Index

A

AbacusMDFormat (class in dpdata.plugins.abacus) AbacusRelaxFormat (class in dpdata.plugins.abacus) AbacusSCFFormat (class in dpdata.plugins.abacus) AbacusSTRUFormat (class in dpdata.plugins.abacus) add_atom_names() (dpdata.System method) (dpdata.system.System method) (in module dpdata.utils) add_format_methods() (in module dpdata.system) affine_map() (dpdata.System method) (dpdata.system.System method) affine_map_fv() (dpdata.LabeledSystem method) (dpdata.system.LabeledSystem method) AmberMDFormat (class in dpdata.plugins.amber) analyze() (in module dpdata.vasp.xml) analyze_atominfo() (in module dpdata.vasp.xml) analyze_block() (in module dpdata.fhi_aims.output) (in module dpdata.pwmat.movement) (in module dpdata.vasp.outcar) analyze_calculation() (in module dpdata.vasp.xml)

AnyInt (class in dpdata.data_type) append() (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) apply_pbc() (dpdata.System method) (dpdata.system.System method) (in module dpdata.md.pbc) apply_type_map() (dpdata.System method) (dpdata.system.System method) as_dict() (dpdata.System method) (dpdata.system.System method) ase_calculator (dpdata.driver.Driver property) ASEDriver (class in dpdata.plugins.ase) ASEMinimizer (class in dpdata.plugins.ase) ASEStructureFormat (class in dpdata.plugins.ase) ASETrajFormat (class in dpdata.plugins.ase) assign_formal_charge_for_atom() (in module dpdata.rdkit.sanitize) Axis (class in dpdata.data_type)

B

BondOrderSystem (class in dpdata) (class in dpdata.bond_order_system)

box2dumpbox() (in module dpdata.lammps.dump) box2lmpbox() (in module dpdata.lammps.lmp)

C

calculated_radius (dpdata.periodic_table.Element property) cell_to_low_triangle() (in module dpdata.cp2k.cell) check() (dpdata.data_type.DataType method) check_atom_names() (dpdata.MultiSystems method) (dpdata.system.MultiSystems method) check_data() (dpdata.System method) (dpdata.system.System method) check_molecule_list() (in module dpdata.rdkit.utils) check_name() (in module dpdata.vasp.xml) check_same_atom() (in module dpdata.rdkit.utils) check_same_molecule() (in module dpdata.rdkit.utils) check_type_map() (dpdata.System method) (dpdata.system.System method) check_unit() (in module dpdata.unit) CheckFile() (in module dpdata.abacus.scf) collect_force() (in module dpdata.abacus.scf) collect_stress() (in module dpdata.abacus.scf) combine_molecules() (in module dpdata.rdkit.utils) compute_bonds() (in module dpdata.md.water) compute_bonds_ase() (in module dpdata.md.water) compute_bonds_naive() (in module dpdata.md.water)

compute_rdf() (in module dpdata.md.rdf) contain_hetero_aromatic() (in module dpdata.rdkit.sanitize) Conversion (class in dpdata.unit) convert() (in module dpdata.cli) convert_by_obabel() (in module dpdata.rdkit.sanitize) convert_celldm() (in module dpdata.qe.traj) convert_to_mixed_type() (dpdata.System method) (dpdata.system.System method) coord_to_xyz() (in module dpdata.xyz.xyz) copy() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) (dpdata.System method) (dpdata.system.System method) correction() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) covert_dimension() (in module dpdata.siesta.aiMD_output) CP2KAIMDOutputFormat (class in dpdata.plugins.cp2k) CP2KOutputFormat (class in dpdata.plugins.cp2k) Cp2kSystems (class in dpdata.cp2k.output)

