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_forces
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_forces() → bool[source]#

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

from_fmt(file_name: Any, fmt: str = 'auto', **kwargs: Any)[source]#

from_fmt_obj(fmtobj: Format, file_name: Any, **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_atom_names() → list[str][source]#: Returns name of atoms.

get_atom_numbs() → list[int][source]#: Returns number of atoms.

get_atom_types() → ndarray[source]#: Returns type of atoms.

get_natoms() → int[source]#: Returns total number of atoms in the system.

get_nframes() → int[source]#: Returns number of frames in the system.

get_ntypes() → int[source]#: Returns total number of atom types in the system.

static load(filename: str)[source]#: Rebuild System obj. from .json or .yaml file.

map_atom_types(type_map: dict[str, int] | list[str] | None = None) → ndarray[source]#

Map the atom types of the system.

Parameters:

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

Returns:

new_atom_typesnp.ndarray: The mapped atom types

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

Minimize the geometry.

Parameters:

*argsiterable: Arguments passing to the minimizer
minimizerstr or Minimizer: The assigned minimizer
**kwargsdict: Other arguments passing to the minimizer

Returns:

labeled_sysLabeledSystem: A new labeled system.

property nopbc#

perturb(pert_num: int, cell_pert_fraction: float, atom_pert_distance: float, atom_pert_style: str = 'normal', atom_pert_prob: float = 1.0)[source]#

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

Parameters:

pert_numint

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

cell_pert_fractionfloat

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

atom_pert_distancefloat

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

atom_pert_stylestr

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

‘normal’: the distance will be object to chi-square distribution with 3 degrees of freedom after normalization.
The mean value of the distance is atom_pert_fraction*side_length
‘uniform’: will generate uniformly random points in a 3D-balls with radius as atom_pert_distance.
These points are treated as vector used by atoms to move. Obviously, the max length of the distance atoms move is atom_pert_distance.
‘const’: The distance atoms move will be a constant atom_pert_distance.

atom_pert_probfloat

Determine the proportion of the total number of atoms in a frame that are perturbed.

Returns:

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

Pick atom index.

Parameters:

idxint or list or slice: atom index
nopbcBoolen (default: None): If nopbc is True or False, set nopbc

Returns:

new_sys: System: new system

pick_by_amber_mask(param: str | parmed.Structure, maskstr: str, pass_coords: bool = False, nopbc: bool | None = None)[source]#

Pick atoms by amber mask.

Parameters:

paramstr or parmed.Structure: filename of Amber param file or parmed.Structure
maskstrstr: Amber masks
pass_coordsBoolen (default: False): If pass_coords is true, the function will pass coordinates and return a MultiSystem. Otherwise, the result is coordinate-independent, and the function will return System or LabeledSystem.
nopbcBoolen (default: None): If nopbc is True or False, set nopbc

post_funcs = <dpdata.plugin.Plugin object>#

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

labeled_sysLabeledSystem: A new labeled system.

Examples

The default driver is DP:

>>> labeled_sys = ori_sys.predict("frozen_model_compressed.pb")

classmethod register_data_type(*data_type: DataType)[source]#

Parameters:

*data_typetuple[DataType]: data type to be regiestered

remove_atom_names(atom_names: str | list[str])[source]#: Remove atom names and all such atoms. For example, you may not remove EP atoms in TIP4P/Ew water, which is not a real atom.

remove_pbc(protect_layer: int = 9)[source]#

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

Parameters:

protect_layerthe protect layer between the atoms and the cell: boundary

replace(initial_atom_type: str, end_atom_type: str, replace_num: int)[source]#

replicate(ncopy: list[int] | tuple[int, int, int])[source]#

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

Parameters:

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

Returns:

tmpSystem: The system after replication.

rot_frame_lower_triangular(f_idx: int | Integral = 0)[source]#

rot_lower_triangular()[source]#

property short_formula: str#: Return the short formula of this system. Elements with zero number will be removed.

property short_name: str#

Return the short name of this system (no more than 255 bytes), in the following order:

formula
short_formula
formula_hash.

shuffle()[source]#: Shuffle frames randomly.

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

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

Parameters:

type_maplist: type_map

sort_atom_types() → ndarray[source]#

Sort atom types.

Returns:

idxnp.ndarray: new atom index in the Axis.NATOMS

sub_system(f_idx: int | slice | list | ndarray)[source]#

Construct a subsystem from the system.

