dpdata package
- 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 extensionvasp/xml
: vasp xmlvasp/outcar
: vasp OUTCARdeepmd/raw
: deepmd-kit rawdeepmd/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 filesiesta/aimd_output
: siesta aimd output filegaussian/log
: gaussian logsgaussian/md
: gaussian ab initio molecular dynamicscp2k/output
: cp2k output filecp2k/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 filepwmat/out.mlmd
: pwmat scf output file
- type_maplist of str
Maps atom type to name. The atom with type ii is mapped to type_map[ii]. If not provided the atom names are assigned to ‘Type_1’, ‘Type_2’, ‘Type_3’…
- beginint
The beginning frame when loading MD trajectory.
- stepint
The number of skipped frames when loading MD trajectory.
- Attributes:
formula
Return the formula of this system, like C3H5O2.
- nopbc
uniq_formula
Return the uniq_formula of this system.
Methods
add_atom_names
(atom_names)Add atom_names that do not exist.
append
(system)Append a system to this system.
apply_pbc
()Append periodic boundary condition.
as_dict
()Returns data dict of System instance.
check_data
()Check if data is correct.
check_type_map
(type_map)Assign atom_names to type_map if type_map is given and different from atom_names.
convert_to_mixed_type
([type_map])Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
copy
()Returns a copy of the system.
correction
(hl_sys)Get energy and force correction between self and a high-level LabeledSystem.
dump
(filename[, indent])Dump .json or .yaml file.
extend
(systems)Extend a system list to this system.
from_3dmol
(file_name, **kwargs)Read data from
dpdata.plugins.3dmol.Py3DMolFormat
format.from_abacus_lcao_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_lcao_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_lcao_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_pw_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_pw_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_pw_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_stru
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSTRUFormat
format.from_amber_md
(file_name, **kwargs)Read data from
dpdata.plugins.amber.AmberMDFormat
format.from_ase_structure
(file_name, **kwargs)Read data from
dpdata.plugins.ase.ASEStructureFormat
format.from_atomconfig
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.from_contcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_cp2k_aimd_output
(file_name, **kwargs)Read data from
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.from_cp2k_output
(file_name, **kwargs)Read data from
dpdata.plugins.cp2k.CP2KOutputFormat
format.from_deepmd
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.from_deepmd_comp
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.from_deepmd_hdf5
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDHDF5Format
format.from_deepmd_npy
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.from_deepmd_npy_mixed
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDMixedFormat
format.from_deepmd_raw
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.from_dict
(d)- param d:
Dict representation.
from_dump
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.from_fhi_aims_md
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.from_fhi_aims_output
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.from_fhi_aims_scf
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiSCFFormat
format.from_finalconfig
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.from_gaussian_gjf
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussiaGJFFormat
format.from_gaussian_log
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussianLogFormat
format.from_gaussian_md
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussianMDFormat
format.from_gro
(file_name, **kwargs)Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.from_gromacs_gro
(file_name, **kwargs)Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.from_lammps_dump
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.from_lammps_lmp
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.from_list
(file_name, **kwargs)Read data from
dpdata.plugins.list.ListFormat
format.from_lmp
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.from_mlmd
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.from_mol
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.MolFormat
format.from_mol_file
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.MolFormat
format.from_movement
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.from_outcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPOutcarFormat
format.from_poscar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_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.Read data from
dpdata.plugins.pymatgen.PyMatgenCSEFormat
format.from_pymatgen_molecule
(file_name, **kwargs)Read data from
dpdata.plugins.pymatgen.PyMatgenMoleculeFormat
format.from_pymatgen_structure
(file_name, **kwargs)Read data from
dpdata.plugins.pymatgen.PyMatgenStructureFormat
format.from_qe_cp_traj
(file_name, **kwargs)Read data from
dpdata.plugins.qe.QECPTrajFormat
format.from_qe_pw_scf
(file_name, **kwargs)Read data from
dpdata.plugins.qe.QECPPWSCFFormat
format.from_quip_gap_xyz
(file_name, **kwargs)Read data from
dpdata.plugins.xyz.QuipGapXYZFormat
format.from_quip_gap_xyz_file
(file_name, **kwargs)Read data from
dpdata.plugins.xyz.QuipGapXYZFormat
format.from_sdf
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.SdfFormat
format.from_sdf_file
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.SdfFormat
format.from_siesta_aiMD_output
(file_name, **kwargs)Read data from
dpdata.plugins.siesta.SiestaAIMDOutputFormat
format.from_siesta_aimd_output
(file_name, **kwargs)Read data from
dpdata.plugins.siesta.SiestaAIMDOutputFormat
format.from_siesta_output
(file_name, **kwargs)Read data from
dpdata.plugins.siesta.SiestaOutputFormat
format.from_sqm_in
(file_name, **kwargs)Read data from
dpdata.plugins.amber.SQMINFormat
format.from_sqm_out
(file_name, **kwargs)Read data from
dpdata.plugins.amber.SQMOutFormat
format.from_stru
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSTRUFormat
format.from_vasp_contcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_vasp_outcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPOutcarFormat
format.from_vasp_poscar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_vasp_string
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPStringFormat
format.from_vasp_xml
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPXMLFormat
format.from_xml
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPXMLFormat
format.from_xyz
(file_name, **kwargs)Read data from
dpdata.plugins.xyz.XYZFormat
format.get_atom_names
()Returns name of atoms.
get_atom_numbs
()Returns number of atoms.
get_atom_types
()Returns type of atoms.
get_natoms
()Returns total number of atoms in the system.
get_nframes
()Returns number of frames in the system.
get_ntypes
()Returns total number of atom types in the system.
load
(filename)Rebuild System obj.
map_atom_types
([type_map])Map the atom types of the system.
minimize
(*args, minimizer, **kwargs)Minimize the geometry.
perturb
(pert_num, cell_pert_fraction, ...[, ...])Perturb each frame in the system randomly.
pick_atom_idx
(idx[, nopbc])Pick atom index.
pick_by_amber_mask
(param, maskstr[, ...])Pick atoms by amber mask.
predict
(*args[, driver])Predict energies and forces by a driver.
remove_atom_names
(atom_names)Remove atom names and all such atoms.
remove_outlier
([threshold])Remove outlier frames from the system.
remove_pbc
([protect_layer])This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
replicate
(ncopy)Replicate the each frame in the system in 3 dimensions.
shuffle
()Shuffle frames randomly.
sort_atom_names
([type_map])Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
sort_atom_types
()Sort atom types.
sub_system
(f_idx)Construct a subsystem from the system.
to
(fmt, *args, **kwargs)Dump systems to the specific format.
to_3dmol
(*args, **kwargs)Dump data to
dpdata.plugins.3dmol.Py3DMolFormat
format.to_abacus_lcao_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_lcao_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_lcao_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_pw_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_pw_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_pw_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_stru
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSTRUFormat
format.to_amber_md
(*args, **kwargs)Dump data to
dpdata.plugins.amber.AmberMDFormat
format.to_ase_structure
(*args, **kwargs)Dump data to
dpdata.plugins.ase.ASEStructureFormat
format.to_atomconfig
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.to_contcar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.to_cp2k_aimd_output
(*args, **kwargs)Dump data to
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.to_cp2k_output
(*args, **kwargs)Dump data to
dpdata.plugins.cp2k.CP2KOutputFormat
format.to_deepmd
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.to_deepmd_comp
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.to_deepmd_hdf5
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDHDF5Format
format.to_deepmd_npy
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.to_deepmd_npy_mixed
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDMixedFormat
format.to_deepmd_raw
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.to_dump
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.to_fhi_aims_md
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.to_fhi_aims_output
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.to_fhi_aims_scf
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiSCFFormat
format.to_finalconfig
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.to_gaussian_gjf
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussiaGJFFormat
format.to_gaussian_log
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussianLogFormat
format.to_gaussian_md
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussianMDFormat
format.to_gro
(*args, **kwargs)Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.to_gromacs_gro
(*args, **kwargs)Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.to_json
()Returns a json string representation of the MSONable object.
to_lammps_dump
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.to_lammps_lmp
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.to_list
(*args, **kwargs)Dump data to
dpdata.plugins.list.ListFormat
format.to_lmp
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.to_mlmd
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.to_mol
(*args, **kwargs)Dump data to
dpdata.plugins.rdkit.MolFormat
format.to_mol_file
(*args, **kwargs)Dump data to
dpdata.plugins.rdkit.MolFormat
format.to_movement
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.to_outcar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPOutcarFormat
format.to_poscar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.to_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
(v)pydantic Validator for MSONable pattern
affine_map
affine_map_fv
apply_type_map
from_fmt
from_fmt_obj
has_virial
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj
- DTYPES = (<dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>)
- 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_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(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.