D

DataError DataType (class in dpdata.data_type) DeePMDCompFormat (class in dpdata.plugins.deepmd) DeePMDHDF5Format (class in dpdata.plugins.deepmd) DeePMDMixedFormat (class in dpdata.plugins.deepmd) DeePMDRawFormat (class in dpdata.plugins.deepmd) detect_multiplicity() (in module dpdata.gaussian.gjf) DFTBplusFormat (class in dpdata.plugins.dftbplus) dir_coord() (in module dpdata.md.pbc) Directory (dpdata.format.Format.MultiModes attribute) dpdata module dpdata.abacus module dpdata.abacus.md module dpdata.abacus.relax module dpdata.abacus.scf module dpdata.abacus.stru module dpdata.amber module dpdata.amber.mask module dpdata.amber.md module dpdata.amber.sqm module dpdata.bond_order_system module dpdata.cli module dpdata.cp2k module dpdata.cp2k.cell module dpdata.cp2k.output module dpdata.data_type module dpdata.deepmd module dpdata.deepmd.comp module dpdata.deepmd.hdf5 module dpdata.deepmd.mixed module dpdata.deepmd.raw module dpdata.dftbplus module dpdata.dftbplus.output module dpdata.driver module dpdata.fhi_aims module dpdata.fhi_aims.output module dpdata.format module dpdata.gaussian module dpdata.gaussian.gjf module dpdata.gaussian.log module dpdata.gromacs module dpdata.gromacs.gro module dpdata.lammps module dpdata.lammps.dump module dpdata.lammps.lmp module dpdata.md module dpdata.md.msd module dpdata.md.pbc module dpdata.md.rdf module dpdata.md.water module dpdata.openmx module dpdata.openmx.omx module dpdata.orca module dpdata.orca.output module dpdata.periodic_table module dpdata.plugin module dpdata.plugins module 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.n2p2 module dpdata.plugins.openmx module dpdata.plugins.orca module dpdata.plugins.psi4 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.psi4 module dpdata.psi4.input module dpdata.psi4.output module dpdata.pwmat module dpdata.pwmat.atomconfig module dpdata.pwmat.movement module dpdata.pymatgen module dpdata.pymatgen.molecule module dpdata.pymatgen.structure module dpdata.qe module dpdata.qe.scf module dpdata.qe.traj module dpdata.rdkit module dpdata.rdkit.sanitize module dpdata.rdkit.utils module dpdata.siesta module dpdata.siesta.aiMD_output module dpdata.siesta.output module dpdata.stat module dpdata.system module dpdata.unit module dpdata.utils module dpdata.vasp module dpdata.vasp.outcar module dpdata.vasp.poscar module dpdata.vasp.xml module dpdata.xyz module dpdata.xyz.quip_gap_xyz module dpdata.xyz.xyz module dpdata_cli() (in module dpdata.cli) dpdata_parser() (in module dpdata.cli) DPDriver (class in dpdata.plugins.deepmd) Driver (class in dpdata.driver) DTYPES (dpdata.bond_order_system.BondOrderSystem attribute) (dpdata.BondOrderSystem attribute) (dpdata.LabeledSystem attribute) (dpdata.System attribute) (dpdata.system.LabeledSystem attribute) (dpdata.system.System attribute) dump() (dpdata.System method) (dpdata.system.System method) (in module dpdata.deepmd.comp) (in module dpdata.deepmd.hdf5) (in module dpdata.deepmd.mixed) (in module dpdata.deepmd.raw) dumpbox2box() (in module dpdata.lammps.dump)

E

e_errors (dpdata.stat.Errors property) (dpdata.stat.ErrorsBase property) (dpdata.stat.MultiErrors property) e_mae (dpdata.stat.ErrorsBase property) e_rmse (dpdata.stat.ErrorsBase property) Element (class in dpdata.periodic_table) elements_index_map() (in module dpdata.utils)

EnergyConversion (class in dpdata.unit) Errors (class in dpdata.stat) ErrorsBase (class in dpdata.stat) extend() (dpdata.System method) (dpdata.system.System method) extract_keyword() (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output)

F

f_errors (dpdata.stat.Errors property) (dpdata.stat.ErrorsBase property) (dpdata.stat.MultiErrors property) f_mae (dpdata.stat.ErrorsBase property) f_rmse (dpdata.stat.ErrorsBase property) FhiMDFormat (class in dpdata.plugins.fhi_aims) FhiSCFFormat (class in dpdata.plugins.fhi_aims) file_to_system_data() (in module dpdata.gromacs.gro) find_ions() (in module dpdata.md.water) ForceConversion (class in dpdata.unit) Format (class in dpdata.format) Format.MultiModes (class in dpdata.format) formula (dpdata.System property) (dpdata.system.System property) formula_hash (dpdata.System property) (dpdata.system.System property) formulate_config() (in module dpdata.vasp.xml) from_3dmol() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_lcao_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_lcao_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_lcao_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_pw_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_pw_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_pw_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_abacus_stru() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_amber_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_ase_structure() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_ase_traj() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_atomconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_bond_order_system() (dpdata.format.Format method) (dpdata.plugins.rdkit.MolFormat method) (dpdata.plugins.rdkit.SdfFormat method) from_contcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_cp2k_aimd_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_cp2k_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd_comp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd_hdf5() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd_npy() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd_npy_mixed() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_deepmd_raw() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_dftbplus() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_dict() (dpdata.System class method) (dpdata.system.System class method) from_dir() (dpdata.MultiSystems class method) (dpdata.system.MultiSystems class method) from_dump() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_fhi_aims_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_fhi_aims_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_fhi_aims_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_file() (dpdata.MultiSystems class method) (dpdata.system.MultiSystems class method) from_finalconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_fmt() (dpdata.System method) (dpdata.system.System method) from_fmt_obj() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_gaussian_gjf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_gaussian_log() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_gaussian_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_gro() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_gromacs_gro() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_labeled_system() (dpdata.format.Format method) (dpdata.plugins.abacus.AbacusMDFormat method) (dpdata.plugins.abacus.AbacusRelaxFormat method) (dpdata.plugins.abacus.AbacusSCFFormat method) (dpdata.plugins.amber.AmberMDFormat method) (dpdata.plugins.amber.SQMOutFormat method) (dpdata.plugins.ase.ASEStructureFormat method) (dpdata.plugins.ase.ASETrajFormat method) (dpdata.plugins.cp2k.CP2KAIMDOutputFormat method) (dpdata.plugins.cp2k.CP2KOutputFormat method) (dpdata.plugins.deepmd.DeePMDCompFormat method) (dpdata.plugins.deepmd.DeePMDHDF5Format method) (dpdata.plugins.deepmd.DeePMDRawFormat method) (dpdata.plugins.dftbplus.DFTBplusFormat method) (dpdata.plugins.fhi_aims.FhiMDFormat method) (dpdata.plugins.fhi_aims.FhiSCFFormat method) (dpdata.plugins.gaussian.GaussianLogFormat method) (dpdata.plugins.gaussian.GaussianMDFormat method) (dpdata.plugins.n2p2.N2P2Format method) (dpdata.plugins.openmx.OPENMXFormat method) (dpdata.plugins.orca.ORCASPOutFormat method) (dpdata.plugins.psi4.PSI4OutFormat method) (dpdata.plugins.pwmat.PwmatOutputFormat method) (dpdata.plugins.qe.QECPPWSCFFormat method) (dpdata.plugins.qe.QECPTrajFormat method) (dpdata.plugins.siesta.SiestaAIMDOutputFormat method) (dpdata.plugins.siesta.SiestaOutputFormat method) (dpdata.plugins.vasp.VASPOutcarFormat method) (dpdata.plugins.vasp.VASPXMLFormat method) (dpdata.plugins.xyz.QuipGapXYZFormat method) from_labeled_system_mix() (dpdata.plugins.deepmd.DeePMDMixedFormat method) from_lammps_dump() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method)

