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.

as_dict()

Returns data dict of System instance.

check_data()

Check if data is correct.

check_type_map(type_map)

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

convert_to_mixed_type([type_map])

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.

copy()

Returns a copy of the system.

dump(filename[, indent])

Dump .json or .yaml file.

extend(systems)

Extend a system list to this system.

from_3dmol(file_name, **kwargs)

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

from_abacus_lcao_md(file_name, **kwargs)

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

from_abacus_lcao_relax(file_name, **kwargs)

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

from_abacus_lcao_scf(file_name, **kwargs)

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

from_abacus_md(file_name, **kwargs)

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

from_abacus_pw_md(file_name, **kwargs)

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

from_abacus_pw_relax(file_name, **kwargs)

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

from_abacus_pw_scf(file_name, **kwargs)

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

from_abacus_relax(file_name, **kwargs)

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

from_abacus_scf(file_name, **kwargs)

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

from_abacus_stru(file_name, **kwargs)

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

from_amber_md(file_name, **kwargs)

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

from_ase_structure(file_name, **kwargs)

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

from_atomconfig(file_name, **kwargs)

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

from_contcar(file_name, **kwargs)

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

from_cp2k_aimd_output(file_name, **kwargs)

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

from_cp2k_output(file_name, **kwargs)

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

from_deepmd(file_name, **kwargs)

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

from_deepmd_comp(file_name, **kwargs)

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

from_deepmd_hdf5(file_name, **kwargs)

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

from_deepmd_npy(file_name, **kwargs)

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

from_deepmd_npy_mixed(file_name, **kwargs)

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

from_deepmd_raw(file_name, **kwargs)

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

from_dftbplus(file_name, **kwargs)

Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dict(d)

param d:

Dict representation.

from_dump(file_name, **kwargs)

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

from_fhi_aims_md(file_name, **kwargs)

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

from_fhi_aims_output(file_name, **kwargs)

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

from_fhi_aims_scf(file_name, **kwargs)

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

from_finalconfig(file_name, **kwargs)

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

from_gaussian_gjf(file_name, **kwargs)

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

from_gaussian_log(file_name, **kwargs)

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

from_gaussian_md(file_name, **kwargs)

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

from_gro(file_name, **kwargs)

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

from_gromacs_gro(file_name, **kwargs)

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

from_lammps_dump(file_name, **kwargs)

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

from_lammps_lmp(file_name, **kwargs)

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

from_list(file_name, **kwargs)

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

from_lmp(file_name, **kwargs)

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

from_mlmd(file_name, **kwargs)

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

from_mol(file_name, **kwargs)

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

from_mol_file(file_name, **kwargs)

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

from_movement(file_name, **kwargs)

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

from_outcar(file_name, **kwargs)

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

from_poscar(file_name, **kwargs)

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

from_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_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_json()

Returns a json string representation of the MSONable object.

to_lammps_dump(*args, **kwargs)

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

to_lammps_lmp(*args, **kwargs)

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

to_list(*args, **kwargs)

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

to_lmp(*args, **kwargs)

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

to_mlmd(*args, **kwargs)

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

to_mol(*args, **kwargs)

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

to_mol_file(*args, **kwargs)

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

to_movement(*args, **kwargs)

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

to_outcar(*args, **kwargs)

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

to_poscar(*args, **kwargs)

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

to_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.

unsafe_hash()

Returns an hash of the current object.

validate_monty_v1(_MSONable__input_value)

Pydantic validator with correct signature for pydantic v1.x

validate_monty_v2(_MSONable__input_value, _)

Pydantic validator with correct signature for pydantic v2.x

affine_map

apply_type_map

from_fmt

from_fmt_obj

replace

rot_frame_lower_triangular

rot_lower_triangular

to_fmt_obj

DTYPES = (<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=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=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.

as_dict()

Returns data dict of System instance.

check_data()

Check if data is correct.

check_type_map(type_map)

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

convert_to_mixed_type([type_map])

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.

copy()

Returns a copy of the system.

correction(hl_sys)

Get energy and force correction between self and a high-level LabeledSystem.

dump(filename[, indent])

Dump .json or .yaml file.

extend(systems)

Extend a system list to this system.

from_3dmol(file_name, **kwargs)

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

from_abacus_lcao_md(file_name, **kwargs)

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

from_abacus_lcao_relax(file_name, **kwargs)

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

from_abacus_lcao_scf(file_name, **kwargs)

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

from_abacus_md(file_name, **kwargs)

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

from_abacus_pw_md(file_name, **kwargs)

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

from_abacus_pw_relax(file_name, **kwargs)

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

from_abacus_pw_scf(file_name, **kwargs)

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

from_abacus_relax(file_name, **kwargs)

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

from_abacus_scf(file_name, **kwargs)

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

from_abacus_stru(file_name, **kwargs)

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

from_amber_md(file_name, **kwargs)

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

from_ase_structure(file_name, **kwargs)

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

from_atomconfig(file_name, **kwargs)

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

from_contcar(file_name, **kwargs)

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

from_cp2k_aimd_output(file_name, **kwargs)

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

from_cp2k_output(file_name, **kwargs)

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

from_deepmd(file_name, **kwargs)

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

from_deepmd_comp(file_name, **kwargs)

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

from_deepmd_hdf5(file_name, **kwargs)

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

from_deepmd_npy(file_name, **kwargs)

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

from_deepmd_npy_mixed(file_name, **kwargs)

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

from_deepmd_raw(file_name, **kwargs)

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

from_dftbplus(file_name, **kwargs)

Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dict(d)

param d:

Dict representation.

from_dump(file_name, **kwargs)

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

from_fhi_aims_md(file_name, **kwargs)

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

from_fhi_aims_output(file_name, **kwargs)

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

from_fhi_aims_scf(file_name, **kwargs)

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

from_finalconfig(file_name, **kwargs)

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

from_gaussian_gjf(file_name, **kwargs)

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

from_gaussian_log(file_name, **kwargs)

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

from_gaussian_md(file_name, **kwargs)

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

from_gro(file_name, **kwargs)

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

from_gromacs_gro(file_name, **kwargs)

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

from_lammps_dump(file_name, **kwargs)

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

from_lammps_lmp(file_name, **kwargs)

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

from_list(file_name, **kwargs)

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

from_lmp(file_name, **kwargs)

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

from_mlmd(file_name, **kwargs)

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

from_mol(file_name, **kwargs)

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

from_mol_file(file_name, **kwargs)

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

from_movement(file_name, **kwargs)

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

from_outcar(file_name, **kwargs)

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

from_poscar(file_name, **kwargs)

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

from_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_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_json()

Returns a json string representation of the MSONable object.

to_lammps_dump(*args, **kwargs)

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

to_lammps_lmp(*args, **kwargs)

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

to_list(*args, **kwargs)

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

to_lmp(*args, **kwargs)

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

to_mlmd(*args, **kwargs)

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

to_mol(*args, **kwargs)

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

to_mol_file(*args, **kwargs)

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

to_movement(*args, **kwargs)

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

to_outcar(*args, **kwargs)

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

to_poscar(*args, **kwargs)

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

to_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.

unsafe_hash()

Returns an hash of the current object.

validate_monty_v1(_MSONable__input_value)

Pydantic validator with correct signature for pydantic v1.x

validate_monty_v2(_MSONable__input_value, _)

Pydantic validator with correct signature for pydantic v2.x

affine_map

affine_map_fv

apply_type_map

from_fmt

from_fmt_obj

has_virial

replace

rot_frame_lower_triangular

rot_lower_triangular

to_fmt_obj

DTYPES = (<dpdata.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)[source]
correction(hl_sys)[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_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_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_out(file_name, **kwargs)

Read data from dpdata.plugins.psi4.PSI4OutFormat format.

from_pwmat_atomconfig(file_name, **kwargs)

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

from_pwmat_finalconfig(file_name, **kwargs)

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

from_pwmat_mlmd(file_name, **kwargs)

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

from_pwmat_movement(file_name, **kwargs)

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

from_pwmat_output(file_name, **kwargs)

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

from_pymatgen_computedstructureentry(file_name, **kwargs)

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

from_pymatgen_molecule(file_name, **kwargs)

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

from_pymatgen_structure(file_name, **kwargs)

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

from_qe_cp_traj(file_name, **kwargs)

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

from_qe_pw_scf(file_name, **kwargs)

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

from_quip_gap_xyz(file_name, **kwargs)

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

from_quip_gap_xyz_file(file_name, **kwargs)

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

from_sdf(file_name, **kwargs)

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

from_sdf_file(file_name, **kwargs)

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

from_siesta_aiMD_output(file_name, **kwargs)

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

from_siesta_aimd_output(file_name, **kwargs)

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

from_siesta_output(file_name, **kwargs)

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

from_sqm_in(file_name, **kwargs)

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

from_sqm_out(file_name, **kwargs)

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

from_stru(file_name, **kwargs)

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

from_vasp_contcar(file_name, **kwargs)

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

from_vasp_outcar(file_name, **kwargs)

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

from_vasp_poscar(file_name, **kwargs)

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

from_vasp_string(file_name, **kwargs)

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

from_vasp_xml(file_name, **kwargs)

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

from_xml(file_name, **kwargs)

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

from_xyz(file_name, **kwargs)

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

has_virial()[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=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_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_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_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_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_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_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_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_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_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)[source]

Append systems or MultiSystems to systems.

Parameters:
*systemsSystem

The system to append

check_atom_names(system)[source]

Make atom_names in all systems equal, prevent inconsistent atom_types.

correction(hl_sys: 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_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, file_name, fmt='auto', type_map=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, **kwargs)[source]
from_finalconfig(file_name, **kwargs)

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

from_fmt_obj(fmtobj, directory, labeled=True, **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_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_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()[source]

Returns number of frames in all systems.

load_systems_from_file(file_name=None, fmt=None, **kwargs)[source]
minimize(*args: Any, minimizer: Union[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_idx(idx, nopbc=None)[source]

Pick atom index.

Parameters:
idxint or list or slice

atom index

nopbcBoolen (default: None)

If nopbc is True or False, set nopbc

Returns:
new_sys: MultiSystems

new system

predict(*args: Any, driver='dp', **kwargs: Any) MultiSystems[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, **kwargs) 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_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, directory, *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_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_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: Union[float, int], seed: Optional[int] = 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=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)[source]

Bases: MSONable

The data System.

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

For example, a water system named d_example has two molecules. The properties can be accessed by
  • d_example[‘atom_numbs’] : [2, 4]

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

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

  • d_example[‘orig’] : [0, 0, 0]

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

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

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

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

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

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

Attributes:
DTYPEStuple[DataType]

data types of this class

Methods

add_atom_names(atom_names)

Add atom_names that do not exist.

append(system)

Append a system to this system.

apply_pbc()

Append periodic boundary condition.

as_dict()

Returns data dict of System instance.

check_data()

Check if data is correct.

check_type_map(type_map)

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

convert_to_mixed_type([type_map])

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.

copy()

Returns a copy of the system.

dump(filename[, indent])

Dump .json or .yaml file.

extend(systems)

Extend a system list to this system.

from_3dmol(file_name, **kwargs)

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

from_abacus_lcao_md(file_name, **kwargs)

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

from_abacus_lcao_relax(file_name, **kwargs)

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

from_abacus_lcao_scf(file_name, **kwargs)

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

from_abacus_md(file_name, **kwargs)

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

from_abacus_pw_md(file_name, **kwargs)

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

from_abacus_pw_relax(file_name, **kwargs)

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

from_abacus_pw_scf(file_name, **kwargs)

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

from_abacus_relax(file_name, **kwargs)

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

from_abacus_scf(file_name, **kwargs)

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

from_abacus_stru(file_name, **kwargs)

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

from_amber_md(file_name, **kwargs)

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

from_ase_structure(file_name, **kwargs)

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

from_atomconfig(file_name, **kwargs)

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

from_contcar(file_name, **kwargs)

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

from_cp2k_aimd_output(file_name, **kwargs)

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

from_cp2k_output(file_name, **kwargs)

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

from_deepmd(file_name, **kwargs)