Parameters:

f_idxint or index: Which frame to use in the subsystem

Returns:

sub_systemSystem: The subsystem

to(fmt: str, *args: Any, **kwargs: Any) → System[source]#

Dump systems to the specific format.

Parameters:

fmtstr: format
*args: arguments
**kwargs: keyword arguments

Returns:

System: self

to_3dmol(*args, **kwargs)#: Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.

to_abacus_lcao_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_lcao_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_lcao_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_pw_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_stru(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_amber_md(*args, **kwargs)#: Dump data to dpdata.plugins.amber.AmberMDFormat format.

to_ase_structure(*args, **kwargs)#: Dump data to dpdata.plugins.ase.ASEStructureFormat format.

to_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, *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.

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

Subpackages#

Submodules#

dpdata.ase_calculator module#

dpdata.bond_order_system module#

class dpdata.bond_order_system.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]#

dpdata.cli module#

Command line interface for dpdata.

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

Convert files from one format to another one.

Parameters:

from_filestr: read data from a file
from_formatstr: the format of from_file
to_filestr: dump data to a file
to_formatstr: the format of to_file
no_labeledbool: labels aren’t provided
multibool: the system contains multiple directories
type_maplist: type map
**kwargsdict: Additional arguments for the format.

dpdata.cli.dpdata_cli()[source]#

Dpdata cli.

Examples

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

dpdata.cli.dpdata_parser() → ArgumentParser[source]#

Returns dpdata cli parser.

Returns:

argparse.ArgumentParser: dpdata cli parser

dpdata.data_type module#

class dpdata.data_type.AnyInt[source]#

Bases: int

AnyInt equals to any other integer.

Attributes:

denominator: the denominator of a rational number in lowest terms
imag: the imaginary part of a complex number
numerator: the numerator of a rational number in lowest terms
real: the real part of a complex number

Methods

`as_integer_ratio`(/)	Return a pair of integers, whose ratio is equal to the original int.
`bit_count`(/)	Number of ones in the binary representation of the absolute value of self.
`bit_length`(/)	Number of bits necessary to represent self in binary.
`conjugate`	Returns self, the complex conjugate of any int.
`from_bytes`(/, bytes[, byteorder, signed])	Return the integer represented by the given array of bytes.
`is_integer`(/)	Returns True.
`to_bytes`(/[, length, byteorder, signed])	Return an array of bytes representing an integer.

class dpdata.data_type.Axis(*values)[source]#

Bases: Enum

Data axis.

NATOMS = 'natoms'#

NBONDS = 'nbonds'#

NFRAMES = 'nframes'#

NTYPES = 'ntypes'#

exception dpdata.data_type.DataError[source]#

Bases: Exception

Data is not correct.

class dpdata.data_type.DataType(name: str, dtype: type, shape: tuple[int | Axis, ...] | None = None, required: bool = True, deepmd_name: str | None = None)[source]#

Bases: object

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

Parameters:

namestr: name of data
dtypetype or tuple[type]: data type, e.g. np.ndarray
shapetuple[int], optional: shape of data. Used when data is list or np.ndarray. Use Axis to represents numbers
requiredbool, default=True: whether this data is required
deepmd_namestr, optional: DeePMD-kit data type name. When not given, it is the same as name.

Methods

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

check(system: System)[source]#

Check if a system has correct data of this type.

Parameters:

systemSystem: checked system

Raises:

DataError: type or shape of data is not correct

real_shape(system: System) → tuple[int][source]#: Returns expected real shape of a system.

dpdata.data_type.get_data_types(labeled: bool)[source]#

Get all registered data types.

Parameters:

labeledbool: whether this data type is for LabeledSystem

dpdata.data_type.register_data_type(data_type: DataType, labeled: bool)[source]#

Parameters:

data_typeDataType: data type to be registered
labeledbool: whether this data type is for LabeledSystem

dpdata.driver module#

Driver plugin system.

class dpdata.driver.Driver(*args, **kwargs)[source]#

Bases: ABC

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

Attributes:

ase_calculator: Returns an ase calculator based on this driver.

Methods

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

dpdata.format module#

Implement the format plugin system.

class dpdata.format.Format[source]#

Bases: ABC

The abstract base class for all formats.