from_lammps_lmp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_list() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_lmp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_mlmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_mol() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_mol_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_movement() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_multi_systems() (dpdata.format.Format method) (dpdata.plugins.ase.ASEStructureFormat method) (dpdata.plugins.deepmd.DeePMDHDF5Format method) (dpdata.plugins.deepmd.DeePMDMixedFormat method) (dpdata.plugins.xyz.QuipGapXYZFormat method) from_n2p2() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_openmx_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_orca_spout() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_outcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_poscar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_psi4_inp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_psi4_out() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pwmat_atomconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pwmat_finalconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pwmat_mlmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pwmat_movement() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pwmat_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pymatgen_computedstructureentry() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pymatgen_molecule() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_pymatgen_structure() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_qe_cp_traj() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_qe_pw_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_quip_gap_xyz() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_quip_gap_xyz_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_rdkit_mol() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) from_sdf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_sdf_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_siesta_aiMD_output() (dpdata.LabeledSystem method) from_siesta_aimd_output() (dpdata.LabeledSystem method) from_siesta_aiMD_output() (dpdata.MultiSystems method) from_siesta_aimd_output() (dpdata.MultiSystems method) from_siesta_aiMD_output() (dpdata.System method) from_siesta_aimd_output() (dpdata.System method) from_siesta_aiMD_output() (dpdata.system.LabeledSystem method) from_siesta_aimd_output() (dpdata.system.LabeledSystem method) from_siesta_aiMD_output() (dpdata.system.MultiSystems method) from_siesta_aimd_output() (dpdata.system.MultiSystems method) from_siesta_aiMD_output() (dpdata.system.System method) from_siesta_aimd_output() (dpdata.system.System method) from_siesta_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_sqm_in() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_sqm_out() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_stru() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_system() (dpdata.format.Format method) (dpdata.plugins.abacus.AbacusSTRUFormat method) (dpdata.plugins.amber.AmberMDFormat method) (dpdata.plugins.amber.SQMOutFormat method) (dpdata.plugins.ase.ASEStructureFormat method) (dpdata.plugins.ase.ASETrajFormat method) (dpdata.plugins.deepmd.DeePMDCompFormat method) (dpdata.plugins.deepmd.DeePMDHDF5Format method) (dpdata.plugins.deepmd.DeePMDRawFormat method) (dpdata.plugins.gaussian.GaussiaGJFFormat method) (dpdata.plugins.gromacs.GromacsGroFormat method) (dpdata.plugins.lammps.LAMMPSDumpFormat method) (dpdata.plugins.lammps.LAMMPSLmpFormat method) (dpdata.plugins.openmx.OPENMXFormat method) (dpdata.plugins.pwmat.PwmatAtomconfigFormat method) (dpdata.plugins.pymatgen.PyMatgenMoleculeFormat method) (dpdata.plugins.pymatgen.PyMatgenStructureFormat method) (dpdata.plugins.qe.QECPTrajFormat method) (dpdata.plugins.siesta.SiestaAIMDOutputFormat method) (dpdata.plugins.siesta.SiestaOutputFormat method) (dpdata.plugins.vasp.VASPPoscarFormat method) (dpdata.plugins.xyz.XYZFormat method) from_system_data() (in module dpdata.gromacs.gro) (in module dpdata.lammps.lmp) (in module dpdata.pwmat.atomconfig) (in module dpdata.pymatgen.structure) (in module dpdata.vasp.poscar) from_system_mix() (dpdata.plugins.deepmd.DeePMDMixedFormat method) from_vasp_contcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_vasp_outcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_vasp_poscar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_vasp_string() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_vasp_xml() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_xml() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_xyz() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) from_Z() (dpdata.periodic_table.Element class method)