- 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.
- to_3dmol(*args, **kwargs)
Dump data to
dpdata.plugins.3dmol.Py3DMolFormat
format.
- to_abacus_lcao_md(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.
- to_abacus_lcao_relax(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- to_abacus_lcao_scf(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.
- to_abacus_md(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.
- to_abacus_pw_md(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.
- to_abacus_pw_relax(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- to_abacus_pw_scf(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.
- to_abacus_relax(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- to_abacus_scf(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.
- to_abacus_stru(*args, **kwargs)
Dump data to
dpdata.plugins.abacus.AbacusSTRUFormat
format.
- to_amber_md(*args, **kwargs)
Dump data to
dpdata.plugins.amber.AmberMDFormat
format.
- to_ase_structure(*args, **kwargs)
Dump data to
dpdata.plugins.ase.ASEStructureFormat
format.
- to_atomconfig(*args, **kwargs)
Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.
- to_contcar(*args, **kwargs)
Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.
- to_cp2k_aimd_output(*args, **kwargs)
Dump data to
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.
- to_cp2k_output(*args, **kwargs)
Dump data to
dpdata.plugins.cp2k.CP2KOutputFormat
format.
- to_deepmd(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.
- to_deepmd_comp(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.
- to_deepmd_hdf5(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDHDF5Format
format.
- to_deepmd_npy(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.
- to_deepmd_npy_mixed(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDMixedFormat
format.
- to_deepmd_raw(*args, **kwargs)
Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.
- to_dump(*args, **kwargs)
Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.
- to_fhi_aims_md(*args, **kwargs)
Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.
- to_fhi_aims_output(*args, **kwargs)
Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.
- to_fhi_aims_scf(*args, **kwargs)
Dump data to
dpdata.plugins.fhi_aims.FhiSCFFormat
format.
- to_finalconfig(*args, **kwargs)
Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.
- to_gaussian_gjf(*args, **kwargs)
Dump data to
dpdata.plugins.gaussian.GaussiaGJFFormat
format.
- to_gaussian_log(*args, **kwargs)
Dump data to
dpdata.plugins.gaussian.GaussianLogFormat
format.
- to_gaussian_md(*args, **kwargs)
Dump data to
dpdata.plugins.gaussian.GaussianMDFormat
format.
- to_gro(*args, **kwargs)
Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.
- to_gromacs_gro(*args, **kwargs)
Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.
- to_lammps_dump(*args, **kwargs)
Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.
- to_lammps_lmp(*args, **kwargs)
Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.
- to_list(*args, **kwargs)
Dump data to
dpdata.plugins.list.ListFormat
format.
- to_lmp(*args, **kwargs)
Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.
- to_mlmd(*args, **kwargs)
Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.
- to_mol(*args, **kwargs)
Dump data to
dpdata.plugins.rdkit.MolFormat
format.
- to_mol_file(*args, **kwargs)
Dump data to
dpdata.plugins.rdkit.MolFormat
format.
- to_movement(*args, **kwargs)
Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.
- to_outcar(*args, **kwargs)
Dump data to
dpdata.plugins.vasp.VASPOutcarFormat
format.
- to_poscar(*args, **kwargs)
Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.
- to_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
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_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(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.
- 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_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, **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.
Append periodic boundary condition.
as_dict
()Returns data dict of System instance.
Check if data is correct.
check_type_map
(type_map)Assign atom_names to type_map if type_map is given and different from atom_names.
convert_to_mixed_type
([type_map])Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
copy
()Returns a copy of the system.
dump
(filename[, indent])Dump .json or .yaml file.
extend
(systems)Extend a system list to this system.
from_3dmol
(file_name, **kwargs)Read data from
dpdata.plugins.3dmol.Py3DMolFormat
format.from_abacus_lcao_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_lcao_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_lcao_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_pw_md
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.from_abacus_pw_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_pw_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_relax
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.from_abacus_scf
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.from_abacus_stru
(file_name, **kwargs)Read data from
dpdata.plugins.abacus.AbacusSTRUFormat
format.from_amber_md
(file_name, **kwargs)Read data from
dpdata.plugins.amber.AmberMDFormat
format.from_ase_structure
(file_name, **kwargs)Read data from
dpdata.plugins.ase.ASEStructureFormat
format.from_atomconfig
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.from_contcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_cp2k_aimd_output
(file_name, **kwargs)Read data from
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.from_cp2k_output
(file_name, **kwargs)Read data from
dpdata.plugins.cp2k.CP2KOutputFormat
format.from_deepmd
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.from_deepmd_comp
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.from_deepmd_hdf5
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDHDF5Format
format.from_deepmd_npy
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.from_deepmd_npy_mixed
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDMixedFormat
format.from_deepmd_raw
(file_name, **kwargs)Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.from_dict
(d)- param d:
Dict representation.
from_dump
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.from_fhi_aims_md
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.from_fhi_aims_output
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.from_fhi_aims_scf
(file_name, **kwargs)Read data from
dpdata.plugins.fhi_aims.FhiSCFFormat
format.from_finalconfig
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.from_gaussian_gjf
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussiaGJFFormat
format.from_gaussian_log
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussianLogFormat
format.from_gaussian_md
(file_name, **kwargs)Read data from
dpdata.plugins.gaussian.GaussianMDFormat
format.from_gro
(file_name, **kwargs)Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.from_gromacs_gro
(file_name, **kwargs)Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.from_lammps_dump
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.from_lammps_lmp
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.from_list
(file_name, **kwargs)Read data from
dpdata.plugins.list.ListFormat
format.from_lmp
(file_name, **kwargs)Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.from_mlmd
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.from_mol
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.MolFormat
format.from_mol_file
(file_name, **kwargs)Read data from
dpdata.plugins.rdkit.MolFormat
format.from_movement
(file_name, **kwargs)Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.from_outcar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPOutcarFormat
format.from_poscar
(file_name, **kwargs)Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.from_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.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.Returns name of atoms.
Returns number of atoms.
Returns type of atoms.
Returns total number of atoms in the system.
Returns number of frames in the system.
Returns total number of atom types in the system.
load
(filename)Rebuild System obj.
map_atom_types
([type_map])Map the atom types of the system.
minimize
(*args, minimizer, **kwargs)Minimize the geometry.
perturb
(pert_num, cell_pert_fraction, ...[, ...])Perturb each frame in the system randomly.
pick_atom_idx
(idx[, nopbc])Pick atom index.
pick_by_amber_mask
(param, maskstr[, ...])Pick atoms by amber mask.
predict
(*args[, driver])Predict energies and forces by a driver.
remove_atom_names
(atom_names)Remove atom names and all such atoms.
remove_pbc
([protect_layer])This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
replicate
(ncopy)Replicate the each frame in the system in 3 dimensions.
shuffle
()Shuffle frames randomly.
sort_atom_names
([type_map])Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
Sort atom types.
sub_system
(f_idx)Construct a subsystem from the system.
to
(fmt, *args, **kwargs)Dump systems to the specific format.