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

from_deepmd_comp(file_name, **kwargs)

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

from_deepmd_hdf5(file_name, **kwargs)

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

from_deepmd_npy(file_name, **kwargs)

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

from_deepmd_npy_mixed(file_name, **kwargs)

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

from_deepmd_raw(file_name, **kwargs)

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

from_dftbplus(file_name, **kwargs)

Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dict(d)

param d:

Dict representation.

from_dump(file_name, **kwargs)

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

from_fhi_aims_md(file_name, **kwargs)

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

from_fhi_aims_output(file_name, **kwargs)

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

from_fhi_aims_scf(file_name, **kwargs)

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

from_finalconfig(file_name, **kwargs)

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

from_gaussian_gjf(file_name, **kwargs)

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

from_gaussian_log(file_name, **kwargs)

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

from_gaussian_md(file_name, **kwargs)

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

from_gro(file_name, **kwargs)

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

from_gromacs_gro(file_name, **kwargs)

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

from_lammps_dump(file_name, **kwargs)

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

from_lammps_lmp(file_name, **kwargs)

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

from_list(file_name, **kwargs)

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

from_lmp(file_name, **kwargs)

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

from_mlmd(file_name, **kwargs)

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

from_mol(file_name, **kwargs)

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

from_mol_file(file_name, **kwargs)

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

from_movement(file_name, **kwargs)

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

from_outcar(file_name, **kwargs)

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

from_poscar(file_name, **kwargs)

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

from_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_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_json()

Returns a json string representation of the MSONable object.

to_lammps_dump(*args, **kwargs)

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

to_lammps_lmp(*args, **kwargs)

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

to_list(*args, **kwargs)

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

to_lmp(*args, **kwargs)

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

to_mlmd(*args, **kwargs)

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

to_mol(*args, **kwargs)

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

to_mol_file(*args, **kwargs)

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

to_movement(*args, **kwargs)

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

to_outcar(*args, **kwargs)

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

to_poscar(*args, **kwargs)

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

to_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.

unsafe_hash()

Returns an hash of the current object.

validate_monty_v1(_MSONable__input_value)

Pydantic validator with correct signature for pydantic v1.x

validate_monty_v2(_MSONable__input_value, _)

Pydantic validator with correct signature for pydantic v2.x

affine_map

apply_type_map

from_fmt

from_fmt_obj

replace

rot_frame_lower_triangular

rot_lower_triangular

to_fmt_obj

DTYPES = (<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)[source]

Add atom_names that do not exist.

affine_map(trans, f_idx=0)[source]
append(system)[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)[source]
as_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)[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=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, indent=4)[source]

Dump .json or .yaml file.

extend(systems)[source]

Extend a system list to this system.

Parameters:
systems[System1, System2, System3 ]

The list to extend

property formula

Return the formula of this system, like C3H5O2.

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_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(file_name, fmt='auto', **kwargs)[source]
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_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_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()[source]

Returns name of atoms.

get_atom_numbs()[source]

Returns number of atoms.

get_atom_types()[source]

Returns type of atoms.

get_natoms()[source]

Returns total number of atoms in the system.

get_nframes()[source]

Returns number of frames in the system.

get_ntypes() int[source]

Returns total number of atom types in the system.

static load(filename)[source]

Rebuild System obj. from .json or .yaml file.

map_atom_types(type_map=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: Union[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, cell_pert_fraction, atom_pert_distance, atom_pert_style='normal')[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.

Returns:
perturbed_systemSystem

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

pick_atom_idx(idx, nopbc=None)[source]

Pick atom index.

Parameters:
idxint or list or slice

atom index

nopbcBoolen (default: None)

If nopbc is True or False, set nopbc

Returns:
new_sys: System

new system

pick_by_amber_mask(param, maskstr, pass_coords=False, nopbc=None)[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 = '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: Tuple[DataType])[source]

Register data type.

Parameters:
*data_typetuple[DataType]

data type to be regiestered

remove_atom_names(atom_names)[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=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, end_atom_type, replace_num)[source]
replicate(ncopy)[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=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=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)[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, **kwargs) 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_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_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_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

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