G

GaussiaGJFFormat (class in dpdata.plugins.gaussian) GaussianDriver (class in dpdata.plugins.gaussian) GaussianLogFormat (class in dpdata.plugins.gaussian) GaussianMDFormat (class in dpdata.plugins.gaussian) get_aiMD_frame() (in module dpdata.siesta.aiMD_output) get_atom_mag_cartesian() (in module dpdata.abacus.stru) get_atom_name() (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output) get_atom_names() (dpdata.System method) (dpdata.system.System method) get_atom_numbs() (dpdata.System method) (dpdata.system.System method) (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output) get_atom_perturb_vector() (in module dpdata.system) get_atom_types() (dpdata.System method) (dpdata.system.System method) (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output) get_atoms() (in module dpdata.lammps.lmp) get_atype() (in module dpdata.lammps.dump) (in module dpdata.lammps.lmp) get_block() (in module dpdata.qe.scf) get_block_generator() (dpdata.xyz.quip_gap_xyz.QuipGapxyzSystems method) get_bond_order() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) get_carteisan_coords() (in module dpdata.abacus.stru) get_cell() (in module dpdata.qe.scf) get_cell_perturb_matrix() (in module dpdata.system) get_charge() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) get_cls_name() (in module dpdata.system) get_coord_dump_freq() (in module dpdata.abacus.md) get_coords() (in module dpdata.qe.scf) get_coords_from_dump() (in module dpdata.abacus.md) get_coords_from_log() (in module dpdata.abacus.relax) get_coordtype_and_scalefactor() (in module dpdata.lammps.dump) get_data_types() (in module dpdata.data_type) get_driver() (dpdata.driver.Driver static method) get_drivers() (dpdata.driver.Driver static method) get_dumpbox() (in module dpdata.lammps.dump) get_energy() (in module dpdata.abacus.md) (in module dpdata.abacus.scf) (in module dpdata.qe.scf) get_explicit_valence() (in module dpdata.rdkit.sanitize) get_fhi_aims_block() (in module dpdata.fhi_aims.output) get_force() (in module dpdata.abacus.scf) (in module dpdata.qe.scf) get_formal_charges() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) get_formats() (dpdata.format.Format static method) get_frame() (in module dpdata.abacus.md) (in module dpdata.abacus.relax) (in module dpdata.abacus.scf) (in module dpdata.qe.scf)

get_frame_from_stru() (in module dpdata.abacus.stru) get_frames() (in module dpdata.cp2k.output) (in module dpdata.fhi_aims.output) (in module dpdata.pwmat.movement) (in module dpdata.vasp.outcar) get_from_methods() (dpdata.format.Format static method) get_geometry_in() (in module dpdata.abacus.scf) get_info() (in module dpdata.fhi_aims.output) get_lmpbox() (in module dpdata.lammps.lmp) get_log_block_generator() (dpdata.cp2k.output.Cp2kSystems method) get_log_file() (in module dpdata.abacus.relax) get_mag_force() (in module dpdata.abacus.scf) get_minimizer() (dpdata.driver.Minimizer static method) get_minimizers() (dpdata.driver.Minimizer static method) get_mol() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) get_movement_block() (in module dpdata.pwmat.movement) get_natoms() (dpdata.System method) (dpdata.system.System method) (in module dpdata.lammps.dump) (in module dpdata.lammps.lmp) get_natoms_vec() (in module dpdata.lammps.dump) (in module dpdata.lammps.lmp) get_natomtypes() (in module dpdata.lammps.dump) (in module dpdata.lammps.lmp) get_nbonds() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) get_nframes() (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) get_ntypes() (dpdata.System method) (dpdata.system.System method) get_outcar_block() (in module dpdata.vasp.outcar) get_path_out() (in module dpdata.abacus.md) (in module dpdata.abacus.scf) get_plugin() (dpdata.plugin.Plugin method) get_posi() (in module dpdata.lammps.lmp) get_single_line_tail() (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output) get_spin() (in module dpdata.lammps.dump) get_spin_keys() (in module dpdata.lammps.dump) get_spins() (in module dpdata.lammps.lmp) get_stress() (in module dpdata.abacus.scf) (in module dpdata.qe.scf) get_terminal_NR2s() (in module dpdata.rdkit.sanitize) get_terminal_oxygens() (in module dpdata.rdkit.sanitize) get_to_methods() (dpdata.format.Format static method) get_varray() (in module dpdata.vasp.xml) get_virial() (in module dpdata.siesta.aiMD_output) (in module dpdata.siesta.output) get_xyz_block_generator() (dpdata.cp2k.output.Cp2kSystems method) GromacsGroFormat (class in dpdata.plugins.gromacs)

