system()
  • dpdata.plugins.gromacs module
    • GromacsGroFormat
      • GromacsGroFormat.from_system()
      • GromacsGroFormat.to_system()
  • dpdata.plugins.lammps module
    • LAMMPSDumpFormat
      • LAMMPSDumpFormat.from_system()
    • LAMMPSLmpFormat
      • LAMMPSLmpFormat.from_system()
      • LAMMPSLmpFormat.to_system()
  • dpdata.plugins.list module
    • ListFormat
      • ListFormat.to_system()
  • dpdata.plugins.pwmat module
    • PwmatAtomconfigFormat
      • PwmatAtomconfigFormat.from_system()
      • PwmatAtomconfigFormat.to_system()
    • PwmatOutputFormat
      • PwmatOutputFormat.from_labeled_system()
  • dpdata.plugins.pymatgen module
    • PyMatgenCSEFormat
      • PyMatgenCSEFormat.to_labeled_system()
    • PyMatgenMoleculeFormat
      • PyMatgenMoleculeFormat.from_system()
      • PyMatgenMoleculeFormat.to_system()
    • PyMatgenStructureFormat
      • PyMatgenStructureFormat.to_system()
  • dpdata.plugins.qe module
    • QECPPWSCFFormat
      • QECPPWSCFFormat.from_labeled_system()
    • QECPTrajFormat
      • QECPTrajFormat.from_labeled_system()
      • QECPTrajFormat.from_system()
  • dpdata.plugins.rdkit module
    • MolFormat
      • MolFormat.from_bond_order_system()
      • MolFormat.to_bond_order_system()
    • SdfFormat
      • SdfFormat.from_bond_order_system()
      • SdfFormat.to_bond_order_system()
  • dpdata.plugins.siesta module
    • SiestaAIMDOutputFormat
      • SiestaAIMDOutputFormat.from_labeled_system()
      • SiestaAIMDOutputFormat.from_system()
    • SiestaOutputFormat
      • SiestaOutputFormat.from_labeled_system()
      • SiestaOutputFormat.from_system()
  • dpdata.plugins.vasp module
    • VASPOutcarFormat
      • VASPOutcarFormat.from_labeled_system()
    • VASPPoscarFormat
      • VASPPoscarFormat.from_system()
      • VASPPoscarFormat.to_system()
    • VASPStringFormat
      • VASPStringFormat.to_system()
    • VASPXMLFormat
      • VASPXMLFormat.from_labeled_system()
  • dpdata.plugins.xyz module
    • QuipGapXYZFormat
      • QuipGapXYZFormat.from_labeled_system()
      • QuipGapXYZFormat.from_multi_systems()
    • XYZFormat
      • XYZFormat.from_system()
      • XYZFormat.to_system()
• dpdata.pwmat package
  • Submodules
  • dpdata.pwmat.atomconfig module
    • from_system_data()
    • to_system_data()
  • dpdata.pwmat.movement module
    • analyze_block()
    • get_frames()
    • get_movement_block()
    • system_info()
• dpdata.pymatgen package
  • Submodules
  • dpdata.pymatgen.molecule module
    • to_system_data()
• dpdata.qe package
  • Submodules
  • dpdata.qe.scf module
    • get_block()
    • get_cell()
    • get_coords()
    • get_energy()
    • get_force()
    • get_frame()
    • get_stress()
  • dpdata.qe.traj module
    • convert_celldm()
    • load_atom_names()
    • load_atom_types()
    • load_block()
    • load_cell_parameters()
    • load_celldm()
    • load_data()
    • load_energy()
    • load_key()
    • load_param_file()
    • to_system_data()
    • to_system_label()
• dpdata.rdkit package
  • Submodules
  • dpdata.rdkit.sanitize module
  • dpdata.rdkit.utils module
    • check_molecule_list()
    • check_same_atom()
    • check_same_molecule()
    • combine_molecules()
    • mol_to_system_data()
    • system_data_to_mol()
• dpdata.siesta package
  • Submodules
  • dpdata.siesta.aiMD_output module
    • covert_dimension()
    • extract_keyword()
    • get_aiMD_frame()
    • get_atom_name()
    • get_atom_numbs()
    • get_atom_types()
    • get_single_line_tail()
    • get_virial()
    • obtain_nframe()
  • dpdata.siesta.output module
    • extract_keyword()
    • get_atom_name()
    • get_atom_numbs()
    • get_atom_types()
    • get_single_line_tail()
    • get_virial()
    • obtain_frame()
• dpdata.vasp package
  • Submodules
  • dpdata.vasp.outcar module
    • analyze_block()
    • get_frames()
    • get_outcar_block()
    • system_info()
  • dpdata.vasp.poscar module
    • from_system_data()
    • to_system_data()
  • dpdata.vasp.xml module
    • analyze()
    • analyze_atominfo()
    • analyze_calculation()
    • check_name()
    • formulate_config()
    • get_varray()
• dpdata.xyz package
  • Submodules
  • dpdata.xyz.quip_gap_xyz module
    • QuipGapxyzSystems
      • QuipGapxyzSystems.get_block_generator()
      • QuipGapxyzSystems.handle_single_xyz_frame()
  • dpdata.xyz.xyz module
    • coord_to_xyz()
    • xyz_to_coord()

Submodules

dpdata.ase_calculator module

dpdata.bond_order_system module

dpdata.cli module

Command line interface for dpdata.

dpdata.cli.convert(*, from_file: str, from_format: str = 'auto', to_file: Optional[str] = None, to_format: Optional[str] = None, no_labeled: bool = False, multi: bool = False, type_map: Optional[list] = None, **kwargs)

Convert files from one format to another one.

Parameters:

from_filestr

read data from a file

from_formatstr

the format of from_file

to_filestr

dump data to a file

to_formatstr

the format of to_file

no_labeledbool

labels aren’t provided

multibool

the system contains multiple directories

type_maplist

type map

dpdata.cli.dpdata_cli()

dpdata cli.

Examples

$ dpdata -iposcar POSCAR -odeepmd/npy -O data -n

dpdata.cli.dpdata_parser() → ArgumentParser

Returns dpdata cli parser.

Returns:

argparse.ArgumentParser

dpdata cli parser

dpdata.driver module

Driver plugin system.

class dpdata.driver.Driver(*args, **kwargs)

Bases: ABC

The base class for a driver plugin. A driver can label a pure System to generate the LabeledSystem.