To add a new format, one should create a new class inherited from this class, and then

implement several methods, such as from_system();
register the format with a key;
add documentation in the class docstring;

The new format can be either insider or outside the package.

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name, **kwargs)	Implement LabeledSystem.from that converts from this format to LabeledSystem.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`(file_name, **kwargs)	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data, args, *kwargs)	Implement System.to that converts from System to this format.

MultiMode = 0#

class MultiModes[source]#

Bases: object

File mode for MultiSystems.

The current implemented modes are:

0 (default): not implemented
1: every directory under the top-level directory is a system.

Directory = 1#

NotImplemented = 0#

from_bond_order_system(file_name, **kwargs)[source]#

Implement BondOrderSystem.from that converts from this format to BondOrderSystem.

Parameters:

file_namestr: file name, i.e. the first argument
**kwargsdict: keyword arguments that will be passed from the method

Returns:

datadict: system data

from_labeled_system(file_name, **kwargs)[source]#

Implement LabeledSystem.from that converts from this format to LabeledSystem.

Parameters:

file_namestr: file name, i.e. the first argument
**kwargsdict: keyword arguments that will be passed from the method

Returns:

datadict: system data, whose keys are defined in LabeledSystem.DTYPES

from_multi_systems(directory, **kwargs)[source]#

Implement MultiSystems.from that converts from this format to MultiSystems.

By default, this method follows MultiMode to implement the conversion.

Parameters:

directorystr: directory of system
**kwargsdict: keyword arguments that will be passed from the method

Returns:

filenames: list[str]: list of filenames

from_system(file_name, **kwargs)[source]#

Implement System.from that converts from this format to System.

Parameters:

file_namestr: file name, i.e. the first argument
**kwargsdict: keyword arguments that will be passed from the method

Returns:

datadict: system data, whose keys are defined in System.DTYPES

static get_formats()[source]#: Get all registered formats.

static get_from_methods()[source]#: Get all registered from methods.

static get_to_methods()[source]#: Get all registered to methods.

mix_system(*system, type_map, **kwargs)[source]#

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

Parameters:

*systemSystem: The systems to mix
type_maplist of str: Maps atom type to name
**kwargsdict: keyword arguments that will be passed from the method

Returns:

mixed_systems: dict: dict of mixed system with key ‘atom_numbs’

static post(func_name)[source]#

Such function will be called after the “from” method is called.

Parameters:

func_namestr or list of str: The name of the post function.

Returns:

function: The decorator function.

Examples

>>> @Format.post('remove_pbc')
... @Format.register('test')
... class TestFormat(Format):
...     pass

static register(key)[source]#

By default, after a format plugin is registered, the following methods will be registered as well for System(), LabeledSystem(), MultiSystems(), and BondOrderSystem():

from_{key.replace(‘/’, ‘_’)}
to_{key.replace(‘/’, ‘_’)}
from({key}, …)
to({key}, …)

The decorator should be explicitly executed before dpdata.system is imported. A module will be imported automatically if it

is a submodule of dpdata.plugins;
is registered at the dpdata.plugins entry point

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

>>> @Format.register('test')
... @Format.register('test2')
... class TestFormat(Format):
...     pass

static register_from(key)[source]#

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

>>> @Format.register_from('from_test_haha')
... @Format.register('test)
... class TestFormat(Format):
...     pass

This will register a from method named from_test_haha, although the format name is test.

static register_to(key)[source]#

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

>>> @Format.register_to('to_test_haha')
... @Format.register('test')
... class TestFormat(Format):
...     pass

This will register a to method named to_test_haha, although the format name is test.

to_bond_order_system(data, rdkit_mol, *args, **kwargs)[source]#

Implement BondOrderSystem.to that converts from BondOrderSystem to this format.

By default, BondOrderSystem.to will fallback to LabeledSystem.to.

Parameters:

datadict: system data
rdkit_molrdkit.Chem.rdchem.Mol: rdkit mol object
*argslist: arguments that will be passed from the method
**kwargsdict: keyword arguments that will be passed from the method

to_labeled_system(data, *args, **kwargs)[source]#

Implement LabeledSystem.to that converts from LabeledSystem to this format.

By default, LabeledSystem.to will fallback to System.to.

Parameters:

datadict: system data, whose keys are defined in LabeledSystem.DTYPES
*argslist: arguments that will be passed from the method
**kwargsdict: keyword arguments that will be passed from the method

to_multi_systems(formulas, directory, **kwargs)[source]#

Implement MultiSystems.to that converts from MultiSystems to this format.