H

handle_single_log_frame() (dpdata.cp2k.output.Cp2kSystems method) handle_single_xyz_frame() (dpdata.cp2k.output.Cp2kSystems method) (dpdata.xyz.quip_gap_xyz.QuipGapxyzSystems static method) has_forces() (dpdata.LabeledSystem method) (dpdata.system.LabeledSystem method)

has_virial() (dpdata.LabeledSystem method) (dpdata.system.LabeledSystem method) HybridDriver (class in dpdata.driver)

I

is_terminal_nitrogen() (in module dpdata.rdkit.sanitize)

is_terminal_NR2() (in module dpdata.rdkit.sanitize) is_terminal_oxygen() (in module dpdata.rdkit.sanitize)

K

kekulize_aromatic_heterocycles() (in module dpdata.rdkit.sanitize)

L

label() (dpdata.driver.Driver method) (dpdata.driver.HybridDriver method) (dpdata.plugins.amber.SQMDriver method) (dpdata.plugins.ase.ASEDriver method) (dpdata.plugins.deepmd.DPDriver method) (dpdata.plugins.gaussian.GaussianDriver method) LabeledSystem (class in dpdata) (class in dpdata.system) LAMMPSDumpFormat (class in dpdata.plugins.lammps) LAMMPSLmpFormat (class in dpdata.plugins.lammps) LengthConversion (class in dpdata.unit) ListFormat (class in dpdata.plugins.list) lmpbox2box() (in module dpdata.lammps.lmp) load() (dpdata.System static method) (dpdata.system.System static method) load_atom() (in module dpdata.openmx.omx) load_atom_names() (in module dpdata.qe.traj) load_atom_types() (in module dpdata.qe.traj)

load_block() (in module dpdata.qe.traj) load_cell_parameters() (in module dpdata.qe.traj) load_celldm() (in module dpdata.qe.traj) load_cells() (in module dpdata.openmx.omx) load_coords() (in module dpdata.openmx.omx) load_data() (in module dpdata.openmx.omx) (in module dpdata.qe.traj) load_energy() (in module dpdata.openmx.omx) (in module dpdata.qe.traj) load_file() (in module dpdata.lammps.dump) load_force() (in module dpdata.openmx.omx) load_format() (in module dpdata.system) load_key() (in module dpdata.qe.traj) load_param_file() (in module dpdata.amber.mask) (in module dpdata.openmx.omx) (in module dpdata.qe.traj) load_systems_from_file() (dpdata.MultiSystems method) (dpdata.system.MultiSystems method) load_type() (in module dpdata.deepmd.raw)

M

mae() (in module dpdata.stat) make_gaussian_input() (in module dpdata.gaussian.gjf) make_sqm_in() (in module dpdata.amber.sqm) make_unlabeled_stru() (in module dpdata.abacus.stru) map_atom_types() (dpdata.System method) (dpdata.system.System method) mass (dpdata.periodic_table.Element property) match_indices() (in module dpdata.plugins.n2p2) minimize() (dpdata.driver.Minimizer method) (dpdata.MultiSystems method) (dpdata.plugins.amber.SQMMinimizer method) (dpdata.plugins.ase.ASEMinimizer method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) Minimizer (class in dpdata.driver) mix_system() (dpdata.format.Format method) (dpdata.plugins.deepmd.DeePMDMixedFormat method) (in module dpdata.deepmd.mixed) module dpdata dpdata.abacus dpdata.abacus.md dpdata.abacus.relax dpdata.abacus.scf dpdata.abacus.stru dpdata.amber dpdata.amber.mask dpdata.amber.md dpdata.amber.sqm dpdata.bond_order_system dpdata.cli dpdata.cp2k dpdata.cp2k.cell dpdata.cp2k.output dpdata.data_type dpdata.deepmd dpdata.deepmd.comp dpdata.deepmd.hdf5 dpdata.deepmd.mixed dpdata.deepmd.raw dpdata.dftbplus dpdata.dftbplus.output dpdata.driver dpdata.fhi_aims dpdata.fhi_aims.output dpdata.format dpdata.gaussian dpdata.gaussian.gjf dpdata.gaussian.log dpdata.gromacs dpdata.gromacs.gro dpdata.lammps dpdata.lammps.dump dpdata.lammps.lmp dpdata.md dpdata.md.msd dpdata.md.pbc dpdata.md.rdf dpdata.md.water dpdata.openmx dpdata.openmx.omx dpdata.orca dpdata.orca.output dpdata.periodic_table dpdata.plugin dpdata.plugins dpdata.plugins.3dmol dpdata.plugins.abacus dpdata.plugins.amber dpdata.plugins.ase dpdata.plugins.cp2k dpdata.plugins.deepmd dpdata.plugins.dftbplus dpdata.plugins.fhi_aims dpdata.plugins.gaussian dpdata.plugins.gromacs dpdata.plugins.lammps dpdata.plugins.list dpdata.plugins.n2p2 dpdata.plugins.openmx dpdata.plugins.orca dpdata.plugins.psi4 dpdata.plugins.pwmat dpdata.plugins.pymatgen dpdata.plugins.qe dpdata.plugins.rdkit dpdata.plugins.siesta dpdata.plugins.vasp dpdata.plugins.xyz dpdata.psi4 dpdata.psi4.input dpdata.psi4.output dpdata.pwmat dpdata.pwmat.atomconfig dpdata.pwmat.movement dpdata.pymatgen dpdata.pymatgen.molecule dpdata.pymatgen.structure dpdata.qe dpdata.qe.scf dpdata.qe.traj dpdata.rdkit dpdata.rdkit.sanitize dpdata.rdkit.utils dpdata.siesta dpdata.siesta.aiMD_output dpdata.siesta.output dpdata.stat dpdata.system dpdata.unit dpdata.utils dpdata.vasp dpdata.vasp.outcar dpdata.vasp.poscar dpdata.vasp.xml dpdata.xyz dpdata.xyz.quip_gap_xyz dpdata.xyz.xyz