See also

dpdata.plugins.deepmd.DPDriver

an example of Driver

Attributes:

ase_calculator

Returns an ase calculator based on this driver.

Methods

get_driver(key)	Get a driver plugin.
get_drivers()	Get all driver plugins.
label(data)	Label a system data.
register(key)	Register a driver plugin.

property ase_calculator: ase.calculators.calculator.Calculator

Returns an ase calculator based on this driver.

static get_driver(key: str) → Driver

Get a driver plugin.

Parameters:

keystr

key of the plugin.

Returns:

Driver

the specific driver class

Raises:

RuntimeError

if the requested driver is not implemented

static get_drivers() → dict

Get all driver plugins.

Returns:

dict

dict for all driver plugisn

abstract label(data: dict) → dict

Label a system data. Returns new data with energy, forces, and virials.

Parameters:

datadict

data with coordinates and atom types

Returns:

dict

labeled data with energies and forces

static register(key: str) → Callable

Register a driver plugin. Used as decorators.

Parameters:

keystr

key of the plugin.

Returns:

Callable

decorator of a class

Examples

>>> @Driver.register("some_driver")
... class SomeDriver(Driver):
...     pass

class dpdata.driver.HybridDriver(drivers: List[Union[dict, Driver]])

Bases: Driver

Hybrid driver, with mixed drivers.

Parameters:

driverslist[dict, Driver]

list of drivers or drivers dict. For a dict, it should contain type as the name of the driver, and others are arguments of the driver.

Raises:

TypeError

The value of drivers is not a dict or Driver.

Examples

>>> driver = HybridDriver([
...     {"type": "sqm", "qm_theory": "DFTB3"},
...     {"type": "dp", "dp": "frozen_model.pb"},
... ])
This driver is the hybrid of SQM and DP.

Attributes:

ase_calculator

Returns an ase calculator based on this driver.

Methods

get_driver(key)	Get a driver plugin.
get_drivers()	Get all driver plugins.
label(data)	Label a system data.
register(key)	Register a driver plugin.

label(data: dict) → dict

Label a system data.

Energies and forces are the sum of those of each driver.

Parameters:

datadict

data with coordinates and atom types

Returns:

dict

labeled data with energies and forces

class dpdata.driver.Minimizer(*args, **kwargs)

Bases: ABC

The base class for a minimizer plugin. A minimizer can minimize geometry.

Methods

get_minimizer(key)	Get a minimizer plugin.
get_minimizers()	Get all minimizer plugins.
minimize(data)	Minimize the geometry.
register(key)	Register a minimizer plugin.

static get_minimizer(key: str) → Minimizer

Get a minimizer plugin.

Parameters:

keystr

key of the plugin.

Returns:

Minimizer

the specific minimizer class

Raises:

RuntimeError

if the requested minimizer is not implemented

static get_minimizers() → dict

Get all minimizer plugins.

Returns:

dict

dict for all minimizer plugisn

abstract minimize(data: dict) → dict

Minimize the geometry.

Parameters:

datadict

data with coordinates and atom types

Returns:

dict

labeled data with minimized coordinates, energies, and forces

static register(key: str) → Callable

Register a minimizer plugin. Used as decorators.

Parameters:

keystr

key of the plugin.

Returns:

Callable

decorator of a class

Examples

>>> @Minimizer.register("some_minimizer")
... class SomeMinimizer(Minimizer):
...     pass

dpdata.format module

Implement the format plugin system.

class dpdata.format.Format

Bases: ABC

Methods

MultiModes()	File mode for MultiSystems 0 (default): not implemented 1: every directory under the top-level directory is a system
from_multi_systems(directory, **kwargs)	MultiSystems.from
from_system(file_name, **kwargs)	System.from
mix_system(*system, type_map, **kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
register(key)	Register a virtual subclass of an ABC.
to_system(data, *args, **kwargs)	System.to

from_bond_order_system
from_labeled_system
get_formats
get_from_methods
get_to_methods
post
register_from
register_to
to_bond_order_system
to_labeled_system
to_multi_systems

MultiMode = 0

class MultiModes

Bases: object

File mode for MultiSystems 0 (default): not implemented 1: every directory under the top-level directory is a system

Directory = 1

NotImplemented = 0

from_bond_order_system(file_name, **kwargs)

from_labeled_system(file_name, **kwargs)

from_multi_systems(directory, **kwargs)

MultiSystems.from

Parameters:

directorystr

directory of system

Returns:

filenames: list[str]

list of filenames

from_system(file_name, **kwargs)

System.from

Parameters:

file_namestr

file name

Returns:

data: dict

system data

static get_formats()

static get_from_methods()

static get_to_methods()

mix_system(*system, type_map, **kwargs)

Mix the systems into mixed_type ones according to the unified given type_map.

Parameters:

*systemSystem

The systems to mix

type_maplist of str

Maps atom type to name

Returns:

mixed_systems: dict

dict of mixed system with key ‘atom_numbs’

static post(func_name)

static register(key)

Register a virtual subclass of an ABC.

Returns the subclass, to allow usage as a class decorator.

static register_from(key)

static register_to(key)

to_bond_order_system(data, rdkit_mol, *args, **kwargs)

to_labeled_system(data, *args, **kwargs)

to_multi_systems(formulas, directory, **kwargs)

to_system(data, *args, **kwargs)

System.to

Parameters:

datadict

system data

dpdata.periodic_table module

class dpdata.periodic_table.Element(symbol: str)

Bases: object

Attributes:

X

Z

calculated_radius

mass

name

radius

Methods

from_Z

property X

property Z

property calculated_radius

classmethod from_Z(Z)

property mass

property name

property radius

dpdata.plugin module

Base of plugin systems.

class dpdata.plugin.Plugin

Bases: object

A class to register plugins.

Examples

>>> Plugin = Register()
>>> @Plugin.register("xx")
    def xxx():
        pass
>>> print(Plugin.plugins['xx'])

Methods

register(key)

Register a plugin.

get_plugin

get_plugin(key)

register(key)

Register a plugin.

Parameters:

keystr

Key of the plugin.

dpdata.stat module

class dpdata.stat.Errors(system_1: object, system_2: object)

Bases: ErrorsBase

Compute errors (deviations) between two LabeledSystems.

