Welcome to dpdata’s documentation!

Try dpdata online

Command line interface

dpdata: Manipulating multiple atomic simulation data formats

usage: dpdata [-h] [--to_file TO_FILE] [--from_format FROM_FORMAT]
              [--to_format TO_FORMAT] [--no-labeled] [--multi]
              [--type-map TYPE_MAP [TYPE_MAP ...]] [--version]
              from_file

Positional Arguments

from_file: read data from a file

Named Arguments

--to_file, -O

dump data to a file

--from_format, -i

the format of from_file

Default: “auto”

--to_format, -o

the format of to_file

--no-labeled, -n

labels aren’t provided

Default: False

--multi, -m

the system contains multiple directories

Default: False

--type-map, -t

type map

--version

show program’s version number and exit

Supported Formats

dpdata supports the following formats:

Supported Formats
Format	Alias	Supported Conversions
psi4/out format	`psi4/out`	LabeledSystem()
psi4/inp format	`psi4/inp`	System.to() LabeledSystem.to()
cp2k/aimd_output format	`cp2k/aimd_output`	LabeledSystem()
cp2k/output format	`cp2k/output`	LabeledSystem()
orca/spout format	`orca/spout`	LabeledSystem()
stru format	`stru` `abacus/stru`	System() System.to() LabeledSystem.to()
abacus/lcao/scf format	`abacus/lcao/scf` `abacus/pw/scf` `abacus/scf`	LabeledSystem()
abacus/lcao/md format	`abacus/lcao/md` `abacus/pw/md` `abacus/md`	LabeledSystem()
abacus/lcao/relax format	`abacus/lcao/relax` `abacus/pw/relax` `abacus/relax`	LabeledSystem()
vasp/contcar format	`vasp/contcar` `vasp/poscar` `contcar` `poscar`	System() System.to() LabeledSystem.to()
vasp/string format	`vasp/string`	System.to() LabeledSystem.to()
vasp/outcar format	`vasp/outcar` `outcar`	LabeledSystem()
vasp/xml format	`vasp/xml` `xml`	LabeledSystem()
deepmd/raw format	`deepmd/raw` `deepmd`	System() System.to() LabeledSystem.to() LabeledSystem() MultiSystems.load_systems_from_file() MultiSystems.to()
deepmd/comp format	`deepmd/comp` `deepmd/npy`	System() System.to() LabeledSystem.to() LabeledSystem() MultiSystems.load_systems_from_file() MultiSystems.to()
deepmd/npy/mixed format	`deepmd/npy/mixed`	System.to() LabeledSystem.to() MultiSystems.load_systems_from_file() MultiSystems.to()
deepmd/hdf5 format	`deepmd/hdf5`	System() System.to() LabeledSystem.to() LabeledSystem() MultiSystems.load_systems_from_file() MultiSystems.to()
siesta/output format	`siesta/output`	System() LabeledSystem()
siesta/aimd_output format	`siesta/aimd_output`	System() LabeledSystem()
pymatgen/structure format	`pymatgen/structure`	System.to() LabeledSystem.to()
pymatgen/molecule format	`pymatgen/molecule`	System() System.to() LabeledSystem.to()
pymatgen/computedstructureentry format	`pymatgen/computedstructureentry`	LabeledSystem.to()
list format	`list`	System.to() LabeledSystem.to()
mol_file format	`mol_file` `mol`	BondOrderSystem() BondOrderSystem.to()
sdf_file format	`sdf_file` `sdf`	BondOrderSystem() BondOrderSystem.to()
lammps/lmp format	`lammps/lmp` `lmp`	System() System.to() LabeledSystem.to()
lammps/dump format	`lammps/dump` `dump`	System()
pwmat/output format	`pwmat/output` `pwmat/mlmd` `pwmat/movement` `mlmd` `movement`	LabeledSystem()
pwmat/final.config format	`pwmat/final.config` `pwmat/atom.config` `final.config` `atom.config`	System() System.to() LabeledSystem.to()
ase/structure format	`ase/structure`	System() System.to() LabeledSystem.to() LabeledSystem() MultiSystems.load_systems_from_file()
ase/traj format	`ase/traj`	System() LabeledSystem()
gaussian/log format	`gaussian/log`	LabeledSystem()
gaussian/md format	`gaussian/md`	LabeledSystem()
gaussian/gjf format	`gaussian/gjf`	System() System.to() LabeledSystem.to()
fhi_aims/output format	`fhi_aims/output` `fhi_aims/md`	LabeledSystem()
fhi_aims/scf format	`fhi_aims/scf`	LabeledSystem()
qe/cp/traj format	`qe/cp/traj`	System() LabeledSystem()
qe/pw/scf format	`qe/pw/scf`	LabeledSystem()
3dmol format	`3dmol`	System.to() LabeledSystem.to()
xyz format	`xyz`	System() System.to() LabeledSystem.to()
quip/gap/xyz_file format	`quip/gap/xyz_file` `quip/gap/xyz`	LabeledSystem() MultiSystems.load_systems_from_file()
gromacs/gro format	`gromacs/gro` `gro`	System() System.to() LabeledSystem.to()
n2p2 format	`n2p2`	LabeledSystem() LabeledSystem.to()
dftbplus format	`dftbplus`	LabeledSystem()
amber/md format	`amber/md`	System() LabeledSystem()
sqm/out format	`sqm/out`	System() LabeledSystem()
sqm/in format	`sqm/in`	System.to() LabeledSystem.to()
openmx/md format	`openmx/md`	System() LabeledSystem()

ase/structure format

Class: ASEStructureFormat

Format for the Atomic Simulation Environment (ase).

ASE supports parsing a few dozen of data formats. As described in i the documentation, many of these formats can be determined automatically. Use the ase_fmt keyword argument to supply the format if automatic detection fails.

Conversions

Convert from this format to System

dpdata.System(atoms: 'ase.Atoms', fmt: Literal['ase/structure'] = None) → dpdata.system.System

dpdata.System.from_ase_structure(atoms: 'ase.Atoms') → dpdata.system.System

Convert ase.Atoms to a System.

Parameters:

atomsase.Atoms: an ASE Atoms, containing a structure

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['ase/structure'])

dpdata.System.to_ase_structure()

Convert System to ASE Atom obj.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['ase/structure'])

dpdata.LabeledSystem.to_ase_structure()

Convert System to ASE Atoms object.

Convert from this format to LabeledSystem

dpdata.LabeledSystem(atoms: 'ase.Atoms', fmt: Literal['ase/structure'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_ase_structure(atoms: 'ase.Atoms') → dpdata.system.LabeledSystem

Convert ase.Atoms to a LabeledSystem. Energies and forces are calculated by the calculator.

Parameters:

atomsase.Atoms: an ASE Atoms, containing a structure

Returns:

LabeledSystem: converted system

Raises:

RuntimeError: ASE will raise RuntimeError if the atoms does not have a calculator

Convert from this format to MultiSystems

dpdata.MultiSystems.from_ase_structure(file_name: str, begin: int | None = None, end: int | None = None, step: int | None = None, ase_fmt: str | None = None) → dpdata.system.MultiSystems

Convert a ASE supported file to ASE Atoms.

It will finally be converted to MultiSystems.

Parameters:

file_namestr: path to file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step
ase_fmtstr, optional: ASE format. See the ASE documentation about supported formats

Returns:

MultiSystems: converted system

ase/traj format

Class: ASETrajFormat

Format for the ASE’s trajectory format <https://wiki.fysik.dtu.dk/ase/ase/io/trajectory.html#module-ase.io.trajectory>`_ (ase).’ a `traj’ contains a sequence of frames, each of which is an `Atoms’ object.

Conversions

Convert from this format to System

dpdata.System(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1, fmt: Literal['ase/traj'] = None) → dpdata.system.System

dpdata.System.from_ase_traj(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1) → dpdata.system.System

Read ASE’s trajectory file to System of multiple frames.

Parameters:

file_namestr: ASE’s trajectory file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1, fmt: Literal['ase/traj'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_ase_traj(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1) → dpdata.system.LabeledSystem

Read ASE’s trajectory file to System of multiple frames.

Parameters:

file_namestr: ASE’s trajectory file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step

Returns:

LabeledSystem: converted system

abacus/lcao/md format

abacus/pw/md format

abacus/md format

Class: AbacusMDFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/lcao/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/pw/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_lcao_md(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_pw_md(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_md(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

abacus/lcao/relax format

abacus/pw/relax format

abacus/relax format

Class: AbacusRelaxFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/lcao/relax'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/pw/relax'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/relax'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_lcao_relax(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_pw_relax(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_relax(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

abacus/lcao/scf format

abacus/pw/scf format

abacus/scf format

Class: AbacusSCFFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/lcao/scf'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/pw/scf'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['abacus/scf'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_lcao_scf(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_pw_scf(file_name) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_abacus_scf(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

stru format

abacus/stru format

Class: AbacusSTRUFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['stru'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['abacus/stru'] = None) → dpdata.system.System

dpdata.System.from_stru(file_name) → dpdata.system.System

dpdata.System.from_abacus_stru(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['stru'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['stru'], file_name, frame_idx=0)

dpdata.System.to_stru(file_name, frame_idx=0)

dpdata.System.to_abacus_stru(file_name, frame_idx=0)

Dump the system into ABACUS STRU format file.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump
pp_filelist of string, optional: List of pseudo potential files
numerical_orbitallist of string, optional: List of orbital files
masslist of float, optional: List of atomic masses
numerical_descriptorstr, optional: numerical descriptor file

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['stru'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['stru'], file_name, frame_idx=0)

dpdata.LabeledSystem.to_stru(file_name, frame_idx=0)

dpdata.LabeledSystem.to_abacus_stru(file_name, frame_idx=0)

Dump the system into ABACUS STRU format file.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump
pp_filelist of string, optional: List of pseudo potential files
numerical_orbitallist of string, optional: List of orbital files
masslist of float, optional: List of atomic masses
numerical_descriptorstr, optional: numerical descriptor file

amber/md format

Class: AmberMDFormat

Conversions

Convert from this format to System

dpdata.System(file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None, fmt: Literal['amber/md'] = None) → dpdata.system.System

dpdata.System.from_amber_md(file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, fmt: Literal['amber/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_amber_md(file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

cp2k/aimd_output format

Class: CP2KAIMDOutputFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, restart=False, fmt: Literal['cp2k/aimd_output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_cp2k_aimd_output(file_name, restart=False) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

cp2k/output format

Class: CP2KOutputFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, restart=False, fmt: Literal['cp2k/output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_cp2k_output(file_name, restart=False) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

dftbplus format

Class: DFTBplusFormat

The DFTBplusFormat class handles files in the DFTB+ format.

This class provides a method to read DFTB+ files from a labeled system and returns a dictionary containing various properties of the system.For more information, please refer to the official documentation at the following URL: https://dftbplus.org/documentation

Attributes:

None

Methods

from_labeled_system(file_paths, **kwargs): Reads system information from files.

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_paths, fmt: Literal['dftbplus'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_dftbplus(file_paths) → dpdata.system.LabeledSystem

Reads system information from the given DFTB+ file paths.

Parameters:

file_pathstuple: A tuple containing the input and output file paths. - Input file (file_in): Contains information about symbols and coord. - Output file (file_out): Contains information about energy and force.

Returns:

LabeledSystem: converted system

deepmd/comp format

deepmd/npy format

Class: DeePMDCompFormat

Conversions

Convert from this format to System

dpdata.System(file_name, type_map=None, fmt: Literal['deepmd/comp'] = None) → dpdata.system.System

dpdata.System(file_name, type_map=None, fmt: Literal['deepmd/npy'] = None) → dpdata.system.System

dpdata.System.from_deepmd_comp(file_name, type_map=None) → dpdata.system.System

dpdata.System.from_deepmd_npy(file_name, type_map=None) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['deepmd/comp'], file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.System.to(fmt: Literal['deepmd/comp'], file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.System.to_deepmd_comp(file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.System.to_deepmd_npy(file_name, set_size=5000, prec=<class 'numpy.float64'>)

Dump the system in deepmd compressed format (numpy binary) to folder.

The frames are firstly split to sets, then dumped to seperated subfolders named as folder/set.000, folder/set.001, ….

Each set contains set_size frames. The last set may have less frames than set_size.

Parameters:

file_namestr: The output folder
set_sizeint: The size of each set.
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['deepmd/comp'], file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.LabeledSystem.to(fmt: Literal['deepmd/comp'], file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.LabeledSystem.to_deepmd_comp(file_name, set_size=5000, prec=<class 'numpy.float64'>)

dpdata.LabeledSystem.to_deepmd_npy(file_name, set_size=5000, prec=<class 'numpy.float64'>)

Dump the system in deepmd compressed format (numpy binary) to folder.

The frames are firstly split to sets, then dumped to seperated subfolders named as folder/set.000, folder/set.001, ….

Each set contains set_size frames. The last set may have less frames than set_size.

Parameters:

file_namestr: The output folder
set_sizeint: The size of each set.
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, type_map=None, fmt: Literal['deepmd/comp'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, type_map=None, fmt: Literal['deepmd/npy'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_deepmd_comp(file_name, type_map=None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_deepmd_npy(file_name, type_map=None) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

Convert from this format to MultiSystems

dpdata.MultiSystems.from_deepmd_comp(directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.from_deepmd_npy(directory) → dpdata.system.MultiSystems

Convert this format to MultiSystems.

Parameters:

directorystr: directory of systems

Returns:

MultiSystems: converted system

Convert from MultiSystems to this format

dpdata.MultiSystems.to(fmt: Literal['deepmd/comp'], directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to(fmt: Literal['deepmd/comp'], directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd_comp(directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd_npy(directory) → dpdata.system.MultiSystems

Convert MultiSystems to this format.

Parameters:

directorystr: directory to save systems

Returns:

MultiSystems: this system

deepmd/hdf5 format

Class: DeePMDHDF5Format

HDF5 format for DeePMD-kit.