mol_edit_log() (in module dpdata.rdkit.sanitize) mol_to_system_data() (in module dpdata.rdkit.utils) MolFormat (class in dpdata.plugins.rdkit) msd() (in module dpdata.md.msd) MultiErrors (class in dpdata.stat) MultiMode (dpdata.format.Format attribute) (dpdata.plugins.deepmd.DeePMDCompFormat attribute) (dpdata.plugins.deepmd.DeePMDMixedFormat attribute) (dpdata.plugins.deepmd.DeePMDRawFormat attribute) MultiSystems (class in dpdata) (class in dpdata.system)

N

N2P2Format (class in dpdata.plugins.n2p2) name (dpdata.periodic_table.Element property) NATOMS (dpdata.data_type.Axis attribute) NBONDS (dpdata.data_type.Axis attribute)

NFRAMES (dpdata.data_type.Axis attribute) nopbc (dpdata.System property) (dpdata.system.System property) NotImplemented (dpdata.format.Format.MultiModes attribute) NTYPES (dpdata.data_type.Axis attribute)

O

obtain_frame() (in module dpdata.siesta.output) obtain_nframe() (in module dpdata.siesta.aiMD_output)

open_file() (in module dpdata.utils) OPENMXFormat (class in dpdata.plugins.openmx) ORCASPOutFormat (class in dpdata.plugins.orca)

P

parse_atomic_species_block() (in module dpdata.abacus.stru) parse_lattice_constant_block() (in module dpdata.abacus.stru) parse_lattice_vectors_block() (in module dpdata.abacus.stru) parse_numerical_orbital_block() (in module dpdata.abacus.stru) parse_pos() (in module dpdata.abacus.stru) parse_pos_oneline() (in module dpdata.abacus.stru) parse_sqm_out() (in module dpdata.amber.sqm) pbc_coords() (in module dpdata.md.water) perturb() (dpdata.System method) (dpdata.system.System method) pick_atom_idx() (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) pick_by_amber_mask() (dpdata.System method) (dpdata.system.System method) (in module dpdata.amber.mask) Plugin (class in dpdata.plugin) posi_diff() (in module dpdata.md.pbc) posi_shift() (in module dpdata.md.pbc)

post() (dpdata.format.Format static method) post_funcs (dpdata.LabeledSystem attribute) (dpdata.System attribute) (dpdata.system.LabeledSystem attribute) (dpdata.system.System attribute) predict() (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) PressureConversion (class in dpdata.unit) print_atoms() (in module dpdata.rdkit.sanitize) print_bonds() (in module dpdata.rdkit.sanitize) PSI4InputFormat (class in dpdata.plugins.psi4) PSI4OutFormat (class in dpdata.plugins.psi4) PwmatAtomconfigFormat (class in dpdata.plugins.pwmat) PwmatOutputFormat (class in dpdata.plugins.pwmat) Py3DMolFormat (class in dpdata.plugins.3dmol) PyMatgenCSEFormat (class in dpdata.plugins.pymatgen) PyMatgenMoleculeFormat (class in dpdata.plugins.pymatgen) PyMatgenStructureFormat (class in dpdata.plugins.pymatgen)

Q

QECPPWSCFFormat (class in dpdata.plugins.qe) QECPTrajFormat (class in dpdata.plugins.qe)

QuipGapXYZFormat (class in dpdata.plugins.xyz) QuipGapxyzSystems (class in dpdata.xyz.quip_gap_xyz)

R

radius (dpdata.periodic_table.Element property) rdf() (in module dpdata.md.rdf) read_amber_traj() (in module dpdata.amber.md) read_dftb_plus() (in module dpdata.dftbplus.output) read_gaussian_input() (in module dpdata.gaussian.gjf) read_orca_sp_output() (in module dpdata.orca.output) read_psi4_output() (in module dpdata.psi4.output) real_shape() (dpdata.data_type.DataType method) register() (dpdata.driver.Driver static method) (dpdata.driver.Minimizer static method) (dpdata.format.Format static method) (dpdata.plugin.Plugin method) register_data_type() (dpdata.System class method) (dpdata.system.System class method) (in module dpdata.data_type) register_from() (dpdata.format.Format static method) register_mag_data() (in module dpdata.plugins.abacus) register_move_data() (in module dpdata.plugins.abacus) (in module dpdata.plugins.vasp) register_spin() (in module dpdata.plugins.deepmd) (in module dpdata.plugins.lammps)

register_to() (dpdata.format.Format static method) regularize_carbon_bond_order() (in module dpdata.rdkit.sanitize) regularize_formal_charges() (in module dpdata.rdkit.sanitize) regularize_nitrogen_bond_order() (in module dpdata.rdkit.sanitize) remove_atom_names() (dpdata.System method) (dpdata.system.System method) remove_outlier() (dpdata.LabeledSystem method) (dpdata.system.LabeledSystem method) remove_pbc() (dpdata.System method) (dpdata.system.System method) (in module dpdata.utils) replace() (dpdata.System method) (dpdata.system.System method) replicate() (dpdata.System method) (dpdata.system.System method) rmse() (in module dpdata.stat) rot_frame_lower_triangular() (dpdata.LabeledSystem method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.System method) rot_lower_triangular() (dpdata.System method) (dpdata.system.System method)

S

safe_get_posi() (in module dpdata.lammps.dump) sanitize() (dpdata.rdkit.sanitize.Sanitizer method) sanitize_carboxyl() (in module dpdata.rdkit.sanitize) sanitize_carboxyl_Catom() (in module dpdata.rdkit.sanitize) sanitize_guanidine() (in module dpdata.rdkit.sanitize) sanitize_guanidine_Catom() (in module dpdata.rdkit.sanitize) sanitize_mol() (in module dpdata.rdkit.sanitize) sanitize_nitrine_Natom() (in module dpdata.rdkit.sanitize) sanitize_nitro() (in module dpdata.rdkit.sanitize) sanitize_nitro_Natom() (in module dpdata.rdkit.sanitize) sanitize_phosphate() (in module dpdata.rdkit.sanitize) sanitize_phosphate_Patom() (in module dpdata.rdkit.sanitize) sanitize_sulfate() (in module dpdata.rdkit.sanitize) sanitize_sulfate_Satom() (in module dpdata.rdkit.sanitize) SanitizeError Sanitizer (class in dpdata.rdkit.sanitize) scipy_constant_value() (in module dpdata.unit) SdfFormat (class in dpdata.plugins.rdkit) set_value() (dpdata.unit.Conversion method) short_formula (dpdata.System property) (dpdata.system.System property) short_name (dpdata.System property) (dpdata.system.System property) shuffle() (dpdata.System method) (dpdata.system.System method) SiestaAIMDOutputFormat (class in dpdata.plugins.siesta)

SiestaOutputFormat (class in dpdata.plugins.siesta) sort_atom_names() (dpdata.System method) (dpdata.system.System method) (in module dpdata.utils) sort_atom_types() (dpdata.System method) (dpdata.system.System method) split_stru_block() (in module dpdata.abacus.stru) split_system() (in module dpdata.deepmd.mixed) split_traj() (in module dpdata.lammps.dump) SQMDriver (class in dpdata.plugins.amber) SQMINFormat (class in dpdata.plugins.amber) SQMMinimizer (class in dpdata.plugins.amber) SQMOutFormat (class in dpdata.plugins.amber) sub_system() (dpdata.System method) (dpdata.system.System method) super_sanitize_mol() (in module dpdata.rdkit.sanitize) System (class in dpdata) (class in dpdata.system) system_data() (in module dpdata.lammps.dump) (in module dpdata.lammps.lmp) system_data_to_mol() (in module dpdata.rdkit.utils) system_info() (in module dpdata.pwmat.movement) (in module dpdata.vasp.outcar) system_pbc_shift() (in module dpdata.md.pbc) SYSTEM_TYPE (dpdata.stat.Errors attribute) (dpdata.stat.ErrorsBase attribute) (dpdata.stat.MultiErrors attribute)

T

to() (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_3dmol() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_lcao_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_lcao_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_lcao_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_pw_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_pw_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_pw_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_relax() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_abacus_stru() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_amber_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_ase_structure() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_ase_traj() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_atomconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_bond_order_system() (dpdata.format.Format method) (dpdata.plugins.rdkit.MolFormat method) (dpdata.plugins.rdkit.SdfFormat method) to_contcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_cp2k_aimd_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_cp2k_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd_comp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd_hdf5() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd_npy() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd_npy_mixed() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_deepmd_raw() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_dftbplus() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_dump() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_fhi_aims_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_fhi_aims_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_fhi_aims_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_finalconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_fmt_obj() (dpdata.bond_order_system.BondOrderSystem method) (dpdata.BondOrderSystem method) (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_gaussian_gjf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_gaussian_log() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_gaussian_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_gro() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_gromacs_gro() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_labeled_system() (dpdata.format.Format method) (dpdata.plugins.ase.ASEStructureFormat method) (dpdata.plugins.ase.ASETrajFormat method) (dpdata.plugins.n2p2.N2P2Format method) (dpdata.plugins.pymatgen.PyMatgenCSEFormat method) to_lammps_dump() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_lammps_lmp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_list() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_lmp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_mlmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method)

to_mol() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_mol_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_movement() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_multi_systems() (dpdata.format.Format method) (dpdata.plugins.deepmd.DeePMDHDF5Format method) to_n2p2() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_openmx_md() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_orca_spout() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_outcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_poscar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_psi4_inp() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_psi4_out() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pwmat_atomconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pwmat_finalconfig() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pwmat_mlmd() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pwmat_movement() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pwmat_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pymatgen_ComputedStructureEntry() (dpdata.LabeledSystem method) to_pymatgen_computedstructureentry() (dpdata.LabeledSystem method) to_pymatgen_ComputedStructureEntry() (dpdata.MultiSystems method) to_pymatgen_computedstructureentry() (dpdata.MultiSystems method) to_pymatgen_ComputedStructureEntry() (dpdata.System method) to_pymatgen_computedstructureentry() (dpdata.System method) to_pymatgen_ComputedStructureEntry() (dpdata.system.LabeledSystem method) to_pymatgen_computedstructureentry() (dpdata.system.LabeledSystem method) to_pymatgen_ComputedStructureEntry() (dpdata.system.MultiSystems method) to_pymatgen_computedstructureentry() (dpdata.system.MultiSystems method) to_pymatgen_ComputedStructureEntry() (dpdata.system.System method) to_pymatgen_computedstructureentry() (dpdata.system.System method) to_pymatgen_molecule() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_pymatgen_structure() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_qe_cp_traj() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_qe_pw_scf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_quip_gap_xyz() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_quip_gap_xyz_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_sdf() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_sdf_file() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_siesta_aimd_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_siesta_output() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_sqm_in() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_sqm_out() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_stru() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_system() (dpdata.format.Format method) (dpdata.plugins.3dmol.Py3DMolFormat method) (dpdata.plugins.abacus.AbacusSTRUFormat method) (dpdata.plugins.amber.SQMINFormat method) (dpdata.plugins.ase.ASEStructureFormat method) (dpdata.plugins.ase.ASETrajFormat method) (dpdata.plugins.deepmd.DeePMDCompFormat method) (dpdata.plugins.deepmd.DeePMDHDF5Format method) (dpdata.plugins.deepmd.DeePMDMixedFormat method) (dpdata.plugins.deepmd.DeePMDRawFormat method) (dpdata.plugins.gaussian.GaussiaGJFFormat method) (dpdata.plugins.gromacs.GromacsGroFormat method) (dpdata.plugins.lammps.LAMMPSLmpFormat method) (dpdata.plugins.list.ListFormat method) (dpdata.plugins.psi4.PSI4InputFormat method) (dpdata.plugins.pwmat.PwmatAtomconfigFormat method) (dpdata.plugins.pymatgen.PyMatgenMoleculeFormat method) (dpdata.plugins.pymatgen.PyMatgenStructureFormat method) (dpdata.plugins.vasp.VASPPoscarFormat method) (dpdata.plugins.vasp.VASPStringFormat method) (dpdata.plugins.xyz.XYZFormat method) to_system_data() (in module dpdata.deepmd.comp) (in module dpdata.deepmd.hdf5) (in module dpdata.deepmd.mixed) (in module dpdata.deepmd.raw) (in module dpdata.gaussian.log) (in module dpdata.lammps.lmp) (in module dpdata.openmx.omx) (in module dpdata.pwmat.atomconfig) (in module dpdata.pymatgen.molecule) (in module dpdata.qe.traj) (in module dpdata.vasp.poscar) to_system_label() (in module dpdata.openmx.omx) (in module dpdata.qe.traj) to_vasp_contcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_vasp_outcar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_vasp_poscar() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_vasp_string() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_vasp_xml() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_xml() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) to_xyz() (dpdata.LabeledSystem method) (dpdata.MultiSystems method) (dpdata.System method) (dpdata.system.LabeledSystem method) (dpdata.system.MultiSystems method) (dpdata.system.System method) train_test_split() (dpdata.MultiSystems method) (dpdata.system.MultiSystems method)

U

uniq_atom_names() (in module dpdata.utils) uniq_formula (dpdata.System property) (dpdata.system.System property)

UnwrapWarning utf8len() (in module dpdata.utils)

V

value() (dpdata.unit.Conversion method) VASPOutcarFormat (class in dpdata.plugins.vasp)

VASPPoscarFormat (class in dpdata.plugins.vasp) VASPStringFormat (class in dpdata.plugins.vasp) VASPXMLFormat (class in dpdata.plugins.vasp)

W

write_psi4_input() (in module dpdata.psi4.input)

X

X (dpdata.periodic_table.Element property)

xyz_to_coord() (in module dpdata.xyz.xyz) XYZFormat (class in dpdata.plugins.xyz)

Z

Z (dpdata.periodic_table.Element property)