By default, this method follows MultiMode to implement the conversion.

Parameters:

formulaslist[str]: list of formulas
directorystr: directory of system
**kwargsdict: keyword arguments that will be passed from the method

to_system(data, *args, **kwargs)[source]#

Implement System.to that converts from System to this format.

Parameters:

datadict: system data, whose keys are defined in System.DTYPES
*argslist: arguments that will be passed from the method
**kwargsdict: keyword arguments that will be passed from the method

dpdata.periodic_table module#

class dpdata.periodic_table.Element(symbol: str)[source]#

Bases: object

Attributes:

X
Z
calculated_radius
mass
name
radius

Methods

from_Z

property X#

property Z#

property calculated_radius#

classmethod from_Z(Z)[source]#

property mass#

property name#

property radius#

dpdata.plugin module#

Base of plugin systems.

class dpdata.plugin.Plugin[source]#

Bases: object

A class to register plugins.

Methods

register(key)

get_plugin

Examples

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

get_plugin(key)[source]#

register(key)[source]#

Parameters:

keystr: Key of the plugin.

dpdata.stat module#

class dpdata.stat.Errors(system_1: SYSTEM_TYPE, system_2: SYSTEM_TYPE)[source]#

Bases: ErrorsBase

Compute errors (deviations) between two LabeledSystems.

Parameters:

system_1object: system 1
system_2object: system 2

Attributes:

e_errors: Energy errors.
e_mae: Energy MAE.
e_rmse: Energy RMSE.
f_errors: Force errors.
f_mae: Force MAE.
f_rmse: Force RMSE.

Methods

SYSTEM_TYPE

alias of LabeledSystem

Examples

Get errors between referenced system and predicted system:

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

SYSTEM_TYPE#: alias of LabeledSystem

property e_errors: ndarray#: Energy errors.

property f_errors: ndarray#: Force errors.

class dpdata.stat.ErrorsBase(system_1: SYSTEM_TYPE, system_2: SYSTEM_TYPE)[source]#

Bases: object

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

Parameters:

system_1object: system 1
system_2object: system 2

Attributes:

e_errors: Energy errors.
e_mae: Energy MAE.
e_rmse: Energy RMSE.
f_errors: Force errors.
f_mae: Force MAE.
f_rmse: Force RMSE.

Methods

SYSTEM_TYPE

alias of object

SYSTEM_TYPE#: alias of object

abstract property e_errors: ndarray#: Energy errors.

property e_mae: floating[Any]#: Energy MAE.

property e_rmse: floating[Any]#: Energy RMSE.

abstract property f_errors: ndarray#: Force errors.

property f_mae: floating[Any]#: Force MAE.

property f_rmse: floating[Any]#: Force RMSE.

class dpdata.stat.MultiErrors(system_1: SYSTEM_TYPE, system_2: SYSTEM_TYPE)[source]#

Bases: ErrorsBase

Compute errors (deviations) between two MultiSystems.

Parameters:

system_1object: system 1
system_2object: system 2

Attributes:

e_errors: Energy errors.
e_mae: Energy MAE.
e_rmse: Energy RMSE.
f_errors: Force errors.
f_mae: Force MAE.
f_rmse: Force RMSE.

Methods

SYSTEM_TYPE

alias of MultiSystems

Examples

Get errors between referenced system and predicted system:

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

SYSTEM_TYPE#: alias of MultiSystems

property e_errors: ndarray#: Energy errors.

property f_errors: ndarray#: Force errors.

dpdata.stat.mae(errors: ndarray) → floating[Any][source]#

Compute the mean absolute error (MAE).

Parameters:

errorsnp.ndarray: errors between two values

Returns:

floating[Any]: mean absolute error (MAE)

dpdata.stat.rmse(errors: ndarray) → floating[Any][source]#

Compute the root mean squared error (RMSE).

Parameters:

errorsnp.ndarray: errors between two values

Returns:

floating[Any]: root mean squared error (RMSE)

dpdata.system module#

class dpdata.system.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_forces
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_forces() → bool[source]#

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]

[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.system.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]#

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.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.