to_3dmol
(*args, **kwargs)Dump data to
dpdata.plugins.3dmol.Py3DMolFormat
format.to_abacus_lcao_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_lcao_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_lcao_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_pw_md
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusMDFormat
format.to_abacus_pw_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_pw_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_relax
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusRelaxFormat
format.to_abacus_scf
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSCFFormat
format.to_abacus_stru
(*args, **kwargs)Dump data to
dpdata.plugins.abacus.AbacusSTRUFormat
format.to_amber_md
(*args, **kwargs)Dump data to
dpdata.plugins.amber.AmberMDFormat
format.to_ase_structure
(*args, **kwargs)Dump data to
dpdata.plugins.ase.ASEStructureFormat
format.to_atomconfig
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.to_contcar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.to_cp2k_aimd_output
(*args, **kwargs)Dump data to
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.to_cp2k_output
(*args, **kwargs)Dump data to
dpdata.plugins.cp2k.CP2KOutputFormat
format.to_deepmd
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.to_deepmd_comp
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.to_deepmd_hdf5
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDHDF5Format
format.to_deepmd_npy
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDCompFormat
format.to_deepmd_npy_mixed
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDMixedFormat
format.to_deepmd_raw
(*args, **kwargs)Dump data to
dpdata.plugins.deepmd.DeePMDRawFormat
format.to_dump
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.to_fhi_aims_md
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.to_fhi_aims_output
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiMDFormat
format.to_fhi_aims_scf
(*args, **kwargs)Dump data to
dpdata.plugins.fhi_aims.FhiSCFFormat
format.to_finalconfig
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.to_gaussian_gjf
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussiaGJFFormat
format.to_gaussian_log
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussianLogFormat
format.to_gaussian_md
(*args, **kwargs)Dump data to
dpdata.plugins.gaussian.GaussianMDFormat
format.to_gro
(*args, **kwargs)Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.to_gromacs_gro
(*args, **kwargs)Dump data to
dpdata.plugins.gromacs.GromacsGroFormat
format.to_json
()Returns a json string representation of the MSONable object.
to_lammps_dump
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSDumpFormat
format.to_lammps_lmp
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.to_list
(*args, **kwargs)Dump data to
dpdata.plugins.list.ListFormat
format.to_lmp
(*args, **kwargs)Dump data to
dpdata.plugins.lammps.LAMMPSLmpFormat
format.to_mlmd
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.to_mol
(*args, **kwargs)Dump data to
dpdata.plugins.rdkit.MolFormat
format.to_mol_file
(*args, **kwargs)Dump data to
dpdata.plugins.rdkit.MolFormat
format.to_movement
(*args, **kwargs)Dump data to
dpdata.plugins.pwmat.PwmatOutputFormat
format.to_outcar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPOutcarFormat
format.to_poscar
(*args, **kwargs)Dump data to
dpdata.plugins.vasp.VASPPoscarFormat
format.to_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
(v)pydantic Validator for MSONable pattern
affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj
- DTYPES = (<dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>, <dpdata.system.DataType object>)
- append(system)[source]
Append a system to this system.
- Parameters:
- systemSystem
The system to append
- 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
- 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.
- from_3dmol(file_name, **kwargs)
Read data from
dpdata.plugins.3dmol.Py3DMolFormat
format.
- from_abacus_lcao_md(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.
- from_abacus_lcao_relax(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- from_abacus_lcao_scf(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.
- from_abacus_md(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.
- from_abacus_pw_md(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusMDFormat
format.
- from_abacus_pw_relax(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- from_abacus_pw_scf(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.
- from_abacus_relax(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusRelaxFormat
format.
- from_abacus_scf(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusSCFFormat
format.
- from_abacus_stru(file_name, **kwargs)
Read data from
dpdata.plugins.abacus.AbacusSTRUFormat
format.
- from_amber_md(file_name, **kwargs)
Read data from
dpdata.plugins.amber.AmberMDFormat
format.
- from_ase_structure(file_name, **kwargs)
Read data from
dpdata.plugins.ase.ASEStructureFormat
format.
- from_atomconfig(file_name, **kwargs)
Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.
- from_contcar(file_name, **kwargs)
Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.
- from_cp2k_aimd_output(file_name, **kwargs)
Read data from
dpdata.plugins.cp2k.CP2KAIMDOutputFormat
format.
- from_cp2k_output(file_name, **kwargs)
Read data from
dpdata.plugins.cp2k.CP2KOutputFormat
format.
- from_deepmd(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.
- from_deepmd_comp(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.
- from_deepmd_hdf5(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDHDF5Format
format.
- from_deepmd_npy(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDCompFormat
format.
- from_deepmd_npy_mixed(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDMixedFormat
format.
- from_deepmd_raw(file_name, **kwargs)
Read data from
dpdata.plugins.deepmd.DeePMDRawFormat
format.
- from_dump(file_name, **kwargs)
Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.
- from_fhi_aims_md(file_name, **kwargs)
Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.
- from_fhi_aims_output(file_name, **kwargs)
Read data from
dpdata.plugins.fhi_aims.FhiMDFormat
format.
- from_fhi_aims_scf(file_name, **kwargs)
Read data from
dpdata.plugins.fhi_aims.FhiSCFFormat
format.
- from_finalconfig(file_name, **kwargs)
Read data from
dpdata.plugins.pwmat.PwmatAtomconfigFormat
format.
- from_gaussian_gjf(file_name, **kwargs)
Read data from
dpdata.plugins.gaussian.GaussiaGJFFormat
format.
- from_gaussian_log(file_name, **kwargs)
Read data from
dpdata.plugins.gaussian.GaussianLogFormat
format.
- from_gaussian_md(file_name, **kwargs)
Read data from
dpdata.plugins.gaussian.GaussianMDFormat
format.
- from_gro(file_name, **kwargs)
Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.
- from_gromacs_gro(file_name, **kwargs)
Read data from
dpdata.plugins.gromacs.GromacsGroFormat
format.
- from_lammps_dump(file_name, **kwargs)
Read data from
dpdata.plugins.lammps.LAMMPSDumpFormat
format.
- from_lammps_lmp(file_name, **kwargs)
Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.
- from_list(file_name, **kwargs)
Read data from
dpdata.plugins.list.ListFormat
format.
- from_lmp(file_name, **kwargs)
Read data from
dpdata.plugins.lammps.LAMMPSLmpFormat
format.
- from_mlmd(file_name, **kwargs)
Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.
- from_mol(file_name, **kwargs)
Read data from
dpdata.plugins.rdkit.MolFormat
format.
- from_mol_file(file_name, **kwargs)
Read data from
dpdata.plugins.rdkit.MolFormat
format.
- from_movement(file_name, **kwargs)
Read data from
dpdata.plugins.pwmat.PwmatOutputFormat
format.
- from_outcar(file_name, **kwargs)
Read data from
dpdata.plugins.vasp.VASPOutcarFormat
format.
- from_poscar(file_name, **kwargs)
Read data from
dpdata.plugins.vasp.VASPPoscarFormat
format.
- from_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.
- 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”)
- 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
- 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.