Examples

Dump a MultiSystems to a HDF5 file:

>>> import dpdata
>>> dpdata.MultiSystems().from_deepmd_npy("data").to_deepmd_hdf5("data.hdf5")

Conversions

Convert from this format to System

dpdata.System(file_name: 'str | (h5py.Group | h5py.File)', type_map: 'list[str] | None' = None, fmt: Literal['deepmd/hdf5'] = None) → dpdata.system.System

dpdata.System.from_deepmd_hdf5(file_name: 'str | (h5py.Group | h5py.File)', type_map: 'list[str] | None' = None) → dpdata.system.System

Convert HDF5 file to System data.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
type_mapdict[str]: type map

Returns:

System: converted system

Raises:

TypeError: file_name is not str or h5py.Group or h5py.File

Convert from System to this format

dpdata.System.to(fmt: Literal['deepmd/hdf5'], file_name: 'str | (h5py.Group | h5py.File)', set_size: 'int' = 5000, comp_prec: 'np.dtype' = <class 'numpy.float64'>)

dpdata.System.to_deepmd_hdf5(file_name: 'str | (h5py.Group | h5py.File)', set_size: 'int' = 5000, comp_prec: 'np.dtype' = <class 'numpy.float64'>)

Convert System data to HDF5 file.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
set_sizeint, default=5000: set size
comp_precnp.dtype: data precision

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['deepmd/hdf5'], file_name: 'str | (h5py.Group | h5py.File)', set_size: 'int' = 5000, comp_prec: 'np.dtype' = <class 'numpy.float64'>)

dpdata.LabeledSystem.to_deepmd_hdf5(file_name: 'str | (h5py.Group | h5py.File)', set_size: 'int' = 5000, comp_prec: 'np.dtype' = <class 'numpy.float64'>)

Convert System data to HDF5 file.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
set_sizeint, default=5000: set size
comp_precnp.dtype: data precision

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name: 'str | (h5py.Group | h5py.File)', type_map: 'list[str] | None' = None, fmt: Literal['deepmd/hdf5'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_deepmd_hdf5(file_name: 'str | (h5py.Group | h5py.File)', type_map: 'list[str] | None' = None) → dpdata.system.LabeledSystem

Convert HDF5 file to LabeledSystem data.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
type_mapdict[str]: type map

Returns:

LabeledSystem: converted system

Raises:

TypeError: file_name is not str or h5py.Group or h5py.File

Convert from this format to MultiSystems

dpdata.MultiSystems.from_deepmd_hdf5(directory: 'str') → dpdata.system.MultiSystems

Generate HDF5 groups from a HDF5 file, which will be passed to from_system.

Parameters:

directorystr: HDF5 file name

Returns:

MultiSystems: converted system

Convert from MultiSystems to this format

dpdata.MultiSystems.to(fmt: Literal['deepmd/hdf5'], directory: 'str') → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd_hdf5(directory: 'str') → dpdata.system.MultiSystems

Generate HDF5 groups, which will be passed to to_system.

Parameters:

directorystr: HDF5 file name

Returns:

MultiSystems: this system

deepmd/npy/mixed format

Class: DeePMDMixedFormat

Mixed type numpy format for DeePMD-kit. Under this format, systems with the same number of atoms but different formula can be put together for a larger system, especially when the frame numbers in systems are sparse. This also helps to mixture the type information together for model training with type embedding network.

Examples

Dump a MultiSystems into a mixed type numpy directory:

>>> import dpdata
>>> dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")

Load a mixed type data into a MultiSystems:

>>> import dpdata
>>> dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['deepmd/npy/mixed'], file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>)

dpdata.System.to_deepmd_npy_mixed(file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>)

Dump the system in deepmd mixed type format (numpy binary) to folder.

The frames were already split to different systems, so these frames can be dumped to one single subfolders: named as folder/set.000, containing less than set_size frames.

Parameters:

file_namestr: The output folder
set_sizeint, default=2000: set size
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['deepmd/npy/mixed'], file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>)

dpdata.LabeledSystem.to_deepmd_npy_mixed(file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>)

Dump the system in deepmd mixed type format (numpy binary) to folder.

The frames were already split to different systems, so these frames can be dumped to one single subfolders: named as folder/set.000, containing less than set_size frames.

Parameters:

file_namestr: The output folder
set_sizeint, default=2000: set size
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data

Convert from this format to MultiSystems

dpdata.MultiSystems.from_deepmd_npy_mixed(directory) → dpdata.system.MultiSystems

Convert this format to MultiSystems.

Parameters:

directorystr: directory of systems

Returns:

MultiSystems: converted system

Convert from MultiSystems to this format

dpdata.MultiSystems.to(fmt: Literal['deepmd/npy/mixed'], directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd_npy_mixed(directory) → dpdata.system.MultiSystems

Convert MultiSystems to this format.

Parameters:

directorystr: directory to save systems

Returns:

MultiSystems: this system

deepmd/raw format

deepmd format

Class: DeePMDRawFormat

Conversions

Convert from this format to System

dpdata.System(file_name, type_map=None, fmt: Literal['deepmd/raw'] = None) → dpdata.system.System

dpdata.System(file_name, type_map=None, fmt: Literal['deepmd'] = None) → dpdata.system.System

dpdata.System.from_deepmd_raw(file_name, type_map=None) → dpdata.system.System

dpdata.System.from_deepmd(file_name, type_map=None) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['deepmd/raw'], file_name)

dpdata.System.to(fmt: Literal['deepmd/raw'], file_name)

dpdata.System.to_deepmd_raw(file_name)

dpdata.System.to_deepmd(file_name)

Dump the system in deepmd raw format to directory file_name.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['deepmd/raw'], file_name)

dpdata.LabeledSystem.to(fmt: Literal['deepmd/raw'], file_name)

dpdata.LabeledSystem.to_deepmd_raw(file_name)

dpdata.LabeledSystem.to_deepmd(file_name)

Dump the system in deepmd raw format to directory file_name.

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, type_map=None, fmt: Literal['deepmd/raw'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, type_map=None, fmt: Literal['deepmd'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_deepmd_raw(file_name, type_map=None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_deepmd(file_name, type_map=None) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

Convert from this format to MultiSystems

dpdata.MultiSystems.from_deepmd_raw(directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.from_deepmd(directory) → dpdata.system.MultiSystems

Convert this format to MultiSystems.

Parameters:

directorystr: directory of systems

Returns:

MultiSystems: converted system

Convert from MultiSystems to this format

dpdata.MultiSystems.to(fmt: Literal['deepmd/raw'], directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to(fmt: Literal['deepmd/raw'], directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd_raw(directory) → dpdata.system.MultiSystems

dpdata.MultiSystems.to_deepmd(directory) → dpdata.system.MultiSystems

Convert MultiSystems to this format.

Parameters:

directorystr: directory to save systems

Returns:

MultiSystems: this system

fhi_aims/output format

fhi_aims/md format

Class: FhiMDFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, md=True, begin=0, step=1, convergence_check=True, fmt: Literal['fhi_aims/output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, md=True, begin=0, step=1, convergence_check=True, fmt: Literal['fhi_aims/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_fhi_aims_output(file_name, md=True, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_fhi_aims_md(file_name, md=True, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

fhi_aims/scf format

Class: FhiSCFFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['fhi_aims/scf'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_fhi_aims_scf(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

gaussian/gjf format

Class: GaussiaGJFFormat

Gaussian input file.

Conversions

Convert from this format to System

dpdata.System(file_name: str, fmt: Literal['gaussian/gjf'] = None) → dpdata.system.System

dpdata.System.from_gaussian_gjf(file_name: str) → dpdata.system.System

Read Gaussian input file.

Parameters:

file_namestr: file name

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['gaussian/gjf'], file_name: str)

dpdata.System.to_gaussian_gjf(file_name: str)

Generate Gaussian input file.

Parameters:

file_namestr: file name

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['gaussian/gjf'], file_name: str)

dpdata.LabeledSystem.to_gaussian_gjf(file_name: str)

Generate Gaussian input file.

Parameters:

file_namestr: file name

gaussian/log format

Class: GaussianLogFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, md=False, fmt: Literal['gaussian/log'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_gaussian_log(file_name, md=False) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

gaussian/md format

Class: GaussianMDFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['gaussian/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_gaussian_md(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

gromacs/gro format

gro format

Class: GromacsGroFormat

Conversions

Convert from this format to System

dpdata.System(file_name, format_atom_name=True, fmt: Literal['gromacs/gro'] = None) → dpdata.system.System

dpdata.System(file_name, format_atom_name=True, fmt: Literal['gro'] = None) → dpdata.system.System

dpdata.System.from_gromacs_gro(file_name, format_atom_name=True) → dpdata.system.System

dpdata.System.from_gro(file_name, format_atom_name=True) → dpdata.system.System

Load gromacs .gro file.

Parameters:

file_namestr: The input file name
format_atom_namebool: Whether to format the atom name

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['gromacs/gro'], file_name=None, frame_idx=-1)

dpdata.System.to(fmt: Literal['gromacs/gro'], file_name=None, frame_idx=-1)

dpdata.System.to_gromacs_gro(file_name=None, frame_idx=-1)

dpdata.System.to_gro(file_name=None, frame_idx=-1)

Dump the system in gromacs .gro format.

Parameters:

file_namestr or None: The output file name. If None, return the file content as a string
frame_idxint: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['gromacs/gro'], file_name=None, frame_idx=-1)

dpdata.LabeledSystem.to(fmt: Literal['gromacs/gro'], file_name=None, frame_idx=-1)

dpdata.LabeledSystem.to_gromacs_gro(file_name=None, frame_idx=-1)

dpdata.LabeledSystem.to_gro(file_name=None, frame_idx=-1)

Dump the system in gromacs .gro format.

Parameters:

file_namestr or None: The output file name. If None, return the file content as a string
frame_idxint: The index of the frame to dump

lammps/dump format

dump format

Class: LAMMPSDumpFormat

Conversions

Convert from this format to System

dpdata.System(file_name, type_map=None, begin=0, step=1, unwrap=False, fmt: Literal['lammps/dump'] = None) → dpdata.system.System

dpdata.System(file_name, type_map=None, begin=0, step=1, unwrap=False, fmt: Literal['dump'] = None) → dpdata.system.System

dpdata.System.from_lammps_dump(file_name, type_map=None, begin=0, step=1, unwrap=False) → dpdata.system.System

dpdata.System.from_dump(file_name, type_map=None, begin=0, step=1, unwrap=False) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

lammps/lmp format

lmp format

Class: LAMMPSLmpFormat

Conversions

Convert from this format to System

dpdata.System(file_name, type_map=None, fmt: Literal['lammps/lmp'] = None) → dpdata.system.System

dpdata.System(file_name, type_map=None, fmt: Literal['lmp'] = None) → dpdata.system.System

dpdata.System.from_lammps_lmp(file_name, type_map=None) → dpdata.system.System

dpdata.System.from_lmp(file_name, type_map=None) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['lammps/lmp'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['lammps/lmp'], file_name, frame_idx=0)

dpdata.System.to_lammps_lmp(file_name, frame_idx=0)

dpdata.System.to_lmp(file_name, frame_idx=0)

Dump the system in lammps data format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['lammps/lmp'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['lammps/lmp'], file_name, frame_idx=0)

dpdata.LabeledSystem.to_lammps_lmp(file_name, frame_idx=0)

dpdata.LabeledSystem.to_lmp(file_name, frame_idx=0)

Dump the system in lammps data format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

list format

Class: ListFormat

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['list'])

dpdata.System.to_list()

Convert system to list, usefull for data collection.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['list'])

dpdata.LabeledSystem.to_list()

Convert system to list, usefull for data collection.

mol_file format

mol format

Class: MolFormat

Conversions

Convert from this format to BondOrderSystem

dpdata.BondOrderSystem(file_name, fmt: Literal['mol_file'] = None) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem(file_name, fmt: Literal['mol'] = None) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem.from_mol_file(file_name) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem.from_mol(file_name) → dpdata.bond_order_system.BondOrderSystem

Convert this format to BondOrderSystem.

Returns:

BondOrderSystem: converted system

Convert from BondOrderSystem to this format

dpdata.BondOrderSystem.to(fmt: Literal['mol_file'], mol, file_name, frame_idx=0)

dpdata.BondOrderSystem.to(fmt: Literal['mol_file'], mol, file_name, frame_idx=0)

dpdata.BondOrderSystem.to_mol_file(mol, file_name, frame_idx=0)

dpdata.BondOrderSystem.to_mol(mol, file_name, frame_idx=0)

Convert BondOrderSystem to this format.

n2p2 format

Class: N2P2Format

n2p2.

This class support the conversion from and to the training data of n2p2 format. For more information about the n2p2 format, please refer to https://compphysvienna.github.io/n2p2/topics/cfg_file.html

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['n2p2'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_n2p2(file_name) → dpdata.system.LabeledSystem

Read from n2p2 format.

Parameters:

file_namestr: file name, i.e. the first argument

Returns:

LabeledSystem: converted system

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['n2p2'], file_name)

dpdata.LabeledSystem.to_n2p2(file_name)

Write n2p2 format.

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

Parameters:

file_namestr: file name, where the data will be written

openmx/md format

Class: OPENMXFormat

Format for the OpenMX <https://www.openmx-square.org/>.

OpenMX (Open source package for Material eXplorer) is a nano-scale material simulation package based on DFT, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

Note that two output files, System.Name.dat and System.Name.md, are required.

Use the openmx/md keyword argument to supply this format.

Conversions

Convert from this format to System

dpdata.System(file_name: str, fmt: Literal['openmx/md'] = None) → dpdata.system.System

dpdata.System.from_openmx_md(file_name: str) → dpdata.system.System

Read from OpenMX output.

Parameters:

file_namestr: file name, which is specified by a input file, i.e. System.Name.dat

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name: str, fmt: Literal['openmx/md'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_openmx_md(file_name: str) → dpdata.system.LabeledSystem

Read from OpenMX output.

Parameters:

file_namestr: file name, which is specified by a input file, i.e. System.Name.dat

Returns:

LabeledSystem: converted system

orca/spout format

Class: ORCASPOutFormat

ORCA single point energy output.

Note that both the energy and the gradient should be printed into the output file.

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name: str, fmt: Literal['orca/spout'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_orca_spout(file_name: str) → dpdata.system.LabeledSystem

Read from ORCA single point energy output.

Parameters:

file_namestr: file name

Returns:

LabeledSystem: converted system

psi4/inp format

Class: PSI4InputFormat

Psi4 input file.

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['psi4/inp'], file_name: str, method: str, basis: str, charge: int = 0, multiplicity: int = 1, frame_idx=0)

dpdata.System.to_psi4_inp(file_name: str, method: str, basis: str, charge: int = 0, multiplicity: int = 1, frame_idx=0)

Write PSI4 input.

Parameters:

file_namestr: file name
methodstr: computational method
basisstr: basis set; see https://psicode.org/psi4manual/master/basissets_tables.html
chargeint, default=0: charge of system
multiplicityint, default=1: multiplicity of system
frame_idxint, default=0: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['psi4/inp'], file_name: str, method: str, basis: str, charge: int = 0, multiplicity: int = 1, frame_idx=0)

dpdata.LabeledSystem.to_psi4_inp(file_name: str, method: str, basis: str, charge: int = 0, multiplicity: int = 1, frame_idx=0)

Write PSI4 input.

Parameters:

file_namestr: file name
methodstr: computational method
basisstr: basis set; see https://psicode.org/psi4manual/master/basissets_tables.html
chargeint, default=0: charge of system
multiplicityint, default=1: multiplicity of system
frame_idxint, default=0: The index of the frame to dump

psi4/out format

Class: PSI4OutFormat

Psi4 output.

Note that both the energy and the gradient should be printed into the output file.

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name: str, fmt: Literal['psi4/out'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_psi4_out(file_name: str) → dpdata.system.LabeledSystem

Read from Psi4 output.

Parameters:

file_namestr: file name

Returns:

LabeledSystem: converted system

pwmat/final.config format

pwmat/atom.config format

final.config format

atom.config format

Class: PwmatAtomconfigFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['pwmat/final.config'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['pwmat/atom.config'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['final.config'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['atom.config'] = None) → dpdata.system.System

dpdata.System.from_pwmat_finalconfig(file_name) → dpdata.system.System

dpdata.System.from_pwmat_atomconfig(file_name) → dpdata.system.System

dpdata.System.from_finalconfig(file_name) → dpdata.system.System

dpdata.System.from_atomconfig(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.System.to_pwmat_finalconfig(file_name, frame_idx=0)

dpdata.System.to_pwmat_atomconfig(file_name, frame_idx=0)

dpdata.System.to_finalconfig(file_name, frame_idx=0)

dpdata.System.to_atomconfig(file_name, frame_idx=0)

Dump the system in pwmat atom.config format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['pwmat/final.config'], file_name, frame_idx=0)

dpdata.LabeledSystem.to_pwmat_finalconfig(file_name, frame_idx=0)

dpdata.LabeledSystem.to_pwmat_atomconfig(file_name, frame_idx=0)

dpdata.LabeledSystem.to_finalconfig(file_name, frame_idx=0)

dpdata.LabeledSystem.to_atomconfig(file_name, frame_idx=0)

Dump the system in pwmat atom.config format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

pwmat/output format

pwmat/mlmd format

pwmat/movement format

mlmd format

movement format

Class: PwmatOutputFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['pwmat/output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['pwmat/mlmd'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['pwmat/movement'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['mlmd'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['movement'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_pwmat_output(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_pwmat_mlmd(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_pwmat_movement(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_mlmd(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_movement(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

3dmol format

Class: Py3DMolFormat

3DMol format.

To use this format, py3Dmol should be installed in advance.

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['3dmol'], f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {'stick': {}, 'sphere': {'radius': 0.4}})

dpdata.System.to_3dmol(f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {'stick': {}, 'sphere': {'radius': 0.4}})

Show 3D structure of a frame in jupyter.

Parameters:

f_idxint: frame index to show
sizetuple[int]: (width, height) of the widget
styledict: style of 3DMol. Read 3DMol documentation for details.

Examples

>>> system.to_3dmol()

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['3dmol'], f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {'stick': {}, 'sphere': {'radius': 0.4}})

dpdata.LabeledSystem.to_3dmol(f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {'stick': {}, 'sphere': {'radius': 0.4}})

Show 3D structure of a frame in jupyter.

Parameters:

f_idxint: frame index to show
sizetuple[int]: (width, height) of the widget
styledict: style of 3DMol. Read 3DMol documentation for details.

Examples

>>> system.to_3dmol()

pymatgen/computedstructureentry format

Class: PyMatgenCSEFormat

Conversions

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['pymatgen/computedstructureentry'])

dpdata.LabeledSystem.to_pymatgen_computedstructureentry()

Convert System to Pymagen ComputedStructureEntry obj.

pymatgen/molecule format

Class: PyMatgenMoleculeFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['pymatgen/molecule'] = None) → dpdata.system.System

dpdata.System.from_pymatgen_molecule(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['pymatgen/molecule'])

dpdata.System.to_pymatgen_molecule()

Convert System to Pymatgen Molecule obj.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['pymatgen/molecule'])

dpdata.LabeledSystem.to_pymatgen_molecule()

Convert System to Pymatgen Molecule obj.

pymatgen/structure format

Class: PyMatgenStructureFormat

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['pymatgen/structure'])

dpdata.System.to_pymatgen_structure()

Convert System to Pymatgen Structure obj.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['pymatgen/structure'])

dpdata.LabeledSystem.to_pymatgen_structure()

Convert System to Pymatgen Structure obj.

qe/pw/scf format

Class: QECPPWSCFFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['qe/pw/scf'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_qe_pw_scf(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

qe/cp/traj format

Class: QECPTrajFormat

Conversions

Convert from this format to System

dpdata.System(file_name, begin=0, step=1, fmt: Literal['qe/cp/traj'] = None) → dpdata.system.System

dpdata.System.from_qe_cp_traj(file_name, begin=0, step=1) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, fmt: Literal['qe/cp/traj'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_qe_cp_traj(file_name, begin=0, step=1) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

quip/gap/xyz_file format

quip/gap/xyz format

Class: QuipGapXYZFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(data, fmt: Literal['quip/gap/xyz_file'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(data, fmt: Literal['quip/gap/xyz'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_quip_gap_xyz_file(data) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_quip_gap_xyz(data) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

Convert from this format to MultiSystems

dpdata.MultiSystems.from_quip_gap_xyz_file(file_name) → dpdata.system.MultiSystems

dpdata.MultiSystems.from_quip_gap_xyz(file_name) → dpdata.system.MultiSystems

Convert this format to MultiSystems.

Parameters:

directorystr: directory of systems

Returns:

MultiSystems: converted system

sqm/in format

Class: SQMINFormat

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['sqm/in'], fname=None, frame_idx=0)

dpdata.System.to_sqm_in(fname=None, frame_idx=0)

Generate input files for semi-emperical calculation in sqm software.

Parameters:

fnamestr: output file name
frame_idxint, default=0: index of frame to write

Other Parameters:

**kwargsdict

valid parameters are:

qm_theorystr, default=dftb3: level of theory. Options includes AM1, RM1, MNDO, PM3-PDDG, MNDO-PDDG, PM3-CARB1, MNDO/d, AM1/d, PM6, DFTB2, DFTB3
chargeint, default=0: total charge in electron units
maxcycint, default=0: maximum number of minimization cycles to allow. 0 represents a single-point calculation
multint, default=1: multiplicity. Only 1 is allowed.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['sqm/in'], fname=None, frame_idx=0)

dpdata.LabeledSystem.to_sqm_in(fname=None, frame_idx=0)

Generate input files for semi-emperical calculation in sqm software.

Parameters:

fnamestr: output file name
frame_idxint, default=0: index of frame to write

Other Parameters:

**kwargsdict

valid parameters are:

qm_theorystr, default=dftb3: level of theory. Options includes AM1, RM1, MNDO, PM3-PDDG, MNDO-PDDG, PM3-CARB1, MNDO/d, AM1/d, PM6, DFTB2, DFTB3
chargeint, default=0: total charge in electron units
maxcycint, default=0: maximum number of minimization cycles to allow. 0 represents a single-point calculation
multint, default=1: multiplicity. Only 1 is allowed.

sqm/out format

Class: SQMOutFormat

Conversions

Convert from this format to System

dpdata.System(fname, fmt: Literal['sqm/out'] = None) → dpdata.system.System

dpdata.System.from_sqm_out(fname) → dpdata.system.System

Read from ambertools sqm.out.

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(fname, fmt: Literal['sqm/out'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_sqm_out(fname) → dpdata.system.LabeledSystem

Read from ambertools sqm.out.

Returns:

LabeledSystem: converted system

sdf_file format

sdf format

Class: SdfFormat

Conversions

Convert from this format to BondOrderSystem

dpdata.BondOrderSystem(file_name, fmt: Literal['sdf_file'] = None) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem(file_name, fmt: Literal['sdf'] = None) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem.from_sdf_file(file_name) → dpdata.bond_order_system.BondOrderSystem

dpdata.BondOrderSystem.from_sdf(file_name) → dpdata.bond_order_system.BondOrderSystem

Note that it requires all molecules in .sdf file must be of the same topology.

Returns:

BondOrderSystem: converted system

Convert from BondOrderSystem to this format

dpdata.BondOrderSystem.to(fmt: Literal['sdf_file'], mol, file_name, frame_idx=-1)

dpdata.BondOrderSystem.to(fmt: Literal['sdf_file'], mol, file_name, frame_idx=-1)

dpdata.BondOrderSystem.to_sdf_file(mol, file_name, frame_idx=-1)

dpdata.BondOrderSystem.to_sdf(mol, file_name, frame_idx=-1)

Convert BondOrderSystem to this format.

siesta/aimd_output format

Class: SiestaAIMDOutputFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['siesta/aimd_output'] = None) → dpdata.system.System

dpdata.System.from_siesta_aimd_output(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['siesta/aimd_output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_siesta_aimd_output(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

siesta/output format

Class: SiestaOutputFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['siesta/output'] = None) → dpdata.system.System

dpdata.System.from_siesta_output(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, fmt: Literal['siesta/output'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_siesta_output(file_name) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

vasp/outcar format

outcar format

Class: VASPOutcarFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['vasp/outcar'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, convergence_check=True, fmt: Literal['outcar'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_vasp_outcar(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_outcar(file_name, begin=0, step=1, convergence_check=True) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

vasp/contcar format

vasp/poscar format

contcar format

poscar format

Class: VASPPoscarFormat

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['vasp/contcar'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['vasp/poscar'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['contcar'] = None) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['poscar'] = None) → dpdata.system.System

dpdata.System.from_vasp_contcar(file_name) → dpdata.system.System

dpdata.System.from_vasp_poscar(file_name) → dpdata.system.System

dpdata.System.from_contcar(file_name) → dpdata.system.System

dpdata.System.from_poscar(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.System.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.System.to_vasp_contcar(file_name, frame_idx=0)

dpdata.System.to_vasp_poscar(file_name, frame_idx=0)

dpdata.System.to_contcar(file_name, frame_idx=0)

dpdata.System.to_poscar(file_name, frame_idx=0)

Dump the system in vasp POSCAR format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.LabeledSystem.to(fmt: Literal['vasp/contcar'], file_name, frame_idx=0)

dpdata.LabeledSystem.to_vasp_contcar(file_name, frame_idx=0)

dpdata.LabeledSystem.to_vasp_poscar(file_name, frame_idx=0)

dpdata.LabeledSystem.to_contcar(file_name, frame_idx=0)

dpdata.LabeledSystem.to_poscar(file_name, frame_idx=0)

Dump the system in vasp POSCAR format.

Parameters:

file_namestr: The output file name
frame_idxint: The index of the frame to dump

vasp/string format

Class: VASPStringFormat

Conversions

Convert from System to this format

dpdata.System.to(fmt: Literal['vasp/string'], frame_idx=0)

dpdata.System.to_vasp_string(frame_idx=0)

Dump the system in vasp POSCAR format string.

Parameters:

frame_idxint: The index of the frame to dump

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['vasp/string'], frame_idx=0)

dpdata.LabeledSystem.to_vasp_string(frame_idx=0)

Dump the system in vasp POSCAR format string.

Parameters:

frame_idxint: The index of the frame to dump

vasp/xml format

xml format

Class: VASPXMLFormat

Conversions

Convert from this format to LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, fmt: Literal['vasp/xml'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem(file_name, begin=0, step=1, fmt: Literal['xml'] = None) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_vasp_xml(file_name, begin=0, step=1) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_xml(file_name, begin=0, step=1) → dpdata.system.LabeledSystem

Convert this format to LabeledSystem.

Returns:

LabeledSystem: converted system

xyz format

Class: XYZFormat

XYZ foramt.

Examples

>>> s.to("xyz", "a.xyz")

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['xyz'] = None) → dpdata.system.System

dpdata.System.from_xyz(file_name) → dpdata.system.System

Convert this format to System.

Returns:

System: converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['xyz'], file_name)

dpdata.System.to_xyz(file_name)

Convert System to this format.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['xyz'], file_name)

dpdata.LabeledSystem.to_xyz(file_name)

Convert LabeledSystem to this format.

Supported Drivers

dpdata supports the following drivers:

Supported Drivers
Class	Alias
`HybridDriver`	`hybrid`
`DPDriver`	`deepmd-kit` `deepmd` `dp`
`ASEDriver`	`ase`
`GaussianDriver`	`gaussian`
`SQMDriver`	`sqm`

Supported Minimizers

dpdata supports the following minimizers:

Supported Minimizers
Class	Alias
`ASEMinimizer`	`ase`
`SQMMinimizer`	`sqm`

API documentation

dpdata package

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

Bases: System

The system with chemical bond and formal charges information.

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

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

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

Attributes:

formula: Return the formula of this system, like C3H5O2.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
uniq_formula: Return the uniq_formula of this system.

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_rdkit_mol`(rdkit_mol)	Initialize from a rdkit.Chem.rdchem.Mol object.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_bond_order`(begin_atom_idx, end_atom_idx)	Return the bond order between given atoms.
`get_charge`()	Return the total formal charge of the moleclue.
`get_formal_charges`()	Return the formal charges on each atom.
`get_mol`()	Return the rdkit.Mol object.
`get_natoms`()	Returns total number of atoms in the system.
`get_nbonds`()	Return the number of bonds.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

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

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

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

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

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

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

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

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

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

class dpdata.LabeledSystem(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)[source]

Bases: System

The labeled data System.

For example, a labeled water system named d_example has two molecules (6 atoms) and nframes frames. The labels can be accessed by

d_example[‘energies’] : a numpy array of size nframes
d_example[‘forces’] : a numpy array of size nframes x 6 x 3
d_example[‘virials’] : optional, a numpy array of size nframes x 3 x 3

It is noted that

The order of frames stored in ‘energies’, ‘forces’ and ‘virials’ should be consistent with ‘atom_types’, ‘cells’ and ‘coords’.
The order of atoms in every frame of ‘forces’ should be consistent with ‘coords’ and ‘atom_types’.

Parameters:

file_namestr

The file to load the system

fmtstr

Format of the file, supported formats are

auto: infered from file_name’s extension
vasp/xml: vasp xml
vasp/outcar: vasp OUTCAR
deepmd/raw: deepmd-kit raw
deepmd/npy: deepmd-kit compressed format (numpy binary)
qe/cp/traj: Quantum Espresso CP trajectory files. should have: file_name+’.in’, file_name+’.pos’, file_name+’.evp’ and file_name+’.for’
qe/pw/scf: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing ‘out’ by ‘in’ from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename.
siesta/output: siesta SCF output file
siesta/aimd_output: siesta aimd output file
gaussian/log: gaussian logs
gaussian/md: gaussian ab initio molecular dynamics
cp2k/output: cp2k output file
cp2k/aimd_output: cp2k aimd output dir(contains pos.xyz and *.log file); optional restart=True if it is a cp2k restarted task.
pwmat/movement: pwmat md output file
pwmat/out.mlmd: pwmat scf output file

type_maplist of str

Maps atom type to name. The atom with type ii is mapped to type_map[ii]. If not provided the atom names are assigned to ‘Type_1’, ‘Type_2’, ‘Type_3’…

beginint

The beginning frame when loading MD trajectory.

stepint

The number of skipped frames when loading MD trajectory.

Attributes:

formula: Return the formula of this system, like C3H5O2.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
uniq_formula: Return the uniq_formula of this system.

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`correction`(hl_sys)	Get energy and force correction between self and a high-level LabeledSystem.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_natoms`()	Returns total number of atoms in the system.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_outlier`([threshold])	Remove outlier frames from the system.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
affine_map_fv
apply_type_map
from_fmt
from_fmt_obj
has_virial
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

affine_map_fv(trans, f_idx)[source]

correction(hl_sys)[source]

Get energy and force correction between self and a high-level LabeledSystem. The self’s coordinates will be kept, but energy and forces will be replaced by the correction between these two systems.

Note: The function will not check whether coordinates and elements of two systems are the same. The user should make sure by itself.

Parameters:

hl_sysLabeledSystem: high-level LabeledSystem

Returns:

corrected_sys: LabeledSystem: Corrected LabeledSystem

from_3dmol(file_name, **kwargs): Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs): Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs): Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

has_virial()[source]

post_funcs = <dpdata.plugin.Plugin object>

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

Remove outlier frames from the system.

Remove the frames whose energies satisfy the condition

\[\frac{\left \| E - \bar{E} \right \|}{\sigma(E)} \geq \text{threshold}\]

where \(\bar{E}\) and \(\sigma(E)\) are the mean and standard deviation of the energies in the system.

Parameters:

thresholdfloat: The threshold of outlier detection. The default value is 8.0.

Returns:

LabeledSystem: The system without outlier frames.

References

[1]

Gao, X.; Ramezanghorbani, F.; Isayev, O.; Smith, J. S.; Roitberg, A. E. TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials. J. Chem. Inf. Model. 2020, 60, 3408-3415.

[2]

Zeng, J.; Tao, Y.; Giese, T. J.; York, D. M.. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. J. Comput. Chem. 2023, 19, 1261-1275.

rot_frame_lower_triangular(f_idx=0)[source]

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

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

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

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

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

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

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

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

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

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

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

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

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

to_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

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

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

class dpdata.MultiSystems(*systems, type_map=None)[source]

Bases: object

A set containing several systems.

Methods

`append`(*systems)	Append systems or MultiSystems to systems.
`check_atom_names`(system)	Make atom_names in all systems equal, prevent inconsistent atom_types.
`correction`(hl_sys)	Get energy and force correction between self (assumed low-level) and a high-level MultiSystems.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dump`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`from_fhi_aims_md`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`from_fhi_aims_output`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`from_fhi_aims_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`from_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_gaussian_gjf`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`from_gaussian_log`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussianLogFormat` format.
`from_gaussian_md`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussianMDFormat` format.
`from_gro`(file_name, **kwargs)	Read data from `dpdata.plugins.gromacs.GromacsGroFormat` format.
`from_gromacs_gro`(file_name, **kwargs)	Read data from `dpdata.plugins.gromacs.GromacsGroFormat` format.
`from_lammps_dump`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`from_lammps_lmp`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`from_list`(file_name, **kwargs)	Read data from `dpdata.plugins.list.ListFormat` format.
`from_lmp`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`from_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_mol`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.MolFormat` format.
`from_mol_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.MolFormat` format.
`from_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_nframes`()	Returns number of frames in all systems.
`minimize`(args, minimizer, *kwargs)	Minimize geometry by a minimizer.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_lammps_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_lammps_lmp`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`to_list`(args, *kwargs)	Dump data to `dpdata.plugins.list.ListFormat` format.
`to_lmp`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`to_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_mol`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.MolFormat` format.
`to_mol_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.MolFormat` format.
`to_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`train_test_split`(test_size[, seed])	Split systems into random train and test subsets.

from_dir
from_file
from_fmt_obj
load_systems_from_file
to_fmt_obj

append(*systems)[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_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

classmethod from_dir(dir_name, file_name, fmt='auto', type_map=None)[source]

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

classmethod from_file(file_name, fmt, **kwargs)[source]

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

get_nframes()[source]: Returns number of frames in all systems.

load_systems_from_file(file_name=None, fmt=None, **kwargs)[source]

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

Minimize geometry by a minimizer.

Parameters:

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

Returns:

MultiSystems: A new labeled MultiSystems.

Examples

Minimize a system using ASE BFGS along with a DP driver:

>>> from dpdata.driver import Driver
>>> from ase.optimize import BFGS
>>> driver = Driver.get_driver("dp")("some_model.pb")
>>> some_system.minimize(minimizer="ase", driver=driver, optimizer=BFGS, fmax=1e-5)

pick_atom_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_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_fmt_obj(fmtobj, directory, *args, **kwargs)[source]

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

train_test_split(test_size: float | int, seed: int | None = None) → Tuple[MultiSystems, MultiSystems, Dict[str, ndarray]][source]

Split systems into random train and test subsets.

Parameters:

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

Returns:

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

class dpdata.System(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)[source]

Bases: MSONable

The data System.

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

For example, a water system named d_example has two molecules. The properties can be accessed by

d_example[‘atom_numbs’] : [2, 4]
d_example[‘atom_names’] : [‘O’, ‘H’]
d_example[‘atom_types’] : [0, 1, 1, 0, 1, 1]
d_example[‘orig’] : [0, 0, 0]
d_example[‘cells’] : a numpy array of size nframes x 3 x 3
d_example[‘coords’] : a numpy array of size nframes x natoms x 3

It is noted that

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

Restrictions:

d_example[‘orig’] is always [0, 0, 0]
d_example[‘cells’][ii] is always lower triangular (lammps cell tensor convention)

Attributes:

DTYPEStuple[DataType]: data types of this class

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_natoms`()	Returns total number of atoms in the system.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

add_atom_names(atom_names)[source]: Add atom_names that do not exist.

affine_map(trans, f_idx=0)[source]

append(system)[source]

Append a system to this system.

Parameters:

systemSystem: The system to append

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

apply_type_map(type_map)[source]

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

check_data()[source]

Check if data is correct.

Raises:

DataError: if data is not correct

check_type_map(type_map)[source]

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

Parameters:

type_maplist: type_map

convert_to_mixed_type(type_map=None)[source]

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms. Change the ‘atom_names’ to one placeholder type ‘MIXED_TOKEN’ and add ‘real_atom_types’ to store the real type vectors according to the given type_map.

Parameters:

type_maplist: type_map

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

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

extend(systems)[source]

Extend a system list to this system.

Parameters:

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

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

property formula_hash: str: Return the hash of the formula of this system.

from_3dmol(file_name, **kwargs): Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs): Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs): Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

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

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

get_atom_names()[source]: Returns name of atoms.

get_atom_numbs()[source]: Returns number of atoms.

get_atom_types()[source]: Returns type of atoms.

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

get_nframes()[source]: Returns number of frames in the system.

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

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

map_atom_types(type_map=None) → ndarray[source]

Map the atom types of the system.

Parameters:

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

Returns:

new_atom_typesnp.ndarray: The mapped atom types

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

Minimize the geometry.

Parameters:

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

Returns:

labeled_sysLabeledSystem: A new labeled system.

property nopbc

perturb(pert_num, cell_pert_fraction, atom_pert_distance, atom_pert_style='normal')[source]

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

Parameters:

pert_numint

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

cell_pert_fractionfloat

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

atom_pert_distancefloat

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

atom_pert_stylestr

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

‘normal’: the distance will be object to chi-square distribution with 3 degrees of freedom after normalization.
The mean value of the distance is atom_pert_fraction*side_length

‘uniform’: will generate uniformly random points in a 3D-balls with radius as atom_pert_distance.
These points are treated as vector used by atoms to move. Obviously, the max length of the distance atoms move is atom_pert_distance.

‘const’: The distance atoms move will be a constant atom_pert_distance.

Returns:

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

pick_atom_idx(idx, nopbc=None)[source]

Pick atom index.

Parameters:

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

Returns:

new_sys: System: new system

pick_by_amber_mask(param, maskstr, pass_coords=False, nopbc=None)[source]

Pick atoms by amber mask.

Parameters:

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

post_funcs = <dpdata.plugin.Plugin object>

predict(*args: Any, driver: str = 'dp', **kwargs: Any) → LabeledSystem[source]

Predict energies and forces by a driver.

Parameters:

*argsiterable: Arguments passing to the driver
driverstr, default=dp: The assigned driver. For compatibility, default is dp
**kwargsdict: Other arguments passing to the driver

Returns:

labeled_sysLabeledSystem: A new labeled system.

Examples

The default driver is DP:

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

classmethod register_data_type(*data_type: Tuple[DataType])[source]

Register data type.

Parameters:

*data_typetuple[DataType]: data type to be regiestered

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

remove_pbc(protect_layer=9)[source]

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

Parameters:

protect_layerthe protect layer between the atoms and the cell: boundary

replace(initial_atom_type, end_atom_type, replace_num)[source]

replicate(ncopy)[source]

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

Parameters:

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

Returns:

tmpSystem: The system after replication.

rot_frame_lower_triangular(f_idx=0)[source]

rot_lower_triangular()[source]

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

property short_name: str

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

formula

short_formula

formula_hash.

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

sort_atom_names(type_map=None)[source]

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

Parameters:

type_maplist: type_map

sort_atom_types() → ndarray[source]

Sort atom types.

Returns:

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

sub_system(f_idx)[source]

Construct a subsystem from the system.

Parameters:

f_idxint or index: Which frame to use in the subsystem

Returns:

sub_systemSystem: The subsystem

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

Dump systems to the specific format.

Parameters:

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

Returns:

System: self

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

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

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

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

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

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

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

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

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

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

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

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

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

to_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

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

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

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

Submodules

dpdata.abacus.md module

dpdata.abacus.md.get_coord_dump_freq(inlines)[source]

dpdata.abacus.md.get_coords_from_dump(dumplines, natoms)[source]

dpdata.abacus.md.get_energy(outlines, ndump, dump_freq)[source]

dpdata.abacus.md.get_frame(fname)[source]

dpdata.abacus.md.get_path_out(fname, inlines)[source]

dpdata.abacus.relax module

dpdata.abacus.relax.get_coords_from_log(loglines, natoms)[source]: NOTICE: unit of coords and cells is Angstrom order:

coordinate cell (no output if cell is not changed) energy (no output, if SCF is not converged) force (no output, if cal_force is not setted or abnormal ending) stress (no output, if set cal_stress is not setted or abnormal ending).

dpdata.abacus.relax.get_frame(fname)[source]

dpdata.abacus.relax.get_log_file(fname, inlines)[source]

dpdata.abacus.scf module

dpdata.abacus.scf.CheckFile(ifile)[source]

dpdata.abacus.scf.collect_force(outlines)[source]

dpdata.abacus.scf.collect_stress(outlines)[source]

dpdata.abacus.scf.get_block(lines, keyword, skip=0, nlines=None)[source]

dpdata.abacus.scf.get_cell(geometry_inlines)[source]

dpdata.abacus.scf.get_coords(celldm, cell, geometry_inlines, inlines=None)[source]

dpdata.abacus.scf.get_energy(outlines)[source]

dpdata.abacus.scf.get_force(outlines, natoms)[source]

dpdata.abacus.scf.get_frame(fname)[source]

dpdata.abacus.scf.get_frame_from_stru(fname)[source]

dpdata.abacus.scf.get_geometry_in(fname, inlines)[source]

dpdata.abacus.scf.get_nele_from_stru(geometry_inlines)[source]

dpdata.abacus.scf.get_path_out(fname, inlines)[source]

dpdata.abacus.scf.get_stress(outlines)[source]

dpdata.abacus.scf.get_stru_block(lines, keyword)[source]

dpdata.abacus.scf.make_unlabeled_stru(data, frame_idx, pp_file=None, numerical_orbital=None, numerical_descriptor=None, mass=None)[source]

dpdata.amber package

Submodules

dpdata.amber.mask module

Amber mask.

dpdata.amber.mask.load_param_file(param_file)[source]

dpdata.amber.mask.pick_by_amber_mask(param, maskstr, coords=None)[source]

Pick atoms by amber masks.

Parameters:

paramstr or parmed.Structure: filename of Amber param file or parmed.Structure
maskstrstr: Amber masks
coordsnp.ndarray (optional): frame coordinates, shape: N*3

dpdata.amber.md module

dpdata.amber.md.read_amber_traj(parm7_file, nc_file, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, labeled=True)[source]

The amber trajectory includes: * nc, NetCDF format, stores coordinates * mdfrc, NetCDF format, stores forces * mden (optional), text format, stores energies * mdout (optional), text format, may store energies if there is no mden_file * parm7, text format, stores types.

Parameters:

parm7_file, nc_file, mdfrc_file, mden_file, mdout_file:: filenames
use_element_symbolsNone or list or str: If use_element_symbols is a list of atom indexes, these atoms will use element symbols instead of amber types. For example, a ligand will use C, H, O, N, and so on instead of h1, hc, o, os, and so on. IF use_element_symbols is str, it will be considered as Amber mask.
labeledbool: Whether to return labeled data

dpdata.amber.sqm module

dpdata.amber.sqm.make_sqm_in(data, fname=None, frame_idx=0, **kwargs)[source]

dpdata.amber.sqm.parse_sqm_out(fname)[source]: Read atom symbols, charges and coordinates from ambertools sqm.out file.

dpdata.cp2k package

Submodules

dpdata.cp2k.cell module

dpdata.cp2k.cell.cell_to_low_triangle(A, B, C, alpha, beta, gamma)[source]

Convert cell to low triangle matrix.

Parameters:

Afloat: cell length A
Bfloat: cell length B
Cfloat: cell length C
alphafloat: radian. The angle between vector B and vector C.
betafloat: radian. The angle between vector A and vector C.
gammafloat: radian. The angle between vector B and vector C.

Returns:

celllist: The cell matrix used by dpdata in low triangle form.

dpdata.cp2k.output module

class dpdata.cp2k.output.Cp2kSystems(log_file_name, xyz_file_name, restart=False)[source]

Bases: object

deal with cp2k outputfile.

Methods

get_log_block_generator
get_xyz_block_generator
handle_single_log_frame
handle_single_xyz_frame

get_log_block_generator()[source]

get_xyz_block_generator()[source]

handle_single_log_frame(lines)[source]

handle_single_xyz_frame(lines)[source]

dpdata.cp2k.output.get_frames(fname)[source]

dpdata.deepmd package

Submodules

dpdata.deepmd.comp module

dpdata.deepmd.comp.dump(folder, data, set_size=5000, comp_prec=<class 'numpy.float32'>, remove_sets=True)[source]

dpdata.deepmd.comp.to_system_data(folder, type_map=None, labels=True)[source]

dpdata.deepmd.hdf5 module

Utils for deepmd/hdf5 format.

dpdata.deepmd.hdf5.dump(f: ~h5py._hl.files.File | ~h5py._hl.group.Group, folder: str, data: dict, set_size=5000, comp_prec=<class 'numpy.float32'>) → None[source]

Dump data to a HDF5 file.

Parameters:

fh5py.File or h5py.Group: HDF5 file or group object
folderstr: path in the HDF5 file
datadict: System or LabeledSystem data
set_sizeint, default: 5000: size of a set
comp_precnp.dtype, default: np.float32: precision of data

dpdata.deepmd.hdf5.to_system_data(f: File | Group, folder: str, type_map: list | None = None, labels: bool = True)[source]

Load a HDF5 file.

Parameters:

fh5py.File or h5py.Group: HDF5 file or group object
folderstr: path in the HDF5 file
type_maplist: type map
labelsbool: labels

dpdata.deepmd.mixed module

dpdata.deepmd.mixed.dump(folder, data, set_size=2000, comp_prec=<class 'numpy.float32'>, remove_sets=True)[source]

dpdata.deepmd.mixed.formula(atom_names, atom_numbs)[source]: Return the formula of this system, like C3H5O2.

dpdata.deepmd.mixed.load_type(folder)[source]

dpdata.deepmd.mixed.mix_system(*system, type_map, **kwargs)[source]

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

Parameters:

*systemSystem: The systems to mix
type_maplist of str: Maps atom type to name
**kwargsdict: Other parameters

Returns:

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

dpdata.deepmd.mixed.split_system(sys, split_num=10000)[source]

dpdata.deepmd.mixed.to_system_data(folder, type_map=None, labels=True)[source]

dpdata.deepmd.raw module

dpdata.deepmd.raw.dump(folder, data)[source]

dpdata.deepmd.raw.load_type(folder, type_map=None)[source]

dpdata.deepmd.raw.to_system_data(folder, type_map=None, labels=True)[source]

dpdata.dftbplus package

Submodules

dpdata.dftbplus.output module

dpdata.dftbplus.output.read_dftb_plus(fn_1: str, fn_2: str) → Tuple[str, ndarray, float, ndarray][source]

Read from DFTB+ input and output.

Parameters:

fn_1str: DFTB+ input file name
fn_2str: DFTB+ output file name

Returns:

str: atomic symbols
np.ndarray: atomic coordinates
float: total potential energy
np.ndarray: atomic forces

dpdata.fhi_aims package

Submodules

dpdata.fhi_aims.output module

dpdata.fhi_aims.output.analyze_block(lines, first_blk=False, md=True)[source]

dpdata.fhi_aims.output.get_fhi_aims_block(fp)[source]

dpdata.fhi_aims.output.get_frames(fname, md=True, begin=0, step=1, convergence_check=True)[source]

dpdata.fhi_aims.output.get_info(lines, type_idx_zero=False)[source]

dpdata.gaussian package

Submodules

dpdata.gaussian.gjf module

Generate Gaussian input file.

dpdata.gaussian.gjf.detect_multiplicity(symbols: ndarray) → int[source]

Find the minimal multiplicity of the given molecules.

Parameters:

symbolsnp.ndarray: element symbols; virtual elements are not supported

Returns:

int: spin multiplicity

dpdata.gaussian.gjf.make_gaussian_input(sys_data: dict, keywords: str | List[str], multiplicity: str | int = 'auto', charge: int = 0, fragment_guesses: bool = False, basis_set: str | None = None, keywords_high_multiplicity: str | None = None, nproc: int = 1) → str[source]

Make gaussian input file.

Parameters:

sys_datadict

system data

keywordsstr or list[str]

Gaussian keywords, e.g. force b3lyp/6-31g**. If a list, run multiple steps

multiplicitystr or int, default=auto

spin multiplicity state. It can be a number. If auto, multiplicity will be detected automatically, with the following rules:

fragment_guesses=True
multiplicity will +1 for each radical, and +2 for each oxygen molecule

fragment_guesses=False
multiplicity will be 1 or 2, but +2 for each oxygen molecule

chargeint, default=0

molecule charge. Only used when charge is not provided by the system

fragment_guessesbool, default=False

initial guess generated from fragment guesses. If True, multiplicity should be auto

basis_setstr, default=None

custom basis set

keywords_high_multiplicitystr, default=None

keywords for points with multiple raicals. multiplicity should be auto. If not set, fallback to normal keywords

nprocint, default=1

Number of CPUs to use

Returns:

str: gjf output string

dpdata.gaussian.gjf.read_gaussian_input(inp: str)[source]

Read Gaussian input.

Parameters:

inpstr: Gaussian input str

Returns:

dict: system data

dpdata.gaussian.log module

dpdata.gaussian.log.to_system_data(file_name, md=False)[source]

Read Gaussian log file.

Parameters:

file_namestr: file name
mdbool, default False: whether to read multiple frames

Returns:

datadict: system data

Raises:

RuntimeError: if the input orientation is not found

dpdata.gromacs package

Submodules

dpdata.gromacs.gro module

dpdata.gromacs.gro.file_to_system_data(fname, format_atom_name=True, **kwargs)[source]

dpdata.gromacs.gro.from_system_data(system, f_idx=0, **kwargs)[source]

dpdata.lammps package

Submodules

dpdata.lammps.dump module

exception dpdata.lammps.dump.UnwrapWarning[source]: Bases: UserWarning

dpdata.lammps.dump.box2dumpbox(orig, box)[source]

dpdata.lammps.dump.dumpbox2box(bounds, tilt)[source]

dpdata.lammps.dump.get_atype(lines, type_idx_zero=False)[source]

dpdata.lammps.dump.get_coordtype_and_scalefactor(keys)[source]

dpdata.lammps.dump.get_dumpbox(lines)[source]

dpdata.lammps.dump.get_natoms(lines)[source]

dpdata.lammps.dump.get_natoms_vec(lines)[source]

dpdata.lammps.dump.get_natomtypes(lines)[source]

dpdata.lammps.dump.load_file(fname, begin=0, step=1)[source]

dpdata.lammps.dump.safe_get_posi(lines, cell, orig=array([0., 0., 0.]), unwrap=False)[source]

dpdata.lammps.dump.split_traj(dump_lines)[source]

dpdata.lammps.dump.system_data(lines, type_map=None, type_idx_zero=True, unwrap=False)[source]

dpdata.lammps.lmp module

dpdata.lammps.lmp.box2lmpbox(orig, box)[source]

dpdata.lammps.lmp.from_system_data(system, f_idx=0)[source]

dpdata.lammps.lmp.get_atoms(lines)[source]

dpdata.lammps.lmp.get_atype(lines, type_idx_zero=False)[source]

dpdata.lammps.lmp.get_lmpbox(lines)[source]

dpdata.lammps.lmp.get_natoms(lines)[source]

dpdata.lammps.lmp.get_natoms_vec(lines)[source]

dpdata.lammps.lmp.get_natomtypes(lines)[source]

dpdata.lammps.lmp.get_posi(lines)[source]

dpdata.lammps.lmp.lmpbox2box(lohi, tilt)[source]

dpdata.lammps.lmp.system_data(lines, type_map=None, type_idx_zero=True)[source]

dpdata.lammps.lmp.to_system_data(lines, type_map=None, type_idx_zero=True)[source]

dpdata.openmx package

Submodules

dpdata.openmx.omx module

dpdata.openmx.omx.load_atom(lines)[source]

dpdata.openmx.omx.load_cells(lines)[source]

dpdata.openmx.omx.load_coords(lines, atom_names, natoms)[source]

dpdata.openmx.omx.load_data(mdname, atom_names, natoms)[source]

dpdata.openmx.omx.load_energy(lines)[source]

dpdata.openmx.omx.load_force(lines, atom_names, atom_numbs)[source]

dpdata.openmx.omx.load_param_file(fname, mdname)[source]

dpdata.openmx.omx.to_system_data(fname, mdname)[source]

dpdata.openmx.omx.to_system_label(fname, mdname)[source]

dpdata.orca package

Submodules

dpdata.orca.output module

dpdata.orca.output.read_orca_sp_output(fn: str) → Tuple[ndarray, ndarray, float, ndarray][source]

Read from ORCA output.

Note that both the energy and the gradient should be printed.

Parameters:

fnstr: file name

Returns:

np.ndarray: atomic symbols
np.ndarray: atomic coordinates
float: total potential energy
np.ndarray: atomic forces

dpdata.plugins package

Submodules

dpdata.plugins.3dmol module

class dpdata.plugins.3dmol.Py3DMolFormat[source]

Bases: Format

3DMol format.

To use this format, py3Dmol should be installed in advance.

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name, **kwargs)	Implement LabeledSystem.from that converts from this format to LabeledSystem.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`(file_name, **kwargs)	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data[, f_idx, size, style])	Show 3D structure of a frame in jupyter.

to_system(data: dict, f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {'sphere': {'radius': 0.4}, 'stick': {}}, **kwargs)[source]

Show 3D structure of a frame in jupyter.

Parameters:

datadict: system data
f_idxint: frame index to show
sizetuple[int]: (width, height) of the widget
styledict: style of 3DMol. Read 3DMol documentation for details.
**kwargsdict: other parameters

Examples

>>> system.to_3dmol()

dpdata.plugins.abacus module

class dpdata.plugins.abacus.AbacusMDFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

class dpdata.plugins.abacus.AbacusRelaxFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

class dpdata.plugins.abacus.AbacusSCFFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

class dpdata.plugins.abacus.AbacusSTRUFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

to_system(data, file_name, frame_idx=0, **kwargs)[source]

Dump the system into ABACUS STRU format file.

Parameters:

datadict: System data
file_namestr: The output file name
frame_idxint: The index of the frame to dump
pp_filelist of string, optional: List of pseudo potential files
numerical_orbitallist of string, optional: List of orbital files
masslist of float, optional: List of atomic masses
numerical_descriptorstr, optional: numerical descriptor file
**kwargsdict: other parameters

dpdata.plugins.amber module

class dpdata.plugins.amber.AmberMDFormat[source]

Bases: Format

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`([file_name, parm7_file, ...])	Implement LabeledSystem.from that converts from this format to LabeledSystem.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`([file_name, parm7_file, ...])	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data, args, *kwargs)	Implement System.to that converts from System to this format.

from_labeled_system(file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

from_system(file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.amber.SQMDriver(sqm_exec: str = 'sqm', **kwargs: dict)[source]

Bases: Driver

AMBER sqm program driver.

Parameters:

sqm_execstr, default=sqm: path to sqm program
**kwargsdict: other arguments to make input files. See SQMINFormat

Examples

Use DFTB3 method to calculate potential energy:

>>> labeled_system = system.predict(theory="DFTB3", driver="sqm")
>>> labeled_system['energies'][0]
-15.41111246

Attributes:

ase_calculator: Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict[source]

Label a system data. Returns new data with energy, forces, and virials.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with energies and forces

class dpdata.plugins.amber.SQMINFormat[source]

Bases: Format

Methods

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

to_system(data, fname=None, frame_idx=0, **kwargs)[source]

Generate input files for semi-emperical calculation in sqm software.

Parameters:

datadict: system data
fnamestr: output file name
frame_idxint, default=0: index of frame to write
**kwargsdict: other parameters

Other Parameters:

**kwargsdict

valid parameters are:

qm_theorystr, default=dftb3: level of theory. Options includes AM1, RM1, MNDO, PM3-PDDG, MNDO-PDDG, PM3-CARB1, MNDO/d, AM1/d, PM6, DFTB2, DFTB3
chargeint, default=0: total charge in electron units
maxcycint, default=0: maximum number of minimization cycles to allow. 0 represents a single-point calculation
multint, default=1: multiplicity. Only 1 is allowed.

class dpdata.plugins.amber.SQMMinimizer(maxcyc=1000, *args, **kwargs)[source]

Bases: Minimizer

SQM minimizer.

Parameters:

maxcycint, default=1000: maximun cycle to minimize

Methods

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

minimize(data: dict) → dict[source]

Minimize the geometry.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with minimized coordinates, energies, and forces

class dpdata.plugins.amber.SQMOutFormat[source]

Bases: Format

Methods

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

from_labeled_system(fname, **kwargs)[source]: Read from ambertools sqm.out.

from_system(fname, **kwargs)[source]: Read from ambertools sqm.out.

dpdata.plugins.ase module

class dpdata.plugins.ase.ASEDriver(calculator: ase.calculators.calculator.Calculator)[source]

Bases: Driver

ASE Driver.

Parameters:

calculatorase.calculators.calculator.Calculato: ASE calculator

Attributes:

ase_calculator: Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict[source]

Label a system data. Returns new data with energy, forces, and virials.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with energies and forces

class dpdata.plugins.ase.ASEMinimizer(driver: Driver, optimizer: Type[Optimizer] | None = None, fmax: float = 0.005, max_steps: int | None = None, optimizer_kwargs: dict = {})[source]

Bases: Minimizer

ASE minimizer.

Parameters:

driverDriver: dpdata driver
optimizertype, optional: ase optimizer class
fmaxfloat, optional, default=5e-3: force convergence criterion
max_stepsint, optional: max steps to optimize
optimizer_kwargsdict, optional: other parameters for optimizer

Methods

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

minimize(data: dict) → dict[source]

Minimize the geometry.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with minimized coordinates, energies, and forces

class dpdata.plugins.ase.ASEStructureFormat[source]

Bases: Format

Format for the Atomic Simulation Environment (ase).

ASE supports parsing a few dozen of data formats. As described in i the documentation, many of these formats can be determined automatically. Use the ase_fmt keyword argument to supply the format if automatic detection fails.

Methods

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

from_labeled_system(atoms: ase.Atoms, **kwargs) → dict[source]

Convert ase.Atoms to a LabeledSystem. Energies and forces are calculated by the calculator.

Parameters:

atomsase.Atoms: an ASE Atoms, containing a structure
**kwargsdict: other parameters

Returns:

dict: data dict

Raises:

RuntimeError: ASE will raise RuntimeError if the atoms does not have a calculator

from_multi_systems(file_name: str, begin: int | None = None, end: int | None = None, step: int | None = None, ase_fmt: str | None = None, **kwargs) → ase.Atoms[source]

Convert a ASE supported file to ASE Atoms.

It will finally be converted to MultiSystems.

Parameters:

file_namestr: path to file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step
ase_fmtstr, optional: ASE format. See the ASE documentation about supported formats
**kwargsdict: other parameters

Yields:

ase.Atoms: ASE atoms in the file

from_system(atoms: ase.Atoms, **kwargs) → dict[source]

Convert ase.Atoms to a System.

Parameters:

atomsase.Atoms: an ASE Atoms, containing a structure
**kwargsdict: other parameters

Returns:

dict: data dict

to_labeled_system(data, *args, **kwargs)[source]: Convert System to ASE Atoms object.

to_system(data, **kwargs)[source]: Convert System to ASE Atom obj.

class dpdata.plugins.ase.ASETrajFormat[source]

Bases: Format

Format for the ASE’s trajectory format <https://wiki.fysik.dtu.dk/ase/ase/io/trajectory.html#module-ase.io.trajectory>`_ (ase).’ a `traj’ contains a sequence of frames, each of which is an `Atoms’ object.

Methods

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

from_labeled_system(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1, **kwargs) → dict[source]

Read ASE’s trajectory file to System of multiple frames.

Parameters:

file_namestr: ASE’s trajectory file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step
**kwargsdict: other parameters

Returns:

dict_frames: dict: a dictionary containing data of multiple frames

from_system(file_name: str, begin: int | None = 0, end: int | None = None, step: int | None = 1, **kwargs) → dict[source]

Read ASE’s trajectory file to System of multiple frames.

Parameters:

file_namestr: ASE’s trajectory file
beginint, optional: begin frame index
endint, optional: end frame index
stepint, optional: frame index step
**kwargsdict: other parameters

Returns:

dict_frames: dict: a dictionary containing data of multiple frames

dpdata.plugins.cp2k module

class dpdata.plugins.cp2k.CP2KAIMDOutputFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, restart=False, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.cp2k.CP2KOutputFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, restart=False, **kwargs)[source]

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

Parameters:

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

Returns:

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

dpdata.plugins.deepmd module

class dpdata.plugins.deepmd.DPDriver(dp: str)[source]

Bases: Driver

DeePMD-kit driver.

Parameters:

dpdeepmd.DeepPot or str: The deepmd-kit potential class or the filename of the model.

Examples

>>> DPDriver("frozen_model.pb")

Attributes:

ase_calculator: Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict[source]

Label a system data by deepmd-kit. Returns new data with energy, forces, and virials.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with energies and forces

class dpdata.plugins.deepmd.DeePMDCompFormat[source]

Bases: Format

Methods

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

MultiMode = 1

from_labeled_system(file_name, type_map=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

from_system(file_name, type_map=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

to_system(data, file_name, set_size=5000, prec=<class 'numpy.float64'>, **kwargs)[source]

Dump the system in deepmd compressed format (numpy binary) to folder.

The frames are firstly split to sets, then dumped to seperated subfolders named as folder/set.000, folder/set.001, ….

Each set contains set_size frames. The last set may have less frames than set_size.

Parameters:

datadict: System data
file_namestr: The output folder
set_sizeint: The size of each set.
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data
**kwargsdict: other parameters

class dpdata.plugins.deepmd.DeePMDHDF5Format[source]

Bases: Format

HDF5 format for DeePMD-kit.

Examples

Dump a MultiSystems to a HDF5 file:

>>> import dpdata
>>> dpdata.MultiSystems().from_deepmd_npy("data").to_deepmd_hdf5("data.hdf5")

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name[, type_map])	Convert HDF5 file to LabeledSystem data.
`from_multi_systems`(directory, **kwargs)	Generate HDF5 groups from a HDF5 file, which will be passed to from_system.
`from_system`(file_name[, type_map])	Convert HDF5 file to System data.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Generate HDF5 groups, which will be passed to to_system.
`to_system`(data, file_name[, set_size, comp_prec])	Convert System data to HDF5 file.

from_labeled_system(file_name: str | Group | File, type_map: list[str] | None = None, **kwargs) → dict[source]

Convert HDF5 file to LabeledSystem data.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
type_mapdict[str]: type map
**kwargsdict: other parameters

Returns:

dict: LabeledSystem data

Raises:

TypeError: file_name is not str or h5py.Group or h5py.File

from_multi_systems(directory: str, **kwargs) → Group[source]

Generate HDF5 groups from a HDF5 file, which will be passed to from_system.

Parameters:

directorystr: HDF5 file name
**kwargsdict: other parameters

Yields:

h5py.Group: a HDF5 group in the HDF5 file

from_system(file_name: str | Group | File, type_map: list[str] | None = None, **kwargs) → dict[source]

Convert HDF5 file to System data.

Parameters:

file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
type_mapdict[str]: type map
**kwargsdict: other parameters

Returns:

dict: System data

Raises:

TypeError: file_name is not str or h5py.Group or h5py.File

to_multi_systems(formulas: list[str], directory: str, **kwargs) → Group[source]

Generate HDF5 groups, which will be passed to to_system.

Parameters:

formulaslist[str]: formulas of MultiSystems
directorystr: HDF5 file name
**kwargsdict: other parameters

Yields:

h5py.Group: a HDF5 group with the name of formula

to_system(data: dict, file_name: str | ~h5py._hl.group.Group | ~h5py._hl.files.File, set_size: int = 5000, comp_prec: ~numpy.dtype = <class 'numpy.float64'>, **kwargs)[source]

Convert System data to HDF5 file.

Parameters:

datadict: data dict
file_namestr or h5py.Group or h5py.File: file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group
set_sizeint, default=5000: set size
comp_precnp.dtype: data precision
**kwargsdict: other parameters

class dpdata.plugins.deepmd.DeePMDMixedFormat[source]

Bases: Format

Mixed type numpy format for DeePMD-kit. Under this format, systems with the same number of atoms but different formula can be put together for a larger system, especially when the frame numbers in systems are sparse. This also helps to mixture the type information together for model training with type embedding network.

Examples

Dump a MultiSystems into a mixed type numpy directory:

>>> import dpdata
>>> dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")

Load a mixed type data into a MultiSystems:

>>> import dpdata
>>> dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")

Methods

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

from_labeled_system_mix
from_system_mix

MultiMode = 1

from_labeled_system_mix(file_name, type_map=None, **kwargs)[source]

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

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

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

Parameters:

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

Returns:

filenames: list[str]: list of filenames

from_system_mix(file_name, type_map=None, **kwargs)[source]

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

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

Parameters:

*systemSystem: The systems to mix
type_maplist of str: Maps atom type to name
**kwargsdict: other parameters

Returns:

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

to_system(data, file_name, set_size: int = 2000, prec=<class 'numpy.float64'>, **kwargs)[source]

Dump the system in deepmd mixed type format (numpy binary) to folder.

The frames were already split to different systems, so these frames can be dumped to one single subfolders: named as folder/set.000, containing less than set_size frames.

Parameters:

datadict: System data
file_namestr: The output folder
set_sizeint, default=2000: set size
prec{numpy.float32, numpy.float64}: The floating point precision of the compressed data
**kwargsdict: other parameters

class dpdata.plugins.deepmd.DeePMDRawFormat[source]

Bases: Format

Methods

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

MultiMode = 1

from_labeled_system(file_name, type_map=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

from_system(file_name, type_map=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

to_system(data, file_name, **kwargs)[source]: Dump the system in deepmd raw format to directory file_name.

dpdata.plugins.dftbplus module

class dpdata.plugins.dftbplus.DFTBplusFormat[source]

Bases: Format

The DFTBplusFormat class handles files in the DFTB+ format.

This class provides a method to read DFTB+ files from a labeled system and returns a dictionary containing various properties of the system.For more information, please refer to the official documentation at the following URL: https://dftbplus.org/documentation

Attributes:

None

Methods

from_labeled_system(file_paths, **kwargs): Reads system information from files.

from_labeled_system(file_paths, **kwargs)[source]

Reads system information from the given DFTB+ file paths.

Parameters:

file_pathstuple: A tuple containing the input and output file paths. - Input file (file_in): Contains information about symbols and coord. - Output file (file_out): Contains information about energy and force.
**kwargsdict: other parameters

dpdata.plugins.fhi_aims module

class dpdata.plugins.fhi_aims.FhiMDFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, md=True, begin=0, step=1, convergence_check=True, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.fhi_aims.FhiSCFFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

dpdata.plugins.gaussian module

class dpdata.plugins.gaussian.GaussiaGJFFormat[source]

Bases: Format

Gaussian input file.

Methods

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

from_system(file_name: str, **kwargs)[source]

Read Gaussian input file.

Parameters:

file_namestr: file name
**kwargsdict: keyword arguments

to_system(data: dict, file_name: str, **kwargs)[source]

Generate Gaussian input file.

Parameters:

datadict: system data
file_namestr: file name
**kwargsdict: Other parameters to make input files. See dpdata.gaussian.gjf.make_gaussian_input()

class dpdata.plugins.gaussian.GaussianDriver(gaussian_exec: str = 'g16', **kwargs: dict)[source]

Bases: Driver

Gaussian driver.

Note that “force” keyword must be added. If the number of atoms is large, “Geom=PrintInputOrient” should be added.

Parameters:

gaussian_execstr, default=g16: path to gaussian program
**kwargsdict: other arguments to make input files. See dpdata.gaussian.gjf.make_gaussian_input()

Examples

Use B3LYP method to calculate potential energy of a methane molecule:

>>> labeled_system = system.predict(keywords="force b3lyp/6-31g**", driver="gaussian")
>>> labeled_system['energies'][0]
-1102.714590995794

Attributes:

ase_calculator: Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict[source]

Label a system data. Returns new data with energy, forces, and virials.

Parameters:

datadict: data with coordinates and atom types

Returns:

dict: labeled data with energies and forces

class dpdata.plugins.gaussian.GaussianLogFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, md=False, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.gaussian.GaussianMDFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

dpdata.plugins.gromacs module

class dpdata.plugins.gromacs.GromacsGroFormat[source]

Bases: Format

Methods

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

from_system(file_name, format_atom_name=True, **kwargs)[source]

Load gromacs .gro file.

Parameters:

file_namestr: The input file name
format_atom_namebool: Whether to format the atom name
**kwargsdict: other parameters

to_system(data, file_name=None, frame_idx=-1, **kwargs)[source]

Dump the system in gromacs .gro format.

Parameters:

datadict: System data
file_namestr or None: The output file name. If None, return the file content as a string
frame_idxint: The index of the frame to dump
**kwargsdict: other parameters

dpdata.plugins.lammps module

class dpdata.plugins.lammps.LAMMPSDumpFormat[source]

Bases: Format

Methods

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

from_system(file_name, type_map=None, begin=0, step=1, unwrap=False, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.lammps.LAMMPSLmpFormat[source]

Bases: Format

Methods

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

from_system(file_name, type_map=None, **kwargs)[source]

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

Parameters:

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

Returns:

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

to_system(data, file_name, frame_idx=0, **kwargs)[source]

Dump the system in lammps data format.

Parameters:

datadict: System data
file_namestr: The output file name
frame_idxint: The index of the frame to dump
**kwargsdict: other parameters

dpdata.plugins.list module

class dpdata.plugins.list.ListFormat[source]

Bases: Format

Methods

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

to_system(data, **kwargs)[source]: Convert system to list, usefull for data collection.

dpdata.plugins.n2p2 module

class dpdata.plugins.n2p2.N2P2Format[source]

Bases: Format

n2p2.

This class support the conversion from and to the training data of n2p2 format. For more information about the n2p2 format, please refer to https://compphysvienna.github.io/n2p2/topics/cfg_file.html

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name, **kwargs)	Read from n2p2 format.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`(file_name, **kwargs)	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, file_name, **kwargs)	Write n2p2 format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data, args, *kwargs)	Implement System.to that converts from System to this format.

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

Read from n2p2 format.

Parameters:

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

Returns:

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

to_labeled_system(data, file_name, **kwargs)[source]

Write n2p2 format.

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

Parameters:

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

dpdata.plugins.n2p2.match_indices(atype1, atype2)[source]

dpdata.plugins.openmx module

class dpdata.plugins.openmx.OPENMXFormat[source]

Bases: Format

Format for the OpenMX <https://www.openmx-square.org/>.

OpenMX (Open source package for Material eXplorer) is a nano-scale material simulation package based on DFT, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

Note that two output files, System.Name.dat and System.Name.md, are required.

Use the openmx/md keyword argument to supply this format.

Methods

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

from_labeled_system(file_name: str, **kwargs) → dict[source]

Read from OpenMX output.

Parameters:

file_namestr: file name, which is specified by a input file, i.e. System.Name.dat
**kwargsdict: other parameters

Returns:

dict: data dict

from_system(file_name: str, **kwargs) → dict[source]

Read from OpenMX output.

Parameters:

file_namestr: file name, which is specified by a input file, i.e. System.Name.dat
**kwargsdict: other parameters

Returns:

dict: data dict

dpdata.plugins.orca module

class dpdata.plugins.orca.ORCASPOutFormat[source]

Bases: Format

ORCA single point energy output.

Note that both the energy and the gradient should be printed into the output file.

Methods

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

from_labeled_system(file_name: str, **kwargs) → dict[source]

Read from ORCA single point energy output.

Parameters:

file_namestr: file name
**kwargs: keyword arguments

Returns:

dict: system data

dpdata.plugins.psi4 module

class dpdata.plugins.psi4.PSI4InputFormat[source]

Bases: Format

Psi4 input file.

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name, **kwargs)	Implement LabeledSystem.from that converts from this format to LabeledSystem.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`(file_name, **kwargs)	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data, file_name, method, basis[, ...])	Write PSI4 input.

to_system(data: dict, file_name: str, method: str, basis: str, charge: int = 0, multiplicity: int = 1, frame_idx=0, **kwargs)[source]

Write PSI4 input.

Parameters:

datadict: system data
file_namestr: file name
methodstr: computational method
basisstr: basis set; see https://psicode.org/psi4manual/master/basissets_tables.html
chargeint, default=0: charge of system
multiplicityint, default=1: multiplicity of system
frame_idxint, default=0: The index of the frame to dump
**kwargs: keyword arguments

class dpdata.plugins.psi4.PSI4OutFormat[source]

Bases: Format

Psi4 output.

Note that both the energy and the gradient should be printed into the output file.

Methods

`MultiModes`()	File mode for MultiSystems.
`from_bond_order_system`(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
`from_labeled_system`(file_name, **kwargs)	Read from Psi4 output.
`from_multi_systems`(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
`from_system`(file_name, **kwargs)	Implement System.from that converts from this format to System.
`get_formats`()	Get all registered formats.
`get_from_methods`()	Get all registered from methods.
`get_to_methods`()	Get all registered to methods.
`mix_system`(system, type_map, *kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
`post`(func_name)	Register a post function for from method.
`register`(key)	Register a format plugin.
`register_from`(key)	Register a from method if the target method name is not default.
`register_to`(key)	Register a to method if the target method name is not default.
`to_bond_order_system`(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
`to_labeled_system`(data, args, *kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
`to_multi_systems`(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
`to_system`(data, args, *kwargs)	Implement System.to that converts from System to this format.

from_labeled_system(file_name: str, **kwargs) → dict[source]

Read from Psi4 output.

Parameters:

file_namestr: file name
**kwargs: keyword arguments

Returns:

dict: system data

dpdata.plugins.pwmat module

class dpdata.plugins.pwmat.PwmatAtomconfigFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

to_system(data, file_name, frame_idx=0, *args, **kwargs)[source]

Dump the system in pwmat atom.config format.

Parameters:

datadict: The system data
file_namestr: The output file name
frame_idxint: The index of the frame to dump
*argslist: other parameters
**kwargsdict: other parameters

class dpdata.plugins.pwmat.PwmatOutputFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, begin=0, step=1, convergence_check=True, **kwargs)[source]

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

Parameters:

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

Returns:

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

dpdata.plugins.pymatgen module

class dpdata.plugins.pymatgen.PyMatgenCSEFormat[source]

Bases: Format

Methods

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

to_labeled_system(data, *args, **kwargs)[source]: Convert System to Pymagen ComputedStructureEntry obj.

class dpdata.plugins.pymatgen.PyMatgenMoleculeFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

to_system(data, **kwargs)[source]: Convert System to Pymatgen Molecule obj.

class dpdata.plugins.pymatgen.PyMatgenStructureFormat[source]

Bases: Format

Methods

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

to_system(data, **kwargs)[source]: Convert System to Pymatgen Structure obj.

dpdata.plugins.qe module

class dpdata.plugins.qe.QECPPWSCFFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

class dpdata.plugins.qe.QECPTrajFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, begin=0, step=1, **kwargs)[source]

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

Parameters:

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

Returns:

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

from_system(file_name, begin=0, step=1, **kwargs)[source]

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

Parameters:

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

Returns:

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

dpdata.plugins.rdkit module

class dpdata.plugins.rdkit.MolFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

datadict: system data

to_bond_order_system(data, mol, file_name, frame_idx=0, **kwargs)[source]

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

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

Parameters:

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

class dpdata.plugins.rdkit.SdfFormat[source]

Bases: Format

Methods

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

from_bond_order_system(file_name, **kwargs)[source]: Note that it requires all molecules in .sdf file must be of the same topology.

to_bond_order_system(data, mol, file_name, frame_idx=-1, **kwargs)[source]

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

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

Parameters:

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

dpdata.plugins.siesta module

class dpdata.plugins.siesta.SiestaAIMDOutputFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

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

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

Parameters:

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

Returns:

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

class dpdata.plugins.siesta.SiestaOutputFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

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

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

Parameters:

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

Returns:

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

dpdata.plugins.vasp module

class dpdata.plugins.vasp.VASPOutcarFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, begin=0, step=1, convergence_check=True, **kwargs)[source]

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

Parameters:

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

Returns:

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

class dpdata.plugins.vasp.VASPPoscarFormat[source]

Bases: Format

Methods

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

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

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

Parameters:

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

Returns:

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

to_system(data, file_name, frame_idx=0, **kwargs)[source]

Dump the system in vasp POSCAR format.

Parameters:

datadict: The system data
file_namestr: The output file name
frame_idxint: The index of the frame to dump
**kwargsdict: other parameters

class dpdata.plugins.vasp.VASPStringFormat[source]

Bases: Format

Methods

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

to_system(data, frame_idx=0, **kwargs)[source]

Dump the system in vasp POSCAR format string.

Parameters:

datadict: The system data
frame_idxint: The index of the frame to dump
**kwargsdict: other parameters

class dpdata.plugins.vasp.VASPXMLFormat[source]

Bases: Format

Methods

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

from_labeled_system(file_name, begin=0, step=1, **kwargs)[source]

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

Parameters:

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

Returns:

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

dpdata.plugins.xyz module

class dpdata.plugins.xyz.QuipGapXYZFormat[source]

Bases: Format

Methods

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

from_labeled_system(data, **kwargs)[source]

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

Parameters:

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

Returns:

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

from_multi_systems(file_name, **kwargs)[source]

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

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

Parameters:

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

Returns:

filenames: list[str]: list of filenames

class dpdata.plugins.xyz.XYZFormat[source]

Bases: Format

XYZ foramt.

Examples

>>> s.to("xyz", "a.xyz")

Methods

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

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

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

Parameters:

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

Returns:

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

to_system(data, file_name, **kwargs)[source]

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

Parameters:

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

dpdata.psi4 package

Submodules

dpdata.psi4.input module

dpdata.psi4.input.write_psi4_input(types: ndarray, coords: ndarray, method: str, basis: str, charge: int = 0, multiplicity: int = 1) → str[source]

Write Psi4 input file.

Parameters:

typesnp.ndarray: atomic symbols
coordsnp.ndarray: atomic coordinates
methodstr: computational method
basisstr: basis set; see https://psicode.org/psi4manual/master/basissets_tables.html
chargeint, default=0: charge of system
multiplicityint, default=1: multiplicity of system

Returns:

str: content of Psi4 input file

dpdata.psi4.output module

dpdata.psi4.output.read_psi4_output(fn: str) → Tuple[str, ndarray, float, ndarray][source]

Read from Psi4 output.

Note that both the energy and the gradient should be printed.

Parameters:

fnstr: file name

Returns:

str: atomic symbols
np.ndarray: atomic coordinates
float: total potential energy
np.ndarray: atomic forces

dpdata.pwmat package

Submodules

dpdata.pwmat.atomconfig module

dpdata.pwmat.atomconfig.from_system_data(system, f_idx=0, skip_zeros=True)[source]

dpdata.pwmat.atomconfig.to_system_data(lines)[source]

dpdata.pwmat.movement module

dpdata.pwmat.movement.analyze_block(lines, ntot, nelm)[source]

dpdata.pwmat.movement.get_frames(fname, begin=0, step=1, convergence_check=True)[source]

dpdata.pwmat.movement.get_movement_block(fp)[source]

dpdata.pwmat.movement.system_info(lines, type_idx_zero=False)[source]

dpdata.pymatgen package

Submodules

dpdata.pymatgen.molecule module

dpdata.pymatgen.molecule.to_system_data(file_name, protect_layer=9)[source]

dpdata.qe package

Submodules

dpdata.qe.scf module

dpdata.qe.scf.get_block(lines, keyword, skip=0)[source]

dpdata.qe.scf.get_cell(lines)[source]

dpdata.qe.scf.get_coords(lines, cell)[source]

dpdata.qe.scf.get_energy(lines)[source]

dpdata.qe.scf.get_force(lines, natoms)[source]

dpdata.qe.scf.get_frame(fname)[source]

dpdata.qe.scf.get_stress(lines)[source]

dpdata.qe.traj module

dpdata.qe.traj.convert_celldm(ibrav, celldm)[source]

dpdata.qe.traj.load_atom_names(lines, ntypes)[source]

dpdata.qe.traj.load_atom_types(lines, natoms, atom_names)[source]

dpdata.qe.traj.load_block(lines, key, nlines)[source]

dpdata.qe.traj.load_cell_parameters(lines)[source]

dpdata.qe.traj.load_celldm(lines)[source]

dpdata.qe.traj.load_data(fname, natoms, begin=0, step=1, convert=1.0)[source]

dpdata.qe.traj.load_energy(fname, begin=0, step=1)[source]

dpdata.qe.traj.load_key(lines, key)[source]

dpdata.qe.traj.load_param_file(fname)[source]

dpdata.qe.traj.to_system_data(input_name, prefix, begin=0, step=1)[source]

dpdata.qe.traj.to_system_label(input_name, prefix, begin=0, step=1)[source]

dpdata.rdkit package

Submodules

dpdata.rdkit.sanitize module

exception dpdata.rdkit.sanitize.SanitizeError(content='Sanitization Failed.')[source]: Bases: Exception

class dpdata.rdkit.sanitize.Sanitizer(level='medium', raise_errors=True, verbose=False)[source]

Bases: object

Methods

sanitize(mol)

Sanitize mol according to self.level.

sanitize(mol)[source]: Sanitize mol according to self.level. If failed, return None.

dpdata.rdkit.sanitize.assign_formal_charge_for_atom(atom, verbose=False)[source]: Assigen formal charge according to 8-electron rule for element B,C,N,O,S,P,As.

dpdata.rdkit.sanitize.contain_hetero_aromatic(mol)[source]

dpdata.rdkit.sanitize.convert_by_obabel(mol, cache_dir='/home/docs/checkouts/readthedocs.org/user_builds/dpdata/checkouts/stable/docs/.cache', obabel_path='obabel')[source]

dpdata.rdkit.sanitize.get_explicit_valence(atom, verbose=False)[source]

dpdata.rdkit.sanitize.get_terminal_NR2s(atom)[source]

dpdata.rdkit.sanitize.get_terminal_oxygens(atom)[source]

dpdata.rdkit.sanitize.is_terminal_NR2(N_atom)[source]

dpdata.rdkit.sanitize.is_terminal_nitrogen(N_atom)[source]

dpdata.rdkit.sanitize.is_terminal_oxygen(O_atom)[source]

dpdata.rdkit.sanitize.kekulize_aromatic_heterocycles(mol_in, assign_formal_charge=True, sanitize=True)[source]

dpdata.rdkit.sanitize.mol_edit_log(mol, i, j)[source]

dpdata.rdkit.sanitize.print_atoms(mol)[source]

dpdata.rdkit.sanitize.print_bonds(mol)[source]

dpdata.rdkit.sanitize.regularize_carbon_bond_order(atom, verbose=True)[source]

dpdata.rdkit.sanitize.regularize_formal_charges(mol, sanitize=True, verbose=False)[source]: Regularize formal charges of atoms.

dpdata.rdkit.sanitize.regularize_nitrogen_bond_order(atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_carboxyl(mol)[source]

dpdata.rdkit.sanitize.sanitize_carboxyl_Catom(C_atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_guanidine(mol)[source]

dpdata.rdkit.sanitize.sanitize_guanidine_Catom(C_atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_mol(mol, verbose=False)[source]

dpdata.rdkit.sanitize.sanitize_nitrine_Natom(atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_nitro(mol)[source]

dpdata.rdkit.sanitize.sanitize_nitro_Natom(N_atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_phosphate(mol)[source]

dpdata.rdkit.sanitize.sanitize_phosphate_Patom(P_atom, verbose=True)[source]

dpdata.rdkit.sanitize.sanitize_sulfate(mol)[source]

dpdata.rdkit.sanitize.sanitize_sulfate_Satom(S_atom, verbose=True)[source]

dpdata.rdkit.sanitize.super_sanitize_mol(mol, name=None, verbose=True)[source]

dpdata.rdkit.utils module

dpdata.rdkit.utils.check_molecule_list(mols)[source]

dpdata.rdkit.utils.check_same_atom(atom_1, atom_2)[source]

dpdata.rdkit.utils.check_same_molecule(mol_1, mol_2)[source]

dpdata.rdkit.utils.combine_molecules(mols)[source]

dpdata.rdkit.utils.mol_to_system_data(mol)[source]

dpdata.rdkit.utils.system_data_to_mol(data)[source]

dpdata.siesta package

Submodules

dpdata.siesta.aiMD_output module

dpdata.siesta.aiMD_output.covert_dimension(arr, num)[source]

dpdata.siesta.aiMD_output.extract_keyword(fout, keyword, down_line_num, begin_column, read_column_num, is_repeated_read, column_num)[source]

dpdata.siesta.aiMD_output.get_aiMD_frame(fname)[source]

dpdata.siesta.aiMD_output.get_atom_name(fout)[source]

dpdata.siesta.aiMD_output.get_atom_numbs(atomtypes)[source]

dpdata.siesta.aiMD_output.get_atom_types(fout, atomnums)[source]

dpdata.siesta.aiMD_output.get_single_line_tail(fin, keyword, num=1)[source]

dpdata.siesta.aiMD_output.get_virial(fout, cell)[source]

dpdata.siesta.aiMD_output.obtain_nframe(fname)[source]

dpdata.siesta.output module

dpdata.siesta.output.extract_keyword(fout, keyword, down_line_num, begin_column, column_num)[source]

dpdata.siesta.output.get_atom_name(fout)[source]

dpdata.siesta.output.get_atom_numbs(atomtypes)[source]

dpdata.siesta.output.get_atom_types(fout, atomnums)[source]

dpdata.siesta.output.get_single_line_tail(fin, keyword, num=1)[source]

dpdata.siesta.output.get_virial(fout, cells)[source]

dpdata.siesta.output.obtain_frame(fname)[source]

dpdata.vasp package

Submodules

dpdata.vasp.outcar module

dpdata.vasp.outcar.analyze_block(lines, ntot, nelm, ml=False)[source]

dpdata.vasp.outcar.get_frames(fname, begin=0, step=1, ml=False, convergence_check=True)[source]

dpdata.vasp.outcar.get_outcar_block(fp, ml=False)[source]

dpdata.vasp.outcar.system_info(lines, type_idx_zero=False)[source]

dpdata.vasp.poscar module

dpdata.vasp.poscar.from_system_data(system, f_idx=0, skip_zeros=True)[source]

dpdata.vasp.poscar.to_system_data(lines)[source]

dpdata.vasp.xml module

dpdata.vasp.xml.analyze(fname, type_idx_zero=False, begin=0, step=1)[source]: Deal with broken xml file.

dpdata.vasp.xml.analyze_atominfo(atominfo_xml)[source]

dpdata.vasp.xml.analyze_calculation(cc)[source]

dpdata.vasp.xml.check_name(item, name)[source]

dpdata.vasp.xml.formulate_config(eles, types, posi, cell, ener, forc, strs_)[source]

dpdata.vasp.xml.get_varray(varray)[source]

dpdata.xyz package

Submodules

dpdata.xyz.quip_gap_xyz module

class dpdata.xyz.quip_gap_xyz.QuipGapxyzSystems(file_name)[source]

Bases: object

deal with QuipGapxyzFile.

Methods

get_block_generator
handle_single_xyz_frame

get_block_generator()[source]

static handle_single_xyz_frame(lines)[source]

dpdata.xyz.xyz module

dpdata.xyz.xyz.coord_to_xyz(coord: ndarray, types: list) → str[source]

Convert coordinates and types to xyz format.

Parameters:

coordnp.ndarray: coordinates, Nx3 array
typeslist: list of types

Returns:

str: xyz format string

Examples

>>> coord_to_xyz(np.ones((1,3)), ["C"])
1

C 1.000000 1.000000 1.000000

dpdata.xyz.xyz.xyz_to_coord(xyz: str) → Tuple[ndarray, list][source]

Convert xyz format to coordinates and types.

Parameters:

xyzstr: xyz format string

Returns:

coordsnp.ndarray: coordinates, Nx3 array
typeslist: list of types

Submodules

dpdata.ase_calculator module

dpdata.bond_order_system module

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

Bases: System

The system with chemical bond and formal charges information.

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

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

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

Attributes:

formula: Return the formula of this system, like C3H5O2.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
uniq_formula: Return the uniq_formula of this system.

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_rdkit_mol`(rdkit_mol)	Initialize from a rdkit.Chem.rdchem.Mol object.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_bond_order`(begin_atom_idx, end_atom_idx)	Return the bond order between given atoms.
`get_charge`()	Return the total formal charge of the moleclue.
`get_formal_charges`()	Return the formal charges on each atom.
`get_mol`()	Return the rdkit.Mol object.
`get_natoms`()	Returns total number of atoms in the system.
`get_nbonds`()	Return the number of bonds.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

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

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

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

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

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

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

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

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

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

dpdata.cli module

Command line interface for dpdata.

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

Convert files from one format to another one.

Parameters:

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

dpdata.cli.dpdata_cli()[source]

Dpdata cli.

Examples

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

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

Returns dpdata cli parser.

Returns:

argparse.ArgumentParser: dpdata cli parser

dpdata.data_type module

class dpdata.data_type.AnyInt[source]

Bases: int

AnyInt equals to any other integer.

Attributes:

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

Methods

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

class dpdata.data_type.Axis(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

Bases: Enum

Data axis.

NATOMS = 'natoms'

NBONDS = 'nbonds'

NFRAMES = 'nframes'

NTYPES = 'ntypes'

exception dpdata.data_type.DataError[source]

Bases: Exception

Data is not correct.

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

Bases: object

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

Parameters:

namestr: name of data
dtypetype or tuple[type]: data type, e.g. np.ndarray
shapetuple[int], optional: shape of data. Used when data is list or np.ndarray. Use Axis to represents numbers
requiredbool, default=True: whether this data is required

Methods

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

check(system: System)[source]

Check if a system has correct data of this type.

Parameters:

systemSystem: checked system

Raises:

DataError: type or shape of data is not correct

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

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

Get all registered data types.

Parameters:

labeledbool: whether this data type is for LabeledSystem

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

Register a data type.

Parameters:

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

dpdata.driver module

Driver plugin system.

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

Bases: ABC

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

dpdata.format module

Implement the format plugin system.

class dpdata.format.Format[source]

Bases: ABC

The abstract base class for all formats.

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

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

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

Methods

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

MultiMode = 0

class MultiModes[source]

Bases: object

File mode for MultiSystems.

The current implemented modes are:

0 (default): not implemented

1: every directory under the top-level directory is a system.

Directory = 1

NotImplemented = 0

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

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

Parameters:

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

Returns:

datadict: system data

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

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

Parameters:

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

Returns:

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

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

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

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

Parameters:

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

Returns:

filenames: list[str]: list of filenames

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

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

Parameters:

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

Returns:

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

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

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

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

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

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

Parameters:

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

Returns:

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

static post(func_name)[source]

Register a post function for from method.

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

Parameters:

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

Returns:

function: The decorator function.

Examples

Register a post function:

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

static register(key)[source]

Register a format plugin.

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

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

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

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

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

Register a format plugin:

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

static register_from(key)[source]

Register a from method if the target method name is not default.

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

Register a from method:

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

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

static register_to(key)[source]

Register a to method if the target method name is not default.

Parameters:

keystr: The key to register the plugin.

Returns:

function: The decorator function.

Examples

Register a to method:

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

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

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

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

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

Parameters:

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

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

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

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

Parameters:

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

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

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

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

Parameters:

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

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

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

Parameters:

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

dpdata.periodic_table module

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

Bases: object

Attributes:

X
Z
calculated_radius
mass
name
radius

Methods

from_Z

property X

property Z

property calculated_radius

classmethod from_Z(Z)[source]

property mass

property name

property radius

dpdata.plugin module

Base of plugin systems.

class dpdata.plugin.Plugin[source]

Bases: object

A class to register plugins.

Examples

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

Methods

register(key)

Register a plugin.

get_plugin

get_plugin(key)[source]

register(key)[source]

Register a plugin.

Parameters:

keystr: Key of the plugin.

dpdata.stat module

class dpdata.stat.Errors(system_1: object, system_2: object)[source]

Bases: ErrorsBase

Compute errors (deviations) between two LabeledSystems.

Parameters:

system_1object: system 1
system_2object: system 2

Examples

Get errors between referenced system and predicted system:

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

Attributes:

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

Methods

SYSTEM_TYPE

alias of LabeledSystem

SYSTEM_TYPE: alias of LabeledSystem

property e_errors: ndarray: Energy errors.

property f_errors: ndarray: Force errors.

class dpdata.stat.ErrorsBase(system_1: object, system_2: object)[source]

Bases: object

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

Parameters:

system_1object: system 1
system_2object: system 2

Attributes:

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

Methods

SYSTEM_TYPE

alias of object

SYSTEM_TYPE: alias of object

abstract property e_errors: ndarray: Energy errors.

property e_mae: float64: Energy MAE.

property e_rmse: float64: Energy RMSE.

abstract property f_errors: ndarray: Force errors.

property f_mae: float64: Force MAE.

property f_rmse: float64: Force RMSE.

class dpdata.stat.MultiErrors(system_1: object, system_2: object)[source]

Bases: ErrorsBase

Compute errors (deviations) between two MultiSystems.

Parameters:

system_1object: system 1
system_2object: system 2

Examples

Get errors between referenced system and predicted system:

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

Attributes:

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

Methods

SYSTEM_TYPE

alias of MultiSystems

SYSTEM_TYPE: alias of MultiSystems

property e_errors: ndarray: Energy errors.

property f_errors: ndarray: Force errors.

dpdata.stat.mae(errors: ndarray) → float64[source]

Compute the mean absolute error (MAE).

Parameters:

errorsnp.ndarray: errors between two values

Returns:

np.float64: mean absolute error (MAE)

dpdata.stat.rmse(errors: ndarray) → float64[source]

Compute the root mean squared error (RMSE).

Parameters:

errorsnp.ndarray: errors between two values

Returns:

np.float64: root mean squared error (RMSE)

dpdata.system module

class dpdata.system.LabeledSystem(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)[source]

Bases: System

The labeled data System.

For example, a labeled water system named d_example has two molecules (6 atoms) and nframes frames. The labels can be accessed by

d_example[‘energies’] : a numpy array of size nframes
d_example[‘forces’] : a numpy array of size nframes x 6 x 3
d_example[‘virials’] : optional, a numpy array of size nframes x 3 x 3

It is noted that

The order of frames stored in ‘energies’, ‘forces’ and ‘virials’ should be consistent with ‘atom_types’, ‘cells’ and ‘coords’.
The order of atoms in every frame of ‘forces’ should be consistent with ‘coords’ and ‘atom_types’.

Parameters:

file_namestr

The file to load the system

fmtstr

Format of the file, supported formats are

auto: infered from file_name’s extension
vasp/xml: vasp xml
vasp/outcar: vasp OUTCAR
deepmd/raw: deepmd-kit raw
deepmd/npy: deepmd-kit compressed format (numpy binary)
qe/cp/traj: Quantum Espresso CP trajectory files. should have: file_name+’.in’, file_name+’.pos’, file_name+’.evp’ and file_name+’.for’
qe/pw/scf: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing ‘out’ by ‘in’ from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename.
siesta/output: siesta SCF output file
siesta/aimd_output: siesta aimd output file
gaussian/log: gaussian logs
gaussian/md: gaussian ab initio molecular dynamics
cp2k/output: cp2k output file
cp2k/aimd_output: cp2k aimd output dir(contains pos.xyz and *.log file); optional restart=True if it is a cp2k restarted task.
pwmat/movement: pwmat md output file
pwmat/out.mlmd: pwmat scf output file

type_maplist of str

Maps atom type to name. The atom with type ii is mapped to type_map[ii]. If not provided the atom names are assigned to ‘Type_1’, ‘Type_2’, ‘Type_3’…

beginint

The beginning frame when loading MD trajectory.

stepint

The number of skipped frames when loading MD trajectory.

Attributes:

formula: Return the formula of this system, like C3H5O2.
formula_hash: Return the hash of the formula of this system.
nopbc
short_formula: Return the short formula of this system.
short_name: Return the short name of this system (no more than 255 bytes), in the following order: - formula - short_formula - formula_hash.
uniq_formula: Return the uniq_formula of this system.

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`correction`(hl_sys)	Get energy and force correction between self and a high-level LabeledSystem.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_natoms`()	Returns total number of atoms in the system.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_outlier`([threshold])	Remove outlier frames from the system.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
affine_map_fv
apply_type_map
from_fmt
from_fmt_obj
has_virial
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

affine_map_fv(trans, f_idx)[source]

correction(hl_sys)[source]

Get energy and force correction between self and a high-level LabeledSystem. The self’s coordinates will be kept, but energy and forces will be replaced by the correction between these two systems.

Note: The function will not check whether coordinates and elements of two systems are the same. The user should make sure by itself.

Parameters:

hl_sysLabeledSystem: high-level LabeledSystem

Returns:

corrected_sys: LabeledSystem: Corrected LabeledSystem

from_3dmol(file_name, **kwargs): Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs): Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs): Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

has_virial()[source]

post_funcs = <dpdata.plugin.Plugin object>

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

Remove outlier frames from the system.

Remove the frames whose energies satisfy the condition

\[\frac{\left \| E - \bar{E} \right \|}{\sigma(E)} \geq \text{threshold}\]

where \(\bar{E}\) and \(\sigma(E)\) are the mean and standard deviation of the energies in the system.

Parameters:

thresholdfloat: The threshold of outlier detection. The default value is 8.0.

Returns:

LabeledSystem: The system without outlier frames.

References

[1]

Gao, X.; Ramezanghorbani, F.; Isayev, O.; Smith, J. S.; Roitberg, A. E. TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials. J. Chem. Inf. Model. 2020, 60, 3408-3415.

[2]

Zeng, J.; Tao, Y.; Giese, T. J.; York, D. M.. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. J. Comput. Chem. 2023, 19, 1261-1275.

rot_frame_lower_triangular(f_idx=0)[source]

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

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

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

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

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

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

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

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

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

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

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

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

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

to_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

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

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

class dpdata.system.MultiSystems(*systems, type_map=None)[source]

Bases: object

A set containing several systems.

Methods

`append`(*systems)	Append systems or MultiSystems to systems.
`check_atom_names`(system)	Make atom_names in all systems equal, prevent inconsistent atom_types.
`correction`(hl_sys)	Get energy and force correction between self (assumed low-level) and a high-level MultiSystems.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dump`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`from_fhi_aims_md`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`from_fhi_aims_output`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`from_fhi_aims_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`from_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_gaussian_gjf`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`from_gaussian_log`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussianLogFormat` format.
`from_gaussian_md`(file_name, **kwargs)	Read data from `dpdata.plugins.gaussian.GaussianMDFormat` format.
`from_gro`(file_name, **kwargs)	Read data from `dpdata.plugins.gromacs.GromacsGroFormat` format.
`from_gromacs_gro`(file_name, **kwargs)	Read data from `dpdata.plugins.gromacs.GromacsGroFormat` format.
`from_lammps_dump`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`from_lammps_lmp`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`from_list`(file_name, **kwargs)	Read data from `dpdata.plugins.list.ListFormat` format.
`from_lmp`(file_name, **kwargs)	Read data from `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`from_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_mol`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.MolFormat` format.
`from_mol_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.MolFormat` format.
`from_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_nframes`()	Returns number of frames in all systems.
`minimize`(args, minimizer, *kwargs)	Minimize geometry by a minimizer.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_lammps_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_lammps_lmp`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`to_list`(args, *kwargs)	Dump data to `dpdata.plugins.list.ListFormat` format.
`to_lmp`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSLmpFormat` format.
`to_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_mol`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.MolFormat` format.
`to_mol_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.MolFormat` format.
`to_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`train_test_split`(test_size[, seed])	Split systems into random train and test subsets.

from_dir
from_file
from_fmt_obj
load_systems_from_file
to_fmt_obj

append(*systems)[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_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

classmethod from_dir(dir_name, file_name, fmt='auto', type_map=None)[source]

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

classmethod from_file(file_name, fmt, **kwargs)[source]

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

get_nframes()[source]: Returns number of frames in all systems.

load_systems_from_file(file_name=None, fmt=None, **kwargs)[source]

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

Minimize geometry by a minimizer.

Parameters:

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

Returns:

MultiSystems: A new labeled MultiSystems.

Examples

Minimize a system using ASE BFGS along with a DP driver:

>>> from dpdata.driver import Driver
>>> from ase.optimize import BFGS
>>> driver = Driver.get_driver("dp")("some_model.pb")
>>> some_system.minimize(minimizer="ase", driver=driver, optimizer=BFGS, fmax=1e-5)

pick_atom_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_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_fmt_obj(fmtobj, directory, *args, **kwargs)[source]

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

train_test_split(test_size: float | int, seed: int | None = None) → Tuple[MultiSystems, MultiSystems, Dict[str, ndarray]][source]

Split systems into random train and test subsets.

Parameters:

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

Returns:

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

class dpdata.system.System(file_name=None, fmt='auto', type_map=None, begin=0, step=1, data=None, convergence_check=True, **kwargs)[source]

Bases: MSONable

The data System.

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

For example, a water system named d_example has two molecules. The properties can be accessed by

d_example[‘atom_numbs’] : [2, 4]
d_example[‘atom_names’] : [‘O’, ‘H’]
d_example[‘atom_types’] : [0, 1, 1, 0, 1, 1]
d_example[‘orig’] : [0, 0, 0]
d_example[‘cells’] : a numpy array of size nframes x 3 x 3
d_example[‘coords’] : a numpy array of size nframes x natoms x 3

It is noted that

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

Restrictions:

d_example[‘orig’] is always [0, 0, 0]
d_example[‘cells’][ii] is always lower triangular (lammps cell tensor convention)

Attributes:

DTYPEStuple[DataType]: data types of this class

Methods

`add_atom_names`(atom_names)	Add atom_names that do not exist.
`append`(system)	Append a system to this system.
`apply_pbc`()	Append periodic boundary condition.
`as_dict`()	Returns data dict of System instance.
`check_data`()	Check if data is correct.
`check_type_map`(type_map)	Assign atom_names to type_map if type_map is given and different from atom_names.
`convert_to_mixed_type`([type_map])	Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms.
`copy`()	Returns a copy of the system.
`dump`(filename[, indent])	Dump .json or .yaml file.
`extend`(systems)	Extend a system list to this system.
`from_3dmol`(file_name, **kwargs)	Read data from `dpdata.plugