dpdata package

dpdata package#

class dpdata.BondOrderSystem(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, rdkit_mol=None, sanitize_level='medium', raise_errors=True, verbose=False, **kwargs)[source]#

Bases: System

The system with chemical bond and formal charges information.

For example, a labeled methane system named d_example has one molecule (5 atoms, 4 bonds) and n_frames frames. The bond order and formal charge information can be accessed by

d_example[‘bonds’]a numpy array of size 4 x 3, and
the first column represents the index of begin atom, the second column represents the index of end atom, the third columen represents the bond order:

1 - single bond, 2 - double bond, 3 - triple bond, 1.5 - aromatic bond
d_example[‘formal_charges’] : a numpy array of size 5 x 1

Attributes:

formula: Return the formula of this system, like C3H5O2.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
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.
`apply_type_map`(type_map)	Customize the element symbol order and it should maintain order consistency in dpgen or deepmd-kit.
`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_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(data)	Construct a System instance from a data dict.
`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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` 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_rdkit_mol`(rdkit_mol)	Initialize from a rdkit.Chem.rdchem.Mol object.
`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_bond_order`(begin_atom_idx, end_atom_idx)	Return the bond order between given atoms.
`get_charge`()	Return the total formal charge of the moleclue.
`get_formal_charges`()	Return the formal charges on each atom.
`get_mol`()	Return the rdkit.Mol object.
`get_natoms`()	Returns total number of atoms in the system.
`get_nbonds`()	Return the number of bonds.
`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.
`register_data_type`(*data_type)	Register data type.
`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_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` 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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` 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.

affine_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES: tuple[DataType, ...] = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)#

copy()[source]#: Returns a copy of the system.

from_fmt_obj(fmtobj, file_name, **kwargs)[source]#

from_rdkit_mol(rdkit_mol)[source]#: Initialize from a rdkit.Chem.rdchem.Mol object.

get_bond_order(begin_atom_idx, end_atom_idx)[source]#: Return the bond order between given atoms.

get_charge()[source]#: Return the total formal charge of the moleclue.

get_formal_charges()[source]#: Return the formal charges on each atom.

get_mol()[source]#: Return the rdkit.Mol object.

get_nbonds()[source]#: Return the number of bonds.

to_fmt_obj(fmtobj, *args, **kwargs)[source]#

class dpdata.LabeledSystem(file_name: Any = None, fmt: str = 'auto', type_map: list[str] | None = None, begin: int = 0, step: int = 1, data: dict[str, Any] | None = None, convergence_check: bool = True, **kwargs)[source]#

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.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
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.
`apply_type_map`(type_map)	Customize the element symbol order and it should maintain order consistency in dpgen or deepmd-kit.
`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_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(data)	Construct a System instance from a data dict.
`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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` 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.
`register_data_type`(*data_type)	Register data type.
`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_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` 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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` 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.

affine_map
affine_map_fv
from_fmt
from_fmt_obj
has_virial
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES: tuple[DataType, ...] = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)#

affine_map_fv(trans, f_idx: int | Integral)[source]#

correction(hl_sys: LabeledSystem) → LabeledSystem[source]#

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_ase_traj(file_name, **kwargs)#: Read data from dpdata.plugins.ase.ASETrajFormat 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_dftbplus(file_name, **kwargs)#: Read data from dpdata.plugins.dftbplus.DFTBplusFormat 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)[source]#

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_n2p2(file_name, **kwargs)#: Read data from dpdata.plugins.n2p2.N2P2Format format.

from_openmx_md(file_name, **kwargs)#: Read data from dpdata.plugins.openmx.OPENMXFormat format.

from_orca_spout(file_name, **kwargs)#: Read data from dpdata.plugins.orca.ORCASPOutFormat 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_psi4_inp(file_name, **kwargs)#: Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs)#: Read data from dpdata.plugins.psi4.PSI4OutFormat 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() → bool[source]#

post_funcs = <dpdata.plugin.Plugin object>#

remove_outlier(threshold: float = 8.0) → LabeledSystem[source]#

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: int | Integral = 0)[source]#

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_ase_traj(*args, **kwargs)#: Dump data to dpdata.plugins.ase.ASETrajFormat 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_dftbplus(*args, **kwargs)#: Dump data to dpdata.plugins.dftbplus.DFTBplusFormat 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)[source]#

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_n2p2(*args, **kwargs)#: Dump data to dpdata.plugins.n2p2.N2P2Format format.

to_openmx_md(*args, **kwargs)#: Dump data to dpdata.plugins.openmx.OPENMXFormat format.

to_orca_spout(*args, **kwargs)#: Dump data to dpdata.plugins.orca.ORCASPOutFormat 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_psi4_inp(*args, **kwargs)#: Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

to_psi4_out(*args, **kwargs)#: Dump data to dpdata.plugins.psi4.PSI4OutFormat 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.MultiSystems(*systems, type_map=None)[source]#

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_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` 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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` 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_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` 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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` 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.
`train_test_split`(test_size[, seed])	Split systems into random train and test subsets.

from_dir
from_file
from_fmt_obj
load_systems_from_file
to_fmt_obj

append(*systems: System | MultiSystems)[source]#

Append systems or MultiSystems to systems.

Parameters:

*systemsSystem: The system to append

check_atom_names(system: System)[source]#: Make atom_names in all systems equal, prevent inconsistent atom_types.

correction(hl_sys: MultiSystems) → MultiSystems[source]#

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_ase_traj(file_name, **kwargs)#: Read data from dpdata.plugins.ase.ASETrajFormat 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_dftbplus(file_name, **kwargs)#: Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

classmethod from_dir(dir_name: str, file_name: str, fmt: str = 'auto', type_map: list[str] | None = None)[source]#

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: str, **kwargs: Any)[source]#

from_finalconfig(file_name, **kwargs)#: Read data from dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

from_fmt_obj(fmtobj: Format, directory, labeled: bool = True, **kwargs: Any)[source]#

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_n2p2(file_name, **kwargs)#: Read data from dpdata.plugins.n2p2.N2P2Format format.

from_openmx_md(file_name, **kwargs)#: Read data from dpdata.plugins.openmx.OPENMXFormat format.

from_orca_spout(file_name, **kwargs)#: Read data from dpdata.plugins.orca.ORCASPOutFormat 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_psi4_inp(file_name, **kwargs)#: Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs)#: Read data from dpdata.plugins.psi4.PSI4OutFormat 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() → int[source]#: Returns number of frames in all systems.

load_systems_from_file(file_name=None, fmt: str | None = None, **kwargs)[source]#

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

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 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: str | Driver = 'dp', **kwargs: Any) → MultiSystems[source]#

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: Any, **kwargs: Any) → MultiSystems[source]#

Dump systems to the specific format.

Parameters:

fmtstr: format
*argslist: arguments
**kwargsdict: keyword arguments

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_ase_traj(*args, **kwargs)#: Dump data to dpdata.plugins.ase.ASETrajFormat 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_dftbplus(*args, **kwargs)#: Dump data to dpdata.plugins.dftbplus.DFTBplusFormat 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: Format, directory, *args: Any, **kwargs: Any)[source]#

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_n2p2(*args, **kwargs)#: Dump data to dpdata.plugins.n2p2.N2P2Format format.

to_openmx_md(*args, **kwargs)#: Dump data to dpdata.plugins.openmx.OPENMXFormat format.

to_orca_spout(*args, **kwargs)#: Dump data to dpdata.plugins.orca.ORCASPOutFormat 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_psi4_inp(*args, **kwargs)#: Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

to_psi4_out(*args, **kwargs)#: Dump data to dpdata.plugins.psi4.PSI4OutFormat 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.

train_test_split(test_size: float | int, seed: int | None = None) → tuple[MultiSystems, MultiSystems, dict[str, ndarray]][source]#

Split systems into random train and test subsets.

Parameters:

test_sizefloat or int: If float, should be between 0.0 and 1.0 and represent the proportion of the dataset to include in the test split. If int, represents the absolute number of test samples.
seedint, default=None: Random seed

Returns:

MultiSystems: The training set
MultiSystems: The testing set
Dict[str, np.ndarray]: The bool array of training and testing sets for each system. False for training set and True for testing set.

class dpdata.System(file_name: Any = None, fmt: str = 'auto', type_map: list[str] | None = None, begin: int = 0, step: int = 1, data: dict[str, Any] | None = None, convergence_check: bool = True, **kwargs)[source]#

Bases: object

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.
`apply_type_map`(type_map)	Customize the element symbol order and it should maintain order consistency in dpgen or deepmd-kit.
`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_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(data)	Construct a System instance from a data dict.
`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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` 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.
`register_data_type`(*data_type)	Register data type.
`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_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` 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_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` 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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` 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_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` 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.

affine_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES: tuple[DataType, ...] = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)#

add_atom_names(atom_names: list[str])[source]#: Add atom_names that do not exist.

affine_map(trans, f_idx: int | Integral = 0)[source]#

append(system: System) → bool[source]#

Append a system to this system.

Parameters:

systemSystem: The system to append

apply_pbc()[source]#: Append periodic boundary condition.

apply_type_map(type_map: list[str])[source]#

Customize the element symbol order and it should maintain order consistency in dpgen or deepmd-kit. It is especially recommended for multiple complexsystems with multiple elements.

Parameters:

type_maplist: type_map

as_dict() → dict[source]#: Returns data dict of System instance.

check_data()[source]#

Check if data is correct.

Raises:

DataError: if data is not correct

check_type_map(type_map: list[str] | None)[source]#

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: list[str] | None = None)[source]#

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()[source]#: Returns a copy of the system.

dump(filename: str, indent: int = 4)[source]#: Dump .json or .yaml file.

extend(systems: Iterable[System])[source]#

Extend a system list to this system.

Parameters:

systems[System1, System2, System3 ]: The list to extend

property formula: str#: Return the formula of this system, like C3H5O2.

property formula_hash: str#: Return the hash of the formula of 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_ase_traj(file_name, **kwargs)#: Read data from dpdata.plugins.ase.ASETrajFormat 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_dftbplus(file_name, **kwargs)#: Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

classmethod from_dict(data: dict)[source]#: Construct a System instance from a data dict.

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, **

dpdata package

Contents

dpdata package#