- 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_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, **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
- dpdata.abacus package
- dpdata.amber package
- dpdata.cp2k package
- dpdata.deepmd package
- dpdata.fhi_aims package
- dpdata.gaussian package
- dpdata.gromacs package
- dpdata.lammps package
- dpdata package
LabeledSystem
LabeledSystem.DTYPES
LabeledSystem.affine_map_fv()
LabeledSystem.correction()
LabeledSystem.from_3dmol()
LabeledSystem.from_abacus_lcao_md()
LabeledSystem.from_abacus_lcao_relax()
LabeledSystem.from_abacus_lcao_scf()
LabeledSystem.from_abacus_md()
LabeledSystem.from_abacus_pw_md()
LabeledSystem.from_abacus_pw_relax()
LabeledSystem.from_abacus_pw_scf()
LabeledSystem.from_abacus_relax()
LabeledSystem.from_abacus_scf()
LabeledSystem.from_abacus_stru()
LabeledSystem.from_amber_md()
LabeledSystem.from_ase_structure()
LabeledSystem.from_atomconfig()
LabeledSystem.from_contcar()
LabeledSystem.from_cp2k_aimd_output()
LabeledSystem.from_cp2k_output()
LabeledSystem.from_deepmd()
LabeledSystem.from_deepmd_comp()
LabeledSystem.from_deepmd_hdf5()
LabeledSystem.from_deepmd_npy()
LabeledSystem.from_deepmd_npy_mixed()
LabeledSystem.from_deepmd_raw()
LabeledSystem.from_dump()
LabeledSystem.from_fhi_aims_md()
LabeledSystem.from_fhi_aims_output()
LabeledSystem.from_fhi_aims_scf()
LabeledSystem.from_finalconfig()
LabeledSystem.from_fmt_obj()
LabeledSystem.from_gaussian_gjf()
LabeledSystem.from_gaussian_log()
LabeledSystem.from_gaussian_md()
LabeledSystem.from_gro()
LabeledSystem.from_gromacs_gro()
LabeledSystem.from_lammps_dump()
LabeledSystem.from_lammps_lmp()
LabeledSystem.from_list()
LabeledSystem.from_lmp()
LabeledSystem.from_mlmd()
LabeledSystem.from_mol()
LabeledSystem.from_mol_file()
LabeledSystem.from_movement()
LabeledSystem.from_outcar()
LabeledSystem.from_poscar()
LabeledSystem.from_psi4_out()
LabeledSystem.from_pwmat_atomconfig()
LabeledSystem.from_pwmat_finalconfig()
LabeledSystem.from_pwmat_mlmd()
LabeledSystem.from_pwmat_movement()
LabeledSystem.from_pwmat_output()
LabeledSystem.from_pymatgen_computedstructureentry()
LabeledSystem.from_pymatgen_molecule()
LabeledSystem.from_pymatgen_structure()
LabeledSystem.from_qe_cp_traj()
LabeledSystem.from_qe_pw_scf()
LabeledSystem.from_quip_gap_xyz()
LabeledSystem.from_quip_gap_xyz_file()
LabeledSystem.from_sdf()
LabeledSystem.from_sdf_file()
LabeledSystem.from_siesta_aiMD_output()
LabeledSystem.from_siesta_aimd_output()
LabeledSystem.from_siesta_output()
LabeledSystem.from_sqm_in()
LabeledSystem.from_sqm_out()
LabeledSystem.from_stru()
LabeledSystem.from_vasp_contcar()
LabeledSystem.from_vasp_outcar()
LabeledSystem.from_vasp_poscar()
LabeledSystem.from_vasp_string()
LabeledSystem.from_vasp_xml()
LabeledSystem.from_xml()
LabeledSystem.from_xyz()
LabeledSystem.has_virial()
LabeledSystem.post_funcs
LabeledSystem.remove_outlier()
LabeledSystem.rot_frame_lower_triangular()
LabeledSystem.to_3dmol()
LabeledSystem.to_abacus_lcao_md()
LabeledSystem.to_abacus_lcao_relax()
LabeledSystem.to_abacus_lcao_scf()
LabeledSystem.to_abacus_md()
LabeledSystem.to_abacus_pw_md()
LabeledSystem.to_abacus_pw_relax()
LabeledSystem.to_abacus_pw_scf()
LabeledSystem.to_abacus_relax()
LabeledSystem.to_abacus_scf()
LabeledSystem.to_abacus_stru()
LabeledSystem.to_amber_md()
LabeledSystem.to_ase_structure()
LabeledSystem.to_atomconfig()
LabeledSystem.to_contcar()
LabeledSystem.to_cp2k_aimd_output()
LabeledSystem.to_cp2k_output()
LabeledSystem.to_deepmd()
LabeledSystem.to_deepmd_comp()
LabeledSystem.to_deepmd_hdf5()
LabeledSystem.to_deepmd_npy()
LabeledSystem.to_deepmd_npy_mixed()
LabeledSystem.to_deepmd_raw()
LabeledSystem.to_dump()
LabeledSystem.to_fhi_aims_md()
LabeledSystem.to_fhi_aims_output()
LabeledSystem.to_fhi_aims_scf()
LabeledSystem.to_finalconfig()
LabeledSystem.to_fmt_obj()
LabeledSystem.to_gaussian_gjf()
LabeledSystem.to_gaussian_log()
LabeledSystem.to_gaussian_md()
LabeledSystem.to_gro()
LabeledSystem.to_gromacs_gro()
LabeledSystem.to_lammps_dump()
LabeledSystem.to_lammps_lmp()
LabeledSystem.to_list()
LabeledSystem.to_lmp()
LabeledSystem.to_mlmd()
LabeledSystem.to_mol()
LabeledSystem.to_mol_file()
LabeledSystem.to_movement()
LabeledSystem.to_outcar()
LabeledSystem.to_poscar()
LabeledSystem.to_psi4_out()
LabeledSystem.to_pwmat_atomconfig()
LabeledSystem.to_pwmat_finalconfig()
LabeledSystem.to_pwmat_mlmd()
LabeledSystem.to_pwmat_movement()
LabeledSystem.to_pwmat_output()
LabeledSystem.to_pymatgen_ComputedStructureEntry()
LabeledSystem.to_pymatgen_computedstructureentry()
LabeledSystem.to_pymatgen_molecule()
LabeledSystem.to_pymatgen_structure()
LabeledSystem.to_qe_cp_traj()
LabeledSystem.to_qe_pw_scf()
LabeledSystem.to_quip_gap_xyz()
LabeledSystem.to_quip_gap_xyz_file()
LabeledSystem.to_sdf()
LabeledSystem.to_sdf_file()
LabeledSystem.to_siesta_aimd_output()
LabeledSystem.to_siesta_output()
LabeledSystem.to_sqm_in()
LabeledSystem.to_sqm_out()
LabeledSystem.to_stru()
LabeledSystem.to_vasp_contcar()
LabeledSystem.to_vasp_outcar()
LabeledSystem.to_vasp_poscar()
LabeledSystem.to_vasp_string()
LabeledSystem.to_vasp_xml()
LabeledSystem.to_xml()
LabeledSystem.to_xyz()
MultiSystems
MultiSystems.append()
MultiSystems.check_atom_names()
MultiSystems.correction()
MultiSystems.from_3dmol()
MultiSystems.from_abacus_lcao_md()
MultiSystems.from_abacus_lcao_relax()
MultiSystems.from_abacus_lcao_scf()
MultiSystems.from_abacus_md()
MultiSystems.from_abacus_pw_md()
MultiSystems.from_abacus_pw_relax()
MultiSystems.from_abacus_pw_scf()
MultiSystems.from_abacus_relax()
MultiSystems.from_abacus_scf()
MultiSystems.from_abacus_stru()
MultiSystems.from_amber_md()
MultiSystems.from_ase_structure()
MultiSystems.from_atomconfig()
MultiSystems.from_contcar()
MultiSystems.from_cp2k_aimd_output()
MultiSystems.from_cp2k_output()
MultiSystems.from_deepmd()
MultiSystems.from_deepmd_comp()
MultiSystems.from_deepmd_hdf5()
MultiSystems.from_deepmd_npy()
MultiSystems.from_deepmd_npy_mixed()
MultiSystems.from_deepmd_raw()
MultiSystems.from_dir()
MultiSystems.from_dump()
MultiSystems.from_fhi_aims_md()
MultiSystems.from_fhi_aims_output()
MultiSystems.from_fhi_aims_scf()
MultiSystems.from_file()
MultiSystems.from_finalconfig()
MultiSystems.from_fmt_obj()