Parameters:

system_1object

system 1

system_2object

system 2

Examples

Get errors between referenced system and predicted system:

>>> e = dpdata.stat.Errors(system_1, system_2)
>>> print("%.4f %.4f %.4f %.4f" % (e.e_mae, e.e_rmse, e.f_mae, e.f_rmse))

Attributes:

e_errors

Energy errors.

e_mae

Energy MAE.

e_rmse

Energy RMSE.

f_errors

Force errors.

f_mae

Force MAE.

f_rmse

Force RMSE.

Methods

SYSTEM_TYPE

alias of LabeledSystem

SYSTEM_TYPE

alias of LabeledSystem

property e_errors: ndarray

Energy errors.

property f_errors: ndarray

Force errors.

class dpdata.stat.ErrorsBase(system_1: object, system_2: object)

Bases: object

Compute errors (deviations) between two systems. The type of system is assigned by SYSTEM_TYPE.

Parameters:

system_1object

system 1

system_2object

system 2

Attributes:

e_errors

Energy errors.

e_mae

Energy MAE.

e_rmse

Energy RMSE.

f_errors

Force errors.

f_mae

Force MAE.

f_rmse

Force RMSE.

Methods

SYSTEM_TYPE

alias of object

SYSTEM_TYPE

alias of object

abstract property e_errors: ndarray

Energy errors.

property e_mae: float64

Energy MAE.

property e_rmse: float64

Energy RMSE.

abstract property f_errors: ndarray

Force errors.

property f_mae: float64

Force MAE.

property f_rmse: float64

Force RMSE.

class dpdata.stat.MultiErrors(system_1: object, system_2: object)

Bases: ErrorsBase

Compute errors (deviations) between two MultiSystems.

Parameters:

system_1object

system 1

system_2object

system 2

Examples

Get errors between referenced system and predicted system:

>>> e = dpdata.stat.MultiErrors(system_1, system_2)
>>> print("%.4f %.4f %.4f %.4f" % (e.e_mae, e.e_rmse, e.f_mae, e.f_rmse))

Attributes:

e_errors

Energy errors.

e_mae

Energy MAE.

e_rmse

Energy RMSE.

f_errors

Force errors.

f_mae

Force MAE.

f_rmse

Force RMSE.

Methods

SYSTEM_TYPE

alias of MultiSystems

SYSTEM_TYPE

alias of MultiSystems

property e_errors: ndarray

Energy errors.

property f_errors: ndarray

Force errors.

dpdata.stat.mae(errors: ndarray) → float64

Compute the mean absolute error (MAE).

Parameters:

errorsnp.ndarray

errors between two values

Returns:

np.float64

mean absolute error (MAE)

dpdata.stat.rmse(errors: ndarray) → float64

Compute the root mean squared error (RMSE).

Parameters:

errorsnp.ndarray

errors between two values

Returns:

np.float64

root mean squared error (RMSE)

dpdata.system module

class dpdata.system.Axis(value)

Bases: Enum

Data axis.

NATOMS = 'natoms'

NBONDS = 'nbonds'

NFRAMES = 'nframes'

NTYPES = 'ntypes'

exception dpdata.system.DataError

Bases: Exception

Data is not correct.

class dpdata.system.DataType(name: str, dtype: type, shape: Optional[Tuple[int, Axis]] = None, required: bool = True)

Bases: object

DataType represents a type of data, like coordinates, energies, etc.

Parameters:

namestr

name of data

dtypetype or tuple[type]

data type, e.g. np.ndarray

shapetuple[int], optional

shape of data. Used when data is list or np.ndarray. Use Axis to represents numbers

requiredbool, default=True

whether this data is required

Methods

check(system)	Check if a system has correct data of this type.
real_shape(system)	Returns expected real shape of a system.

check(system: System)

Check if a system has correct data of this type.

Parameters:

systemSystem

checked system

Raises:

DataError

type or shape of data is not correct

real_shape(system: System) → Tuple[int]

Returns expected real shape of a system.

class dpdata.system.LabeledSystem(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)

Bases: System

The labeled data System

For example, a labeled water system named d_example has two molecules (6 atoms) and nframes frames. The labels can be accessed by

• d_example[‘energies’] : a numpy array of size nframes

• d_example[‘forces’] : a numpy array of size nframes x 6 x 3

• d_example[‘virials’] : optional, a numpy array of size nframes x 3 x 3

It is noted that

• The order of frames stored in ‘energies’, ‘forces’ and ‘virials’ should be consistent with ‘atom_types’, ‘cells’ and ‘coords’.

• The order of atoms in every frame of ‘forces’ should be consistent with ‘coords’ and ‘atom_types’.

Parameters:

file_namestr

The file to load the system

fmtstr

Format of the file, supported formats are

• auto: infered from file_name’s extension

• vasp/xml: vasp xml

• vasp/outcar: vasp OUTCAR

• deepmd/raw: deepmd-kit raw

• deepmd/npy: deepmd-kit compressed format (numpy binary)

• qe/cp/traj: Quantum Espresso CP trajectory files. should have: file_name+’.in’, file_name+’.pos’, file_name+’.evp’ and file_name+’.for’

• qe/pw/scf: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing ‘out’ by ‘in’ from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename.

• siesta/output: siesta SCF output file

• siesta/aimd_output: siesta aimd output file

• gaussian/log: gaussian logs

• gaussian/md: gaussian ab initio molecular dynamics

• cp2k/output: cp2k output file

• cp2k/aimd_output: cp2k aimd output dir(contains pos.xyz and *.log file); optional restart=True if it is a cp2k restarted task.

• pwmat/movement: pwmat md output file

• pwmat/out.mlmd: pwmat scf output file

type_maplist of str

Maps atom type to name. The atom with type ii is mapped to type_map[ii]. If not provided the atom names are assigned to ‘Type_1’, ‘Type_2’, ‘Type_3’…

beginint

The beginning frame when loading MD trajectory.

stepint

The number of skipped frames when loading MD trajectory.

Attributes:

formula

Return the formula of this system, like C3H5O2

nopbc

uniq_formula

Return the uniq_formula of this system.