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]#

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

from_fmt(file_name: Any, fmt: str = 'auto', **kwargs: Any)[source]#

from_fmt_obj(fmtobj: Format, file_name: Any, **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_atom_names() → list[str][source]#: Returns name of atoms.

get_atom_numbs() → list[int][source]#: Returns number of atoms.

get_atom_types() → ndarray[source]#: Returns type of atoms.

get_natoms() → int[source]#: Returns total number of atoms in the system.

get_nframes() → int[source]#: Returns number of frames in the system.

get_ntypes() → int[source]#: Returns total number of atom types in the system.

static load(filename: str)[source]#: Rebuild System obj. from .json or .yaml file.

map_atom_types(type_map: dict[str, int] | list[str] | None = None) → ndarray[source]#

Map the atom types of the system.

Parameters:

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

Returns:

new_atom_typesnp.ndarray: The mapped atom types

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

Minimize the geometry.

Parameters:

*argsiterable: Arguments passing to the minimizer
minimizerstr or Minimizer: The assigned minimizer
**kwargsdict: Other arguments passing to the minimizer

Returns:

labeled_sysLabeledSystem: A new labeled system.

property nopbc#

perturb(pert_num: int, cell_pert_fraction: float, atom_pert_distance: float, atom_pert_style: str = 'normal', atom_pert_prob: float = 1.0)[source]#

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

Parameters:

pert_numint

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

cell_pert_fractionfloat

atom_pert_distancefloat

atom_pert_stylestr

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

‘normal’: the distance will be object to chi-square distribution with 3 degrees of freedom after normalization.
The mean value of the distance is atom_pert_fraction*side_length
‘uniform’: will generate uniformly random points in a 3D-balls with radius as atom_pert_distance.
These points are treated as vector used by atoms to move. Obviously, the max length of the distance atoms move is atom_pert_distance.
‘const’: The distance atoms move will be a constant atom_pert_distance.

atom_pert_probfloat

Determine the proportion of the total number of atoms in a frame that are perturbed.

Returns:

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

Pick atom index.

Parameters:

idxint or list or slice: atom index
nopbcBoolen (default: None): If nopbc is True or False, set nopbc

Returns:

new_sys: System: new system

pick_by_amber_mask(param: str | parmed.Structure, maskstr: str, pass_coords: bool = False, nopbc: bool | None = None)[source]#

Pick atoms by amber mask.

Parameters:

paramstr or parmed.Structure: filename of Amber param file or parmed.Structure
maskstrstr: Amber masks
pass_coordsBoolen (default: False): If pass_coords is true, the function will pass coordinates and return a MultiSystem. Otherwise, the result is coordinate-independent, and the function will return System or LabeledSystem.
nopbcBoolen (default: None): If nopbc is True or False, set nopbc

post_funcs = <dpdata.plugin.Plugin object>#

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

labeled_sysLabeledSystem: A new labeled system.

Examples

The default driver is DP:

>>> labeled_sys = ori_sys.predict("frozen_model_compressed.pb")

classmethod register_data_type(*data_type: DataType)[source]#

Parameters:

*data_typetuple[DataType]: data type to be regiestered

remove_atom_names(atom_names: str | list[str])[source]#: Remove atom names and all such atoms. For example, you may not remove EP atoms in TIP4P/Ew water, which is not a real atom.

remove_pbc(protect_layer: int = 9)[source]#

Parameters:

protect_layerthe protect layer between the atoms and the cell: boundary

replace(initial_atom_type: str, end_atom_type: str, replace_num: int)[source]#

replicate(ncopy: list[int] | tuple[int, int, int])[source]#

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

Parameters:

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

Returns:

tmpSystem: The system after replication.

rot_frame_lower_triangular(f_idx: int | Integral = 0)[source]#

rot_lower_triangular()[source]#

property short_formula: str#: Return the short formula of this system. Elements with zero number will be removed.

property short_name: str#

Return the short name of this system (no more than 255 bytes), in the following order:

formula
short_formula
formula_hash.

shuffle()[source]#: Shuffle frames randomly.

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

Parameters:

type_maplist: type_map

sort_atom_types() → ndarray[source]#

Sort atom types.

Returns:

idxnp.ndarray: new atom index in the Axis.NATOMS

sub_system(f_idx: int | slice | list | ndarray)[source]#

Construct a subsystem from the system.

Parameters:

f_idxint or index: Which frame to use in the subsystem

Returns:

sub_systemSystem: The subsystem

to(fmt: str, *args: Any, **kwargs: Any) → System[source]#

Dump systems to the specific format.

Parameters:

fmtstr: format
*args: arguments
**kwargs: keyword arguments

Returns:

System: self

to_3dmol(*args, **kwargs)#: Dump data to dpdata.plugins.3dmol.Py3DMolFormat format.

to_abacus_lcao_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_lcao_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_lcao_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_md(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusMDFormat format.

to_abacus_pw_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_pw_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_relax(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusRelaxFormat format.

to_abacus_scf(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSCFFormat format.

to_abacus_stru(*args, **kwargs)#: Dump data to dpdata.plugins.abacus.AbacusSTRUFormat format.

to_amber_md(*args, **kwargs)#: Dump data to dpdata.plugins.amber.AmberMDFormat format.

to_ase_structure(*args, **kwargs)#: Dump data to dpdata.plugins.ase.ASEStructureFormat format.

to_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, *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.

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

dpdata.system.add_format_methods()[source]#

Add format methods to System, LabeledSystem, and MultiSystems; add data types to System and LabeledSystem.

Notes

Ensure all plugins have been loaded before execuating this function!

dpdata.system.get_atom_perturb_vector(atom_pert_distance: float, atom_pert_style: str = 'normal')[source]#

dpdata.system.get_cell_perturb_matrix(cell_pert_fraction: float)[source]#

dpdata.system.get_cls_name(cls: type[Any]) → str[source]#

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

Parameters:

clsobject: the class

Returns:

str: the fully qualified name of a class

dpdata.system.load_format(fmt)[source]#

dpdata.unit module#

class dpdata.unit.Conversion(unitA, unitB, check=True)[source]#

Bases: ABC

Methods

set_value
value

set_value(value)[source]#

value()[source]#

class dpdata.unit.EnergyConversion(unitA, unitB)[source]#

Bases: Conversion

Methods

set_value
value

class dpdata.unit.ForceConversion(unitA, unitB)[source]#

Bases: Conversion

Methods

set_value
value

class dpdata.unit.LengthConversion(unitA, unitB)[source]#

Bases: Conversion

Methods

set_value
value

class dpdata.unit.PressureConversion(unitA, unitB)[source]#

Bases: Conversion

Methods

set_value
value

dpdata.unit.check_unit(unit)[source]#

dpdata.unit.scipy_constant_value(key: str) → float[source]#

dpdata.utils module#

dpdata.utils.add_atom_names(data, atom_names)[source]#: Add atom_names that do not exist.

dpdata.utils.elements_index_map(elements: list[str], standard: bool, inverse: Literal[True]) → dict[int, str][source]#
dpdata.utils.elements_index_map(elements: list[str], standard: bool, inverse: Literal[False] = False) → dict[str, int]
dpdata.utils.elements_index_map(elements: list[str], standard: bool, inverse: bool = False) → dict[str, int] | dict[int, str]

dpdata.utils.open_file(file: FileType, *args, **kwargs) → Generator[io.IOBase, None, None][source]#

A context manager that yields a file object.

Parameters:

filefile object or file path: A file object or a file path.

Yields:

fileio.IOBase: A file object.
*args: parameters to open
**kwargs: other parameters

Raises:

ValueError: If file is not a file object or a file

Examples

>>> with open_file("file.txt") as file:
...     print(file.read())

dpdata.utils.remove_pbc(system, protect_layer=9)[source]#

dpdata.utils.sort_atom_names(data, type_map=None)[source]#

Parameters:

datadict: system data
type_maplist: type_map

dpdata.utils.uniq_atom_names(data)[source]#

Make the atom names uniq. For example [‘O’, ‘H’, ‘O’, ‘H’, ‘O’] -> [‘O’, ‘H’].

Parameters:

datadict: data dict of System, LabeledSystem

dpdata.utils.utf8len(s: str) → int[source]#: Return the byte length of a string.

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

dpdata package

Contents

dpdata package#

Subpackages#

Submodules#

dpdata.ase_calculator module#

dpdata.bond_order_system module#

dpdata.cli module#

dpdata.data_type module#

dpdata.driver module#

dpdata.format module#

dpdata.periodic_table module#

dpdata.plugin module#

dpdata.stat module#

dpdata.system module#

dpdata.unit module#

dpdata.utils module#