MultiSystems.from_gaussian_gjf()
MultiSystems.from_gaussian_log()
MultiSystems.from_gaussian_md()
MultiSystems.from_gro()
MultiSystems.from_gromacs_gro()
MultiSystems.from_lammps_dump()
MultiSystems.from_lammps_lmp()
MultiSystems.from_list()
MultiSystems.from_lmp()
MultiSystems.from_mlmd()
MultiSystems.from_mol()
MultiSystems.from_mol_file()
MultiSystems.from_movement()
MultiSystems.from_outcar()
MultiSystems.from_poscar()
MultiSystems.from_psi4_out()
MultiSystems.from_pwmat_atomconfig()
MultiSystems.from_pwmat_finalconfig()
MultiSystems.from_pwmat_mlmd()
MultiSystems.from_pwmat_movement()
MultiSystems.from_pwmat_output()
MultiSystems.from_pymatgen_computedstructureentry()
MultiSystems.from_pymatgen_molecule()
MultiSystems.from_pymatgen_structure()
MultiSystems.from_qe_cp_traj()
MultiSystems.from_qe_pw_scf()
MultiSystems.from_quip_gap_xyz()
MultiSystems.from_quip_gap_xyz_file()
MultiSystems.from_sdf()
MultiSystems.from_sdf_file()
MultiSystems.from_siesta_aiMD_output()
MultiSystems.from_siesta_aimd_output()
MultiSystems.from_siesta_output()
MultiSystems.from_sqm_in()
MultiSystems.from_sqm_out()
MultiSystems.from_stru()
MultiSystems.from_vasp_contcar()
MultiSystems.from_vasp_outcar()
MultiSystems.from_vasp_poscar()
MultiSystems.from_vasp_string()
MultiSystems.from_vasp_xml()
MultiSystems.from_xml()
MultiSystems.from_xyz()
MultiSystems.get_nframes()
MultiSystems.load_systems_from_file()
MultiSystems.minimize()
MultiSystems.pick_atom_idx()
MultiSystems.predict()
MultiSystems.to()
MultiSystems.to_3dmol()
MultiSystems.to_abacus_lcao_md()
MultiSystems.to_abacus_lcao_relax()
MultiSystems.to_abacus_lcao_scf()
MultiSystems.to_abacus_md()
MultiSystems.to_abacus_pw_md()
MultiSystems.to_abacus_pw_relax()
MultiSystems.to_abacus_pw_scf()
MultiSystems.to_abacus_relax()
MultiSystems.to_abacus_scf()
MultiSystems.to_abacus_stru()
MultiSystems.to_amber_md()
MultiSystems.to_ase_structure()
MultiSystems.to_atomconfig()
MultiSystems.to_contcar()
MultiSystems.to_cp2k_aimd_output()
MultiSystems.to_cp2k_output()
MultiSystems.to_deepmd()
MultiSystems.to_deepmd_comp()
MultiSystems.to_deepmd_hdf5()
MultiSystems.to_deepmd_npy()
MultiSystems.to_deepmd_npy_mixed()
MultiSystems.to_deepmd_raw()
MultiSystems.to_dump()
MultiSystems.to_fhi_aims_md()
MultiSystems.to_fhi_aims_output()
MultiSystems.to_fhi_aims_scf()
MultiSystems.to_finalconfig()
MultiSystems.to_fmt_obj()
MultiSystems.to_gaussian_gjf()
MultiSystems.to_gaussian_log()
MultiSystems.to_gaussian_md()
MultiSystems.to_gro()
MultiSystems.to_gromacs_gro()
MultiSystems.to_lammps_dump()
MultiSystems.to_lammps_lmp()
MultiSystems.to_list()
MultiSystems.to_lmp()
MultiSystems.to_mlmd()
MultiSystems.to_mol()
MultiSystems.to_mol_file()
MultiSystems.to_movement()
MultiSystems.to_outcar()
MultiSystems.to_poscar()
MultiSystems.to_psi4_out()
MultiSystems.to_pwmat_atomconfig()
MultiSystems.to_pwmat_finalconfig()
MultiSystems.to_pwmat_mlmd()
MultiSystems.to_pwmat_movement()
MultiSystems.to_pwmat_output()
MultiSystems.to_pymatgen_ComputedStructureEntry()
MultiSystems.to_pymatgen_computedstructureentry()
MultiSystems.to_pymatgen_molecule()
MultiSystems.to_pymatgen_structure()
MultiSystems.to_qe_cp_traj()
MultiSystems.to_qe_pw_scf()
MultiSystems.to_quip_gap_xyz()
MultiSystems.to_quip_gap_xyz_file()
MultiSystems.to_sdf()
MultiSystems.to_sdf_file()
MultiSystems.to_siesta_aimd_output()
MultiSystems.to_siesta_output()
MultiSystems.to_sqm_in()
MultiSystems.to_sqm_out()
MultiSystems.to_stru()
MultiSystems.to_vasp_contcar()
MultiSystems.to_vasp_outcar()
MultiSystems.to_vasp_poscar()
MultiSystems.to_vasp_string()
MultiSystems.to_vasp_xml()
MultiSystems.to_xml()
MultiSystems.to_xyz()
MultiSystems.train_test_split()
System
System.DTYPES
System.add_atom_names()
System.affine_map()
System.append()
System.apply_pbc()
System.apply_type_map()
System.as_dict()
System.check_data()
System.check_type_map()
System.convert_to_mixed_type()
System.copy()
System.dump()
System.extend()
System.formula
System.from_3dmol()
System.from_abacus_lcao_md()
System.from_abacus_lcao_relax()
System.from_abacus_lcao_scf()
System.from_abacus_md()
System.from_abacus_pw_md()
System.from_abacus_pw_relax()
System.from_abacus_pw_scf()
System.from_abacus_relax()
System.from_abacus_scf()
System.from_abacus_stru()
System.from_amber_md()
System.from_ase_structure()
System.from_atomconfig()
System.from_contcar()
System.from_cp2k_aimd_output()
System.from_cp2k_output()
System.from_deepmd()
System.from_deepmd_comp()
System.from_deepmd_hdf5()
System.from_deepmd_npy()
System.from_deepmd_npy_mixed()
System.from_deepmd_raw()
System.from_dump()
System.from_fhi_aims_md()
System.from_fhi_aims_output()
System.from_fhi_aims_scf()
System.from_finalconfig()
System.from_fmt()
System.from_fmt_obj()
System.from_gaussian_gjf()
System.from_gaussian_log()
System.from_gaussian_md()
System.from_gro()
System.from_gromacs_gro()
System.from_lammps_dump()
System.from_lammps_lmp()
System.from_list()
System.from_lmp()
System.from_mlmd()
System.from_mol()
System.from_mol_file()
System.from_movement()
System.from_outcar()
System.from_poscar()
System.from_psi4_out()
System.from_pwmat_atomconfig()
System.from_pwmat_finalconfig()
System.from_pwmat_mlmd()
System.from_pwmat_movement()
System.from_pwmat_output()
System.from_pymatgen_computedstructureentry()
System.from_pymatgen_molecule()
System.from_pymatgen_structure()
System.from_qe_cp_traj()
System.from_qe_pw_scf()
System.from_quip_gap_xyz()
System.from_quip_gap_xyz_file()
System.from_sdf()
System.from_sdf_file()
System.from_siesta_aiMD_output()
System.from_siesta_aimd_output()
System.from_siesta_output()
System.from_sqm_in()
System.from_sqm_out()
System.from_stru()
System.from_vasp_contcar()
System.from_vasp_outcar()
System.from_vasp_poscar()
System.from_vasp_string()
System.from_vasp_xml()
System.from_xml()
System.from_xyz()
System.get_atom_names()
System.get_atom_numbs()
System.get_atom_types()
System.get_natoms()
System.get_nframes()
System.get_ntypes()
System.load()
System.map_atom_types()
System.minimize()
System.nopbc
System.perturb()
System.pick_atom_idx()
System.pick_by_amber_mask()
System.post_funcs
System.predict()
System.remove_atom_names()
System.remove_pbc()
System.replace()
System.replicate()
System.rot_frame_lower_triangular()
System.rot_lower_triangular()
System.shuffle()
System.sort_atom_names()
System.sort_atom_types()
System.sub_system()
System.to()
System.to_3dmol()
System.to_abacus_lcao_md()
System.to_abacus_lcao_relax()
System.to_abacus_lcao_scf()
System.to_abacus_md()
System.to_abacus_pw_md()
System.to_abacus_pw_relax()
System.to_abacus_pw_scf()
System.to_abacus_relax()
System.to_abacus_scf()
System.to_abacus_stru()
System.to_amber_md()
System.to_ase_structure()
System.to_atomconfig()
System.to_contcar()
System.to_cp2k_aimd_output()
System.to_cp2k_output()
System.to_deepmd()
System.to_deepmd_comp()
System.to_deepmd_hdf5()
System.to_deepmd_npy()
System.to_deepmd_npy_mixed()
System.to_deepmd_raw()
System.to_dump()
System.to_fhi_aims_md()
System.to_fhi_aims_output()
System.to_fhi_aims_scf()
System.to_finalconfig()
System.to_fmt_obj()
System.to_gaussian_gjf()
System.to_gaussian_log()
System.to_gaussian_md()
System.to_gro()
System.to_gromacs_gro()
System.to_lammps_dump()
System.to_lammps_lmp()
System.to_list()
System.to_lmp()
System.to_mlmd()
System.to_mol()
System.to_mol_file()
System.to_movement()
System.to_outcar()
System.to_poscar()
System.to_psi4_out()
System.to_pwmat_atomconfig()
System.to_pwmat_finalconfig()
System.to_pwmat_mlmd()
System.to_pwmat_movement()
System.to_pwmat_output()
System.to_pymatgen_ComputedStructureEntry()
System.to_pymatgen_computedstructureentry()
System.to_pymatgen_molecule()
System.to_pymatgen_structure()
System.to_qe_cp_traj()
System.to_qe_pw_scf()
System.to_quip_gap_xyz()
System.to_quip_gap_xyz_file()
System.to_sdf()
System.to_sdf_file()
System.to_siesta_aimd_output()
System.to_siesta_output()
System.to_sqm_in()
System.to_sqm_out()
System.to_stru()
System.to_vasp_contcar()
System.to_vasp_outcar()
System.to_vasp_poscar()
System.to_vasp_string()
System.to_vasp_xml()
System.to_xml()
System.to_xyz()
System.uniq_formula
- Subpackages
- dpdata.abacus package
- dpdata.amber package
- dpdata.cp2k package
- dpdata.deepmd package
- dpdata.fhi_aims package
- dpdata.gaussian package
- dpdata.gromacs package
- dpdata.lammps package
- dpdata.plugins package
- Submodules
- dpdata.plugins.3dmol module
- dpdata.plugins.abacus module
- dpdata.plugins.amber module
- dpdata.plugins.ase module
- dpdata.plugins.cp2k module
- dpdata.plugins.deepmd module
- dpdata.plugins.dftbplus module
- dpdata.plugins.fhi_aims module
- dpdata.plugins.gaussian module
- dpdata.plugins.gromacs module
- dpdata.plugins.lammps module
- dpdata.plugins.list module
- dpdata.plugins.psi4 module
- dpdata.plugins.pwmat module
- dpdata.plugins.pymatgen module
- dpdata.plugins.qe module
- dpdata.plugins.rdkit module
- dpdata.plugins.siesta module
- dpdata.plugins.vasp module
- dpdata.plugins.xyz module
- dpdata.psi4 package
- dpdata.pwmat package
- dpdata.pymatgen package
- dpdata.qe package
- dpdata.rdkit package
- dpdata.siesta package
- dpdata.vasp package
- dpdata.xyz package
- Submodules
- dpdata.ase_calculator module
- dpdata.bond_order_system module
- dpdata.cli module
- dpdata.driver module
- dpdata.format module
Format
Format.MultiMode
Format.MultiModes
Format.from_bond_order_system()
Format.from_labeled_system()
Format.from_multi_systems()
Format.from_system()
Format.get_formats()
Format.get_from_methods()
Format.get_to_methods()
Format.mix_system()
Format.post()
Format.register()
Format.register_from()
Format.register_to()
Format.to_bond_order_system()
Format.to_labeled_system()
Format.to_multi_systems()
Format.to_system()
- dpdata.periodic_table module
- dpdata.plugin module
- dpdata.stat module
- dpdata.system module
Axis
DataError
DataType
LabeledSystem
LabeledSystem.DTYPES
LabeledSystem.affine_map_fv()
LabeledSystem.correction()
LabeledSystem.from_3dmol()
LabeledSystem.from_abacus_lcao_md()
LabeledSystem.from_abacus_lcao_relax()
LabeledSystem.from_abacus_lcao_scf()
LabeledSystem.from_abacus_md()
LabeledSystem.from_abacus_pw_md()
LabeledSystem.from_abacus_pw_relax()
LabeledSystem.from_abacus_pw_scf()
LabeledSystem.from_abacus_relax()
LabeledSystem.from_abacus_scf()
LabeledSystem.from_abacus_stru()
LabeledSystem.from_amber_md()
LabeledSystem.from_ase_structure()
LabeledSystem.from_atomconfig()
LabeledSystem.from_contcar()
LabeledSystem.from_cp2k_aimd_output()
LabeledSystem.from_cp2k_output()
LabeledSystem.from_deepmd()
LabeledSystem.from_deepmd_comp()
LabeledSystem.from_deepmd_hdf5()
LabeledSystem.from_deepmd_npy()
LabeledSystem.from_deepmd_npy_mixed()
LabeledSystem.from_deepmd_raw()
LabeledSystem.from_dump()
LabeledSystem.from_fhi_aims_md()
LabeledSystem.from_fhi_aims_output()
LabeledSystem.from_fhi_aims_scf()
LabeledSystem.from_finalconfig()
LabeledSystem.from_fmt_obj()
LabeledSystem.from_gaussian_gjf()
LabeledSystem.from_gaussian_log()
LabeledSystem.from_gaussian_md()
LabeledSystem.from_gro()
LabeledSystem.from_gromacs_gro()
LabeledSystem.from_lammps_dump()
LabeledSystem.from_lammps_lmp()
LabeledSystem.from_list()
LabeledSystem.from_lmp()
LabeledSystem.from_mlmd()
LabeledSystem.from_mol()
LabeledSystem.from_mol_file()
LabeledSystem.from_movement()
LabeledSystem.from_outcar()
LabeledSystem.from_poscar()
LabeledSystem.from_psi4_out()
LabeledSystem.from_pwmat_atomconfig()
LabeledSystem.from_pwmat_finalconfig()
LabeledSystem.from_pwmat_mlmd()
LabeledSystem.from_pwmat_movement()
LabeledSystem.from_pwmat_output()
LabeledSystem.from_pymatgen_computedstructureentry()
LabeledSystem.from_pymatgen_molecule()
LabeledSystem.from_pymatgen_structure()
LabeledSystem.from_qe_cp_traj()
LabeledSystem.from_qe_pw_scf()
LabeledSystem.from_quip_gap_xyz()
LabeledSystem.from_quip_gap_xyz_file()
LabeledSystem.from_sdf()
LabeledSystem.from_sdf_file()
LabeledSystem.from_siesta_aiMD_output()
LabeledSystem.from_siesta_aimd_output()
LabeledSystem.from_siesta_output()
LabeledSystem.from_sqm_in()
LabeledSystem.from_sqm_out()
LabeledSystem.from_stru()
LabeledSystem.from_vasp_contcar()
LabeledSystem.from_vasp_outcar()
LabeledSystem.from_vasp_poscar()
LabeledSystem.from_vasp_string()
LabeledSystem.from_vasp_xml()
LabeledSystem.from_xml()
LabeledSystem.from_xyz()
LabeledSystem.has_virial()
LabeledSystem.post_funcs
LabeledSystem.remove_outlier()
LabeledSystem.rot_frame_lower_triangular()
LabeledSystem.to_3dmol()
LabeledSystem.to_abacus_lcao_md()
LabeledSystem.to_abacus_lcao_relax()
LabeledSystem.to_abacus_lcao_scf()
LabeledSystem.to_abacus_md()
LabeledSystem.to_abacus_pw_md()
LabeledSystem.to_abacus_pw_relax()
LabeledSystem.to_abacus_pw_scf()
LabeledSystem.to_abacus_relax()
LabeledSystem.to_abacus_scf()
LabeledSystem.to_abacus_stru()
LabeledSystem.to_amber_md()
LabeledSystem.to_ase_structure()
LabeledSystem.to_atomconfig()
LabeledSystem.to_contcar()
LabeledSystem.to_cp2k_aimd_output()
LabeledSystem.to_cp2k_output()
LabeledSystem.to_deepmd()
LabeledSystem.to_deepmd_comp()
LabeledSystem.to_deepmd_hdf5()
LabeledSystem.to_deepmd_npy()
LabeledSystem.to_deepmd_npy_mixed()
LabeledSystem.to_deepmd_raw()
LabeledSystem.to_dump()
LabeledSystem.to_fhi_aims_md()
LabeledSystem.to_fhi_aims_output()
LabeledSystem.to_fhi_aims_scf()
LabeledSystem.to_finalconfig()
LabeledSystem.to_fmt_obj()
LabeledSystem.to_gaussian_gjf()
LabeledSystem.to_gaussian_log()
LabeledSystem.to_gaussian_md()
LabeledSystem.to_gro()
LabeledSystem.to_gromacs_gro()
LabeledSystem.to_lammps_dump()
LabeledSystem.to_lammps_lmp()
LabeledSystem.to_list()
LabeledSystem.to_lmp()
LabeledSystem.to_mlmd()
LabeledSystem.to_mol()
LabeledSystem.to_mol_file()
LabeledSystem.to_movement()
LabeledSystem.to_outcar()
LabeledSystem.to_poscar()
LabeledSystem.to_psi4_out()
LabeledSystem.to_pwmat_atomconfig()
LabeledSystem.to_pwmat_finalconfig()
LabeledSystem.to_pwmat_mlmd()
LabeledSystem.to_pwmat_movement()
LabeledSystem.to_pwmat_output()
LabeledSystem.to_pymatgen_ComputedStructureEntry()
LabeledSystem.to_pymatgen_computedstructureentry()
LabeledSystem.to_pymatgen_molecule()
LabeledSystem.to_pymatgen_structure()
LabeledSystem.to_qe_cp_traj()
LabeledSystem.to_qe_pw_scf()
LabeledSystem.to_quip_gap_xyz()
LabeledSystem.to_quip_gap_xyz_file()
LabeledSystem.to_sdf()
LabeledSystem.to_sdf_file()
LabeledSystem.to_siesta_aimd_output()
LabeledSystem.to_siesta_output()
LabeledSystem.to_sqm_in()
LabeledSystem.to_sqm_out()
LabeledSystem.to_stru()
LabeledSystem.to_vasp_contcar()
LabeledSystem.to_vasp_outcar()
LabeledSystem.to_vasp_poscar()
LabeledSystem.to_vasp_string()
LabeledSystem.to_vasp_xml()
LabeledSystem.to_xml()
LabeledSystem.to_xyz()
MultiSystems
MultiSystems.append()
MultiSystems.check_atom_names()
MultiSystems.correction()
MultiSystems.from_3dmol()
MultiSystems.from_abacus_lcao_md()
MultiSystems.from_abacus_lcao_relax()
MultiSystems.from_abacus_lcao_scf()
MultiSystems.from_abacus_md()
MultiSystems.from_abacus_pw_md()
MultiSystems.from_abacus_pw_relax()
MultiSystems.from_abacus_pw_scf()
MultiSystems.from_abacus_relax()
MultiSystems.from_abacus_scf()
MultiSystems.from_abacus_stru()
MultiSystems.from_amber_md()
MultiSystems.from_ase_structure()
MultiSystems.from_atomconfig()
MultiSystems.from_contcar()
MultiSystems.from_cp2k_aimd_output()
MultiSystems.from_cp2k_output()
MultiSystems.from_deepmd()
MultiSystems.from_deepmd_comp()
MultiSystems.from_deepmd_hdf5()
MultiSystems.from_deepmd_npy()
MultiSystems.from_deepmd_npy_mixed()
MultiSystems.from_deepmd_raw()
MultiSystems.from_dir()
MultiSystems.from_dump()
MultiSystems.from_fhi_aims_md()
MultiSystems.from_fhi_aims_output()
MultiSystems.from_fhi_aims_scf()
MultiSystems.from_file()
MultiSystems.from_finalconfig()
MultiSystems.from_fmt_obj()
MultiSystems.from_gaussian_gjf()
MultiSystems.from_gaussian_log()
MultiSystems.from_gaussian_md()
MultiSystems.from_gro()
MultiSystems.from_gromacs_gro()
MultiSystems.from_lammps_dump()
MultiSystems.from_lammps_lmp()
MultiSystems.from_list()
MultiSystems.from_lmp()
MultiSystems.from_mlmd()
MultiSystems.from_mol()
MultiSystems.from_mol_file()
MultiSystems.from_movement()
MultiSystems.from_outcar()
MultiSystems.from_poscar()
MultiSystems.from_psi4_out()
MultiSystems.from_pwmat_atomconfig()
MultiSystems.from_pwmat_finalconfig()
MultiSystems.from_pwmat_mlmd()
MultiSystems.from_pwmat_movement()
MultiSystems.from_pwmat_output()
MultiSystems.from_pymatgen_computedstructureentry()
MultiSystems.from_pymatgen_molecule()
MultiSystems.from_pymatgen_structure()
MultiSystems.from_qe_cp_traj()
MultiSystems.from_qe_pw_scf()
MultiSystems.from_quip_gap_xyz()
MultiSystems.from_quip_gap_xyz_file()
MultiSystems.from_sdf()
MultiSystems.from_sdf_file()
MultiSystems.from_siesta_aiMD_output()
MultiSystems.from_siesta_aimd_output()
MultiSystems.from_siesta_output()
MultiSystems.from_sqm_in()
MultiSystems.from_sqm_out()
MultiSystems.from_stru()
MultiSystems.from_vasp_contcar()
MultiSystems.from_vasp_outcar()
MultiSystems.from_vasp_poscar()
MultiSystems.from_vasp_string()
MultiSystems.from_vasp_xml()
MultiSystems.from_xml()
MultiSystems.from_xyz()
MultiSystems.get_nframes()
MultiSystems.load_systems_from_file()
MultiSystems.minimize()
MultiSystems.pick_atom_idx()
MultiSystems.predict()
MultiSystems.to()
MultiSystems.to_3dmol()
MultiSystems.to_abacus_lcao_md()
MultiSystems.to_abacus_lcao_relax()
MultiSystems.to_abacus_lcao_scf()
MultiSystems.to_abacus_md()
MultiSystems.to_abacus_pw_md()
MultiSystems.to_abacus_pw_relax()
MultiSystems.to_abacus_pw_scf()
MultiSystems.to_abacus_relax()
MultiSystems.to_abacus_scf()
MultiSystems.to_abacus_stru()
MultiSystems.to_amber_md()
MultiSystems.to_ase_structure()
MultiSystems.to_atomconfig()
MultiSystems.to_contcar()
MultiSystems.to_cp2k_aimd_output()
MultiSystems.to_cp2k_output()
MultiSystems.to_deepmd()
MultiSystems.to_deepmd_comp()
MultiSystems.to_deepmd_hdf5()
MultiSystems.to_deepmd_npy()
MultiSystems.to_deepmd_npy_mixed()
MultiSystems.to_deepmd_raw()
MultiSystems.to_dump()
MultiSystems.to_fhi_aims_md()
MultiSystems.to_fhi_aims_output()
MultiSystems.to_fhi_aims_scf()
MultiSystems.to_finalconfig()
MultiSystems.to_fmt_obj()
MultiSystems.to_gaussian_gjf()
MultiSystems.to_gaussian_log()
MultiSystems.to_gaussian_md()
MultiSystems.to_gro()
MultiSystems.to_gromacs_gro()
MultiSystems.to_lammps_dump()
MultiSystems.to_lammps_lmp()
MultiSystems.to_list()
MultiSystems.to_lmp()
MultiSystems.to_mlmd()
MultiSystems.to_mol()
MultiSystems.to_mol_file()
MultiSystems.to_movement()
MultiSystems.to_outcar()
MultiSystems.to_poscar()
MultiSystems.to_psi4_out()
MultiSystems.to_pwmat_atomconfig()
MultiSystems.to_pwmat_finalconfig()
MultiSystems.to_pwmat_mlmd()
MultiSystems.to_pwmat_movement()
MultiSystems.to_pwmat_output()
MultiSystems.to_pymatgen_ComputedStructureEntry()
MultiSystems.to_pymatgen_computedstructureentry()
MultiSystems.to_pymatgen_molecule()
MultiSystems.to_pymatgen_structure()
MultiSystems.to_qe_cp_traj()
MultiSystems.to_qe_pw_scf()
MultiSystems.to_quip_gap_xyz()
MultiSystems.to_quip_gap_xyz_file()
MultiSystems.to_sdf()
MultiSystems.to_sdf_file()
MultiSystems.to_siesta_aimd_output()
MultiSystems.to_siesta_output()
MultiSystems.to_sqm_in()
MultiSystems.to_sqm_out()
MultiSystems.to_stru()
MultiSystems.to_vasp_contcar()
MultiSystems.to_vasp_outcar()
MultiSystems.to_vasp_poscar()
MultiSystems.to_vasp_string()
MultiSystems.to_vasp_xml()
MultiSystems.to_xml()
MultiSystems.to_xyz()
MultiSystems.train_test_split()
System
System.DTYPES
System.add_atom_names()
System.affine_map()
System.append()
System.apply_pbc()
System.apply_type_map()
System.as_dict()
System.check_data()
System.check_type_map()
System.convert_to_mixed_type()
System.copy()
System.dump()
System.extend()
System.formula
System.from_3dmol()
System.from_abacus_lcao_md()
System.from_abacus_lcao_relax()
System.from_abacus_lcao_scf()
System.from_abacus_md()
System.from_abacus_pw_md()
System.from_abacus_pw_relax()
System.from_abacus_pw_scf()
System.from_abacus_relax()
System.from_abacus_scf()
System.from_abacus_stru()
System.from_amber_md()
System.from_ase_structure()
System.from_atomconfig()
System.from_contcar()
System.from_cp2k_aimd_output()
System.from_cp2k_output()
System.from_deepmd()
System.from_deepmd_comp()
System.from_deepmd_hdf5()
System.from_deepmd_npy()
System.from_deepmd_npy_mixed()
System.from_deepmd_raw()
System.from_dump()
System.from_fhi_aims_md()
System.from_fhi_aims_output()
System.from_fhi_aims_scf()
System.from_finalconfig()
System.from_fmt()
System.from_fmt_obj()
System.from_gaussian_gjf()
System.from_gaussian_log()
System.from_gaussian_md()
System.from_gro()
System.from_gromacs_gro()
System.from_lammps_dump()
System.from_lammps_lmp()
System.from_list()
System.from_lmp()
System.from_mlmd()
System.from_mol()
System.from_mol_file()
System.from_movement()
System.from_outcar()
System.from_poscar()
System.from_psi4_out()
System.from_pwmat_atomconfig()
System.from_pwmat_finalconfig()
System.from_pwmat_mlmd()
System.from_pwmat_movement()
System.from_pwmat_output()
System.from_pymatgen_computedstructureentry()
System.from_pymatgen_molecule()
System.from_pymatgen_structure()
System.from_qe_cp_traj()
System.from_qe_pw_scf()
System.from_quip_gap_xyz()
System.from_quip_gap_xyz_file()
System.from_sdf()
System.from_sdf_file()
System.from_siesta_aiMD_output()
System.from_siesta_aimd_output()
System.from_siesta_output()
System.from_sqm_in()
System.from_sqm_out()
System.from_stru()
System.from_vasp_contcar()
System.from_vasp_outcar()
System.from_vasp_poscar()
System.from_vasp_string()
System.from_vasp_xml()
System.from_xml()
System.from_xyz()
System.get_atom_names()
System.get_atom_numbs()
System.get_atom_types()
System.get_natoms()
System.get_nframes()
System.get_ntypes()
System.load()
System.map_atom_types()
System.minimize()
System.nopbc
System.perturb()
System.pick_atom_idx()
System.pick_by_amber_mask()
System.post_funcs
System.predict()
System.remove_atom_names()
System.remove_pbc()
System.replace()
System.replicate()
System.rot_frame_lower_triangular()
System.rot_lower_triangular()
System.shuffle()
System.sort_atom_names()
System.sort_atom_types()
System.sub_system()
System.to()
System.to_3dmol()
System.to_abacus_lcao_md()
System.to_abacus_lcao_relax()
System.to_abacus_lcao_scf()
System.to_abacus_md()
System.to_abacus_pw_md()
System.to_abacus_pw_relax()
System.to_abacus_pw_scf()
System.to_abacus_relax()
System.to_abacus_scf()
System.to_abacus_stru()
System.to_amber_md()
System.to_ase_structure()
System.to_atomconfig()
System.to_contcar()
System.to_cp2k_aimd_output()
System.to_cp2k_output()
System.to_deepmd()
System.to_deepmd_comp()
System.to_deepmd_hdf5()
System.to_deepmd_npy()
System.to_deepmd_npy_mixed()
System.to_deepmd_raw()
System.to_dump()
System.to_fhi_aims_md()
System.to_fhi_aims_output()
System.to_fhi_aims_scf()
System.to_finalconfig()
System.to_fmt_obj()
System.to_gaussian_gjf()
System.to_gaussian_log()
System.to_gaussian_md()
System.to_gro()
System.to_gromacs_gro()
System.to_lammps_dump()
System.to_lammps_lmp()
System.to_list()
System.to_lmp()
System.to_mlmd()
System.to_mol()
System.to_mol_file()
System.to_movement()
System.to_outcar()
System.to_poscar()
System.to_psi4_out()
System.to_pwmat_atomconfig()
System.to_pwmat_finalconfig()
System.to_pwmat_mlmd()
System.to_pwmat_movement()
System.to_pwmat_output()
System.to_pymatgen_ComputedStructureEntry()
System.to_pymatgen_computedstructureentry()
System.to_pymatgen_molecule()
System.to_pymatgen_structure()
System.to_qe_cp_traj()
System.to_qe_pw_scf()
System.to_quip_gap_xyz()
System.to_quip_gap_xyz_file()
System.to_sdf()
System.to_sdf_file()
System.to_siesta_aimd_output()
System.to_siesta_output()
System.to_sqm_in()
System.to_sqm_out()
System.to_stru()
System.to_vasp_contcar()
System.to_vasp_outcar()
System.to_vasp_poscar()
System.to_vasp_string()
System.to_vasp_xml()
System.to_xml()
System.to_xyz()
System.uniq_formula
add_format_methods()
get_atom_perturb_vector()
get_cell_perturb_matrix()
get_cls_name()
load_format()
- dpdata.unit module
- dpdata.utils module
- dpdata.plugins package
- Submodules
- dpdata.plugins.3dmol module
- dpdata.plugins.abacus module
- dpdata.plugins.amber module
- dpdata.plugins.ase module
- dpdata.plugins.cp2k module
- dpdata.plugins.deepmd module
- dpdata.plugins.dftbplus module
- dpdata.plugins.fhi_aims module
- dpdata.plugins.gaussian module
- dpdata.plugins.gromacs module
- dpdata.plugins.lammps module
- dpdata.plugins.list module
- dpdata.plugins.psi4 module
- dpdata.plugins.pwmat module
- dpdata.plugins.pymatgen module
- dpdata.plugins.qe module
- dpdata.plugins.rdkit module
- dpdata.plugins.siesta module
- dpdata.plugins.vasp module
- dpdata.plugins.xyz module
- dpdata.psi4 package
- dpdata.pwmat package
- dpdata.pymatgen package
- dpdata.qe package
- dpdata.rdkit package
- dpdata.siesta package
- dpdata.vasp package
- dpdata.xyz package
Submodules
dpdata.ase_calculator module
dpdata.bond_order_system module
dpdata.cli module
Command line interface for dpdata.