Methods

add_atom_names(atom_names)	Add atom_names that do not exist.
append(system)	Append a system to this system
apply_pbc()	Append periodic boundary condition
as_dict()	Returns data dict of System instance
check_data()	Check if data is correct.
check_type_map(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
convert_to_mixed_type([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
copy()	Returns a copy of the system.
correction(hl_sys)	Get energy and force correction between self and a high-level LabeledSystem.
dump(filename[, indent])	dump .json or .yaml file
extend(systems)	Extend a system list to this system
from_3dmol(file_name, **kwargs)	Read data from dpdata.plugins.3dmol.Py3DMolFormat format.
from_abacus_lcao_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_lcao_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_lcao_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_amber_md(file_name, **kwargs)	Read data from dpdata.plugins.amber.AmberMDFormat format.
from_ase_structure(file_name, **kwargs)	Read data from dpdata.plugins.ase.ASEStructureFormat format.
from_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_cp2k_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
from_cp2k_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.
from_deepmd(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_deepmd_comp(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_hdf5(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.
from_deepmd_npy(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_npy_mixed(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.
from_deepmd_raw(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_dict(d)	param d: Dict representation.
from_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_fhi_aims_md(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_output(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_scf(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.
from_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_gaussian_gjf(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.
from_gaussian_log(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianLogFormat format.
from_gaussian_md(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianMDFormat format.
from_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_gromacs_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_lammps_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_lammps_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_list(file_name, **kwargs)	Read data from dpdata.plugins.list.ListFormat format.
from_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_mol(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_mol_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_pwmat_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_output(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pymatgen_computedstructureentry(...)	Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
from_pymatgen_molecule(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
from_pymatgen_structure(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
from_qe_cp_traj(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPTrajFormat format.
from_qe_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPPWSCFFormat format.
from_quip_gap_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_quip_gap_xyz_file(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_sdf(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_sdf_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_siesta_aiMD_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaOutputFormat format.
from_sqm_in(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMINFormat format.
from_sqm_out(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMOutFormat format.
from_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_vasp_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_vasp_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_string(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPStringFormat format.
from_vasp_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.XYZFormat format.
get_atom_names()	Returns name of atoms
get_atom_numbs()	Returns number of atoms
get_atom_types()	Returns type of atoms
get_natoms()	Returns total number of atoms in the system
get_nframes()	Returns number of frames in the system
get_ntypes()	Returns total number of atom types in the system.
load(filename)	rebuild System obj.
map_atom_types([type_map])	Map the atom types of the system
minimize(*args, minimizer, **kwargs)	Minimize the geometry.
perturb(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
pick_atom_idx(idx[, nopbc])	Pick atom index
pick_by_amber_mask(param, maskstr[, ...])	Pick atoms by amber mask
predict(*args[, driver])	Predict energies and forces by a driver.
remove_atom_names(atom_names)	Remove atom names and all such atoms.
remove_outlier([threshold])	Remove outlier frames from the system.
remove_pbc([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
replicate(ncopy)	Replicate the each frame in the system in 3 dimensions.
shuffle()	Shuffle frames randomly.
sort_atom_names([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
sort_atom_types()	Sort atom types.
sub_system(f_idx)	Construct a subsystem from the system
to(fmt, *args, **kwargs)	Dump systems to the specific format.
to_3dmol(*args, **kwargs)	Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.
to_abacus_lcao_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_lcao_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_lcao_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_amber_md(*args, **kwargs)	Dump data to dpdata.plugins.amber.AmberMDFormat format.
to_ase_structure(*args, **kwargs)	Dump data to dpdata.plugins.ase.ASEStructureFormat format.
to_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_cp2k_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
to_cp2k_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.
to_deepmd(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_deepmd_comp(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_hdf5(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.
to_deepmd_npy(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_npy_mixed(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.
to_deepmd_raw(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_fhi_aims_md(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_output(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_scf(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.
to_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_gaussian_gjf(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.
to_gaussian_log(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.
to_gaussian_md(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.
to_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_gromacs_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_json()	Returns a json string representation of the MSONable object.
to_lammps_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_lammps_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_list(*args, **kwargs)	Dump data to dpdata.plugins.list.ListFormat format.
to_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_mol(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_mol_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_pwmat_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_output(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pymatgen_ComputedStructureEntry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_computedstructureentry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_molecule(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
to_pymatgen_structure(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
to_qe_cp_traj(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPTrajFormat format.
to_qe_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.
to_quip_gap_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_quip_gap_xyz_file(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_sdf(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_sdf_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_siesta_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
to_siesta_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.
to_sqm_in(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMINFormat format.
to_sqm_out(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMOutFormat format.
to_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_vasp_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_vasp_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_string(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPStringFormat format.
to_vasp_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.XYZFormat format.
unsafe_hash()	Returns an hash of the current object.
validate_monty(v)	pydantic Validator for MSONable pattern

affine_map
affine_map_fv
apply_type_map
from_fmt
from_fmt_obj
has_virial
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>)

affine_map_fv(trans, f_idx)

correction(hl_sys)

Get energy and force correction between self and a high-level LabeledSystem. The self’s coordinates will be kept, but energy and forces will be replaced by the correction between these two systems.

Note: The function will not check whether coordinates and elements of two systems are the same. The user should make sure by itself.

Parameters:

hl_sysLabeledSystem

high-level LabeledSystem

Returns:

corrected_sys: LabeledSystem

Corrected LabeledSystem

from_3dmol(file_name, **kwargs)

Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs)

Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs)

Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

from_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_fmt_obj(fmtobj, file_name, **kwargs)

from_gaussian_gjf(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs)

Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_pwmat_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.XYZFormat format.

has_virial()

post_funcs = <dpdata.plugin.Plugin object>

remove_outlier(threshold: float = 8.0) → LabeledSystem

Remove outlier frames from the system.

Remove the frames whose energies satisfy the condition

\[\frac{\left \| E - \bar{E} \right \|}{\sigma(E)} \geq \text{threshold}\]

where \(\bar{E}\) and \(\sigma(E)\) are the mean and standard deviation of the energies in the system.

Parameters:

thresholdfloat

The threshold of outlier detection. The default value is 8.0.

Returns:

LabeledSystem

The system without outlier frames.

References

[1]

Gao, X.; Ramezanghorbani, F.; Isayev, O.; Smith, J. S.; Roitberg, A. E. TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials. J. Chem. Inf. Model. 2020, 60, 3408-3415.

[2]

Zeng, J.; Tao, Y.; Giese, T. J.; York, D. M.. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. J. Comput. Chem. 2023, 19, 1261-1275.

rot_frame_lower_triangular(f_idx=0)

to_3dmol(*args, **kwargs)

Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.

to_abacus_lcao_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_lcao_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_lcao_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_amber_md(*args, **kwargs)

Dump data to dpdata.plugins.amber.AmberMDFormat format.

to_ase_structure(*args, **kwargs)

Dump data to dpdata.plugins.ase.ASEStructureFormat format.

to_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_fmt_obj(fmtobj, *args, **kwargs)

to_gaussian_gjf(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs)

Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_pwmat_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMOutFormat format.

to_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_vasp_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.XYZFormat format.

class dpdata.system.MultiSystems(*systems, type_map=None)

Bases: object

A set containing several systems.

Methods

append(*systems)	Append systems or MultiSystems to systems
check_atom_names(system)	Make atom_names in all systems equal, prevent inconsistent atom_types.
correction(hl_sys)	Get energy and force correction between self (assumed low-level) and a high-level MultiSystems.
from_3dmol(file_name, **kwargs)	Read data from dpdata.plugins.3dmol.Py3DMolFormat format.
from_abacus_lcao_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_lcao_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_lcao_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_amber_md(file_name, **kwargs)	Read data from dpdata.plugins.amber.AmberMDFormat format.
from_ase_structure(file_name, **kwargs)	Read data from dpdata.plugins.ase.ASEStructureFormat format.
from_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_cp2k_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
from_cp2k_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.
from_deepmd(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_deepmd_comp(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_hdf5(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.
from_deepmd_npy(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_npy_mixed(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.
from_deepmd_raw(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_fhi_aims_md(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_output(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_scf(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.
from_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_gaussian_gjf(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.
from_gaussian_log(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianLogFormat format.
from_gaussian_md(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianMDFormat format.
from_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_gromacs_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_lammps_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_lammps_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_list(file_name, **kwargs)	Read data from dpdata.plugins.list.ListFormat format.
from_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_mol(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_mol_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_pwmat_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_output(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pymatgen_computedstructureentry(...)	Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
from_pymatgen_molecule(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
from_pymatgen_structure(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
from_qe_cp_traj(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPTrajFormat format.
from_qe_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPPWSCFFormat format.
from_quip_gap_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_quip_gap_xyz_file(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_sdf(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_sdf_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_siesta_aiMD_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaOutputFormat format.
from_sqm_in(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMINFormat format.
from_sqm_out(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMOutFormat format.
from_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_vasp_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_vasp_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_string(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPStringFormat format.
from_vasp_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.XYZFormat format.
get_nframes()	Returns number of frames in all systems
minimize(*args, minimizer, **kwargs)	Minimize geometry by a minimizer.
pick_atom_idx(idx[, nopbc])	Pick atom index
predict(*args[, driver])	Predict energies and forces by a driver.
to(fmt, *args, **kwargs)	Dump systems to the specific format.
to_3dmol(*args, **kwargs)	Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.
to_abacus_lcao_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_lcao_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_lcao_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_amber_md(*args, **kwargs)	Dump data to dpdata.plugins.amber.AmberMDFormat format.
to_ase_structure(*args, **kwargs)	Dump data to dpdata.plugins.ase.ASEStructureFormat format.
to_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_cp2k_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
to_cp2k_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.
to_deepmd(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_deepmd_comp(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_hdf5(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.
to_deepmd_npy(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_npy_mixed(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.
to_deepmd_raw(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_fhi_aims_md(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_output(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_scf(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.
to_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_gaussian_gjf(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.
to_gaussian_log(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.
to_gaussian_md(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.
to_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_gromacs_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_lammps_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_lammps_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_list(*args, **kwargs)	Dump data to dpdata.plugins.list.ListFormat format.
to_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_mol(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_mol_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_pwmat_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_output(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pymatgen_ComputedStructureEntry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_computedstructureentry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_molecule(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
to_pymatgen_structure(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
to_qe_cp_traj(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPTrajFormat format.
to_qe_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.
to_quip_gap_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_quip_gap_xyz_file(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_sdf(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_sdf_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_siesta_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
to_siesta_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.
to_sqm_in(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMINFormat format.
to_sqm_out(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMOutFormat format.
to_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_vasp_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_vasp_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_string(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPStringFormat format.
to_vasp_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.XYZFormat format.

from_dir
from_file
from_fmt_obj
load_systems_from_file
to_fmt_obj

append(*systems)

Append systems or MultiSystems to systems

Parameters:

systemSystem

The system to append

check_atom_names(system)

Make atom_names in all systems equal, prevent inconsistent atom_types.

correction(hl_sys: MultiSystems)

Get energy and force correction between self (assumed low-level) and a high-level MultiSystems. The self’s coordinates will be kept, but energy and forces will be replaced by the correction between these two systems.

Parameters:

hl_sysMultiSystems

high-level MultiSystems

Returns:

corrected_sysMultiSystems

Corrected MultiSystems

Notes

This method will not check whether coordinates and elements of two systems are the same. The user should make sure by itself.

Examples

Get correction between a low-level system and a high-level system:

>>> low_level = dpdata.MultiSystems().from_deepmd_hdf5("low_level.hdf5")
>>> high_level = dpdata.MultiSystems().from_deepmd_hdf5("high_level.hdf5")
>>> corr = low_level.correction(high_lebel)
>>> corr.to_deepmd_hdf5("corr.hdf5")

from_3dmol(file_name, **kwargs)

Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs)

Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs)

Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

classmethod from_dir(dir_name, file_name, fmt='auto', type_map=None)

from_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

classmethod from_file(file_name, fmt, **kwargs)

from_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_fmt_obj(fmtobj, directory, labeled=True, **kwargs)

from_gaussian_gjf(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs)

Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_pwmat_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.XYZFormat format.

get_nframes()

Returns number of frames in all systems

load_systems_from_file(file_name=None, fmt=None, **kwargs)

minimize(*args: Any, minimizer: Union[str, Minimizer], **kwargs: Any) → MultiSystems

Minimize geometry by a minimizer.

Parameters:

*argsiterable

Arguments passing to the minimizer

minimizerstr or Minimizer

The assigned minimizer

**kwargsdict

Other arguments passing to the minimizer

Returns:

MultiSystems

A new labeled MultiSystems.

Examples

Minimize a system using ASE BFGS along with a DP driver: >>> from dpdata.driver import Driver >>> from ase.optimize import BFGS >>> driver = driver.get_driver(“dp”)(“some_model.pb”) >>> some_system.minimize(minimizer=”ase”, driver=driver, optimizer=BFGS, fmax=1e-5)

pick_atom_idx(idx, nopbc=None)

Pick atom index

Parameters:

idxint or list or slice

atom index

nopbcBoolen (default: None)

If nopbc is True or False, set nopbc

Returns:

new_sys: MultiSystems

new system

predict(*args: Any, driver='dp', **kwargs: Any) → MultiSystems

Predict energies and forces by a driver.

Parameters:

*argsiterable

Arguments passing to the driver

driverstr, default=dp

The assigned driver. For compatibility, default is dp

**kwargsdict

Other arguments passing to the driver

Returns:

MultiSystems

A new labeled MultiSystems.

to(fmt: str, *args, **kwargs) → MultiSystems

Dump systems to the specific format.

Parameters:

fmtstr

format

Returns:

MultiSystems

self

to_3dmol(*args, **kwargs)

Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.

to_abacus_lcao_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_lcao_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_lcao_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_amber_md(*args, **kwargs)

Dump data to dpdata.plugins.amber.AmberMDFormat format.

to_ase_structure(*args, **kwargs)

Dump data to dpdata.plugins.ase.ASEStructureFormat format.

to_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_fmt_obj(fmtobj, directory, *args, **kwargs)

to_gaussian_gjf(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs)

Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_pwmat_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMOutFormat format.

to_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_vasp_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.XYZFormat format.

class dpdata.system.System(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)

Bases: MSONable

The data System

A data System (a concept used by deepmd-kit) contains frames (e.g. produced by an MD simulation) that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one System.

For example, a water system named d_example has two molecules. The properties can be accessed by

• d_example[‘atom_numbs’] : [2, 4]

• d_example[‘atom_names’] : [‘O’, ‘H’]

• d_example[‘atom_types’] : [0, 1, 1, 0, 1, 1]

• d_example[‘orig’] : [0, 0, 0]

• d_example[‘cells’] : a numpy array of size nframes x 3 x 3

• d_example[‘coords’] : a numpy array of size nframes x natoms x 3

It is noted that

• The order of frames stored in ‘atom_types’, ‘cells’ and ‘coords’ should be consistent.

• The order of atoms in all frames of ‘atom_types’ and ‘coords’ should be consistent.

Restrictions:

• d_example[‘orig’] is always [0, 0, 0]

• d_example[‘cells’][ii] is always lower triangular (lammps cell tensor convention)

Attributes:

DTYPEStuple[DataType]

data types of this class

Methods

add_atom_names(atom_names)	Add atom_names that do not exist.
append(system)	Append a system to this system
apply_pbc()	Append periodic boundary condition
as_dict()	Returns data dict of System instance
check_data()	Check if data is correct.
check_type_map(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
convert_to_mixed_type([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
copy()	Returns a copy of the system.
dump(filename[, indent])	dump .json or .yaml file
extend(systems)	Extend a system list to this system
from_3dmol(file_name, **kwargs)	Read data from dpdata.plugins.3dmol.Py3DMolFormat format.
from_abacus_lcao_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_lcao_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_lcao_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_md(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusMDFormat format.
from_abacus_pw_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_relax(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.
from_abacus_scf(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSCFFormat format.
from_abacus_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_amber_md(file_name, **kwargs)	Read data from dpdata.plugins.amber.AmberMDFormat format.
from_ase_structure(file_name, **kwargs)	Read data from dpdata.plugins.ase.ASEStructureFormat format.
from_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_cp2k_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
from_cp2k_output(file_name, **kwargs)	Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.
from_deepmd(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_deepmd_comp(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_hdf5(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.
from_deepmd_npy(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.
from_deepmd_npy_mixed(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.
from_deepmd_raw(file_name, **kwargs)	Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.
from_dict(d)	param d: Dict representation.
from_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_fhi_aims_md(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_output(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.
from_fhi_aims_scf(file_name, **kwargs)	Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.
from_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_gaussian_gjf(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.
from_gaussian_log(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianLogFormat format.
from_gaussian_md(file_name, **kwargs)	Read data from dpdata.plugins.gaussian.GaussianMDFormat format.
from_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_gromacs_gro(file_name, **kwargs)	Read data from dpdata.plugins.gromacs.GromacsGroFormat format.
from_lammps_dump(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.
from_lammps_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_list(file_name, **kwargs)	Read data from dpdata.plugins.list.ListFormat format.
from_lmp(file_name, **kwargs)	Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.
from_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_mol(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_mol_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.MolFormat format.
from_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_pwmat_atomconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_finalconfig(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
from_pwmat_mlmd(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_movement(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pwmat_output(file_name, **kwargs)	Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.
from_pymatgen_computedstructureentry(...)	Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
from_pymatgen_molecule(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
from_pymatgen_structure(file_name, **kwargs)	Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
from_qe_cp_traj(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPTrajFormat format.
from_qe_pw_scf(file_name, **kwargs)	Read data from dpdata.plugins.qe.QECPPWSCFFormat format.
from_quip_gap_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_quip_gap_xyz_file(file_name, **kwargs)	Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.
from_sdf(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_sdf_file(file_name, **kwargs)	Read data from dpdata.plugins.rdkit.SdfFormat format.
from_siesta_aiMD_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_aimd_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
from_siesta_output(file_name, **kwargs)	Read data from dpdata.plugins.siesta.SiestaOutputFormat format.
from_sqm_in(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMINFormat format.
from_sqm_out(file_name, **kwargs)	Read data from dpdata.plugins.amber.SQMOutFormat format.
from_stru(file_name, **kwargs)	Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.
from_vasp_contcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_outcar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPOutcarFormat format.
from_vasp_poscar(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPPoscarFormat format.
from_vasp_string(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPStringFormat format.
from_vasp_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xml(file_name, **kwargs)	Read data from dpdata.plugins.vasp.VASPXMLFormat format.
from_xyz(file_name, **kwargs)	Read data from dpdata.plugins.xyz.XYZFormat format.
get_atom_names()	Returns name of atoms
get_atom_numbs()	Returns number of atoms
get_atom_types()	Returns type of atoms
get_natoms()	Returns total number of atoms in the system
get_nframes()	Returns number of frames in the system
get_ntypes()	Returns total number of atom types in the system.
load(filename)	rebuild System obj.
map_atom_types([type_map])	Map the atom types of the system
minimize(*args, minimizer, **kwargs)	Minimize the geometry.
perturb(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
pick_atom_idx(idx[, nopbc])	Pick atom index
pick_by_amber_mask(param, maskstr[, ...])	Pick atoms by amber mask
predict(*args[, driver])	Predict energies and forces by a driver.
remove_atom_names(atom_names)	Remove atom names and all such atoms.
remove_pbc([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
replicate(ncopy)	Replicate the each frame in the system in 3 dimensions.
shuffle()	Shuffle frames randomly.
sort_atom_names([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
sort_atom_types()	Sort atom types.
sub_system(f_idx)	Construct a subsystem from the system
to(fmt, *args, **kwargs)	Dump systems to the specific format.
to_3dmol(*args, **kwargs)	Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.
to_abacus_lcao_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_lcao_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_lcao_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_md(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusMDFormat format.
to_abacus_pw_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_relax(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.
to_abacus_scf(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.
to_abacus_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_amber_md(*args, **kwargs)	Dump data to dpdata.plugins.amber.AmberMDFormat format.
to_ase_structure(*args, **kwargs)	Dump data to dpdata.plugins.ase.ASEStructureFormat format.
to_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_cp2k_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.
to_cp2k_output(*args, **kwargs)	Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.
to_deepmd(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_deepmd_comp(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_hdf5(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.
to_deepmd_npy(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.
to_deepmd_npy_mixed(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.
to_deepmd_raw(*args, **kwargs)	Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.
to_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_fhi_aims_md(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_output(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.
to_fhi_aims_scf(*args, **kwargs)	Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.
to_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_gaussian_gjf(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.
to_gaussian_log(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.
to_gaussian_md(*args, **kwargs)	Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.
to_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_gromacs_gro(*args, **kwargs)	Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.
to_json()	Returns a json string representation of the MSONable object.
to_lammps_dump(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.
to_lammps_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_list(*args, **kwargs)	Dump data to dpdata.plugins.list.ListFormat format.
to_lmp(*args, **kwargs)	Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.
to_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_mol(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_mol_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.MolFormat format.
to_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_pwmat_atomconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_finalconfig(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.
to_pwmat_mlmd(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_movement(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pwmat_output(*args, **kwargs)	Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.
to_pymatgen_ComputedStructureEntry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_computedstructureentry(*args, ...)	Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.
to_pymatgen_molecule(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.
to_pymatgen_structure(*args, **kwargs)	Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.
to_qe_cp_traj(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPTrajFormat format.
to_qe_pw_scf(*args, **kwargs)	Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.
to_quip_gap_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_quip_gap_xyz_file(*args, **kwargs)	Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.
to_sdf(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_sdf_file(*args, **kwargs)	Dump data to dpdata.plugins.rdkit.SdfFormat format.
to_siesta_aimd_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.
to_siesta_output(*args, **kwargs)	Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.
to_sqm_in(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMINFormat format.
to_sqm_out(*args, **kwargs)	Dump data to dpdata.plugins.amber.SQMOutFormat format.
to_stru(*args, **kwargs)	Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.
to_vasp_contcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_outcar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.
to_vasp_poscar(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.
to_vasp_string(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPStringFormat format.
to_vasp_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xml(*args, **kwargs)	Dump data to dpdata.plugins.vasp.VASPXMLFormat format.
to_xyz(*args, **kwargs)	Dump data to dpdata.plugins.xyz.XYZFormat format.
unsafe_hash()	Returns an hash of the current object.
validate_monty(v)	pydantic Validator for MSONable pattern

affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>)

add_atom_names(atom_names)

Add atom_names that do not exist.

affine_map(trans, f_idx=0)

append(system)

Append a system to this system

Parameters:

systemSystem

The system to append

apply_pbc()

Append periodic boundary condition

apply_type_map(type_map)

as_dict()

Returns data dict of System instance

check_data()

Check if data is correct.

Raises:

DataError

if data is not correct

check_type_map(type_map)

Assign atom_names to type_map if type_map is given and different from atom_names.

Parameters:

type_maplist

type_map

convert_to_mixed_type(type_map=None)

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms. Change the ‘atom_names’ to one placeholder type ‘MIXED_TOKEN’ and add ‘real_atom_types’ to store the real type vectors according to the given type_map.

Parameters:

type_maplist

type_map

copy()

Returns a copy of the system.

dump(filename, indent=4)

dump .json or .yaml file

extend(systems)

Extend a system list to this system

Parameters:

systems[System1, System2, System3 ]

The list to extend

property formula

Return the formula of this system, like C3H5O2

from_3dmol(file_name, **kwargs)

Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs)

Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs)

Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs)

Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs)

Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs)

Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

from_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_fmt(file_name, fmt='auto', **kwargs)

from_fmt_obj(fmtobj, file_name, **kwargs)

from_gaussian_gjf(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs)

Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs)

Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs)

Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs)

Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_pwmat_atomconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_finalconfig(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_pwmat_mlmd(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs)

Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs)

Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs)

Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs)

Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs)

Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs)

Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs)

Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs)

Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs)

Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs)

Read data from dpdata.plugins.xyz.XYZFormat format.

get_atom_names()

Returns name of atoms

get_atom_numbs()

Returns number of atoms

get_atom_types()

Returns type of atoms

get_natoms()

Returns total number of atoms in the system

get_nframes()

Returns number of frames in the system

get_ntypes() → int

Returns total number of atom types in the system.

static load(filename)

rebuild System obj. from .json or .yaml file

map_atom_types(type_map=None) → ndarray

Map the atom types of the system

Parameters:

type_map

dict : {“H”:0,”O”:1} or list [“H”,”C”,”O”,”N”] The map between elements and index if no map_dict is given, index will be set according to atomic number

Returns:

new_atom_typesnp.ndarray

The mapped atom types

minimize(*args: Any, minimizer: Union[str, Minimizer], **kwargs: Any) → LabeledSystem

Minimize the geometry.

Parameters:

*argsiterable

Arguments passing to the minimizer

minimizerstr or Minimizer

The assigned minimizer

**kwargsdict

Other arguments passing to the minimizer

Returns:

labeled_sysLabeledSystem

A new labeled system.

property nopbc

perturb(pert_num, cell_pert_fraction, atom_pert_distance, atom_pert_style='normal')

Perturb each frame in the system randomly. The cell will be deformed randomly, and atoms will be displaced by a random distance in random direction.

Parameters:

pert_numint

Each frame in the system will make pert_num copies, and all the copies will be perturbed. That means the system to be returned will contain pert_num * frame_num of the input system.

cell_pert_fractionfloat

A fraction determines how much (relatively) will cell deform. The cell of each frame is deformed by a symmetric matrix perturbed from identity. The perturbation to the diagonal part is subject to a uniform distribution in [-cell_pert_fraction, cell_pert_fraction), and the perturbation to the off-diagonal part is subject to a uniform distribution in [-0.5*cell_pert_fraction, 0.5*cell_pert_fraction).

atom_pert_distancefloat

unit: Angstrom. A distance determines how far atoms will move. Atoms will move about atom_pert_distance in random direction. The distribution of the distance atoms move is determined by atom_pert_style

atom_pert_stylestr

Determines the distribution of the distance atoms move is subject to. Avaliable options are

• ‘normal’: the distance will be object to chi-square distribution with 3 degrees of freedom after normalization.

  The mean value of the distance is atom_pert_fraction*side_length

• ‘uniform’: will generate uniformly random points in a 3D-balls with radius as atom_pert_distance.

  These points are treated as vector used by atoms to move. Obviously, the max length of the distance atoms move is atom_pert_distance.

• ‘const’: The distance atoms move will be a constant atom_pert_distance.

Returns:

perturbed_systemSystem

The perturbed_system. It contains pert_num * frame_num of the input system frames.

pick_atom_idx(idx, nopbc=None)

Pick atom index

Parameters:

idxint or list or slice

atom index

nopbcBoolen (default: None)

If nopbc is True or False, set nopbc

Returns:

new_sys: System

new system

pick_by_amber_mask(param, maskstr, pass_coords=False, nopbc=None)

Pick atoms by amber mask

Parameters:

paramstr or parmed.Structure

filename of Amber param file or parmed.Structure

maskstrstr

Amber masks

pass_coordsBoolen (default: False)

If pass_coords is true, the function will pass coordinates and return a MultiSystem. Otherwise, the result is coordinate-independent, and the function will return System or LabeledSystem.

nopbcBoolen (default: None)

If nopbc is True or False, set nopbc

post_funcs = <dpdata.plugin.Plugin object>

predict(*args: Any, driver: str = 'dp', **kwargs: Any) → LabeledSystem

Predict energies and forces by a driver.

Parameters:

*argsiterable

Arguments passing to the driver

driverstr, default=dp

The assigned driver. For compatibility, default is dp

**kwargsdict

Other arguments passing to the driver

Returns:

labeled_sysLabeledSystem

A new labeled system.

Examples

The default driver is DP: >>> labeled_sys = ori_sys.predict(“frozen_model_compressed.pb”)

remove_atom_names(atom_names)

Remove atom names and all such atoms. For example, you may not remove EP atoms in TIP4P/Ew water, which is not a real atom.

remove_pbc(protect_layer=9)

This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.

Parameters:

protect_layerthe protect layer between the atoms and the cell

boundary

replace(initial_atom_type, end_atom_type, replace_num)

replicate(ncopy)

Replicate the each frame in the system in 3 dimensions. Each frame in the system will become a supercell.

Parameters:

ncopy

list: [4,2,3] or tuple: (4,2,3,) make ncopy[0] copys in x dimensions, make ncopy[1] copys in y dimensions, make ncopy[2] copys in z dimensions.

Returns:

tmpSystem

The system after replication.

rot_frame_lower_triangular(f_idx=0)

rot_lower_triangular()

shuffle()

Shuffle frames randomly.

sort_atom_names(type_map=None)

Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names. If type_map is not given, atom_names will be sorted by alphabetical order. If type_map is given, atom_names will be type_map.

Parameters:

type_maplist

type_map

sort_atom_types() → ndarray

Sort atom types.

Returns:

idxnp.ndarray

new atom index in the Axis.NATOMS

sub_system(f_idx)

Construct a subsystem from the system

Parameters:

f_idxint or index

Which frame to use in the subsystem

Returns:

sub_systemSystem

The subsystem

to(fmt: str, *args, **kwargs) → System

Dump systems to the specific format.

Parameters:

fmtstr

format

Returns:

System

self

to_3dmol(*args, **kwargs)

Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.

to_abacus_lcao_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_lcao_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_lcao_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_md(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_relax(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_scf(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_amber_md(*args, **kwargs)

Dump data to dpdata.plugins.amber.AmberMDFormat format.

to_ase_structure(*args, **kwargs)

Dump data to dpdata.plugins.ase.ASEStructureFormat format.

to_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs)

Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs)

Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs)

Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_fmt_obj(fmtobj, *args, **kwargs)

to_gaussian_gjf(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs)

Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs)

Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs)

Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs)

Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_pwmat_atomconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs)

Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs)

Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs)

Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs)

Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs)

Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs)

Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs)

Dump data to dpdata.plugins.amber.SQMOutFormat format.

to_stru(*args, **kwargs)

Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_vasp_contcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs)

Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs)

Dump data to dpdata.plugins.xyz.XYZFormat format.

property uniq_formula

Return the uniq_formula of this system. The uniq_formula sort the elements in formula by names. Systems with the same uniq_formula can be append together.

dpdata.system.add_format_methods()

Add format methods to System, LabeledSystem, and MultiSystems.

Notes

Ensure all plugins have been loaded before execuating this function!

dpdata.system.get_atom_perturb_vector(atom_pert_distance, atom_pert_style='normal')

dpdata.system.get_cell_perturb_matrix(cell_pert_fraction)

dpdata.system.get_cls_name(cls: object) → str

Returns the fully qualified name of a class, such as np.ndarray.

Parameters:

clsobject

the class

Returns:

str

the fully qualified name of a class

dpdata.system.load_format(fmt)

dpdata.unit module

class dpdata.unit.Conversion(unitA, unitB, check=True)

Bases: ABC

Methods

set_value
value

set_value(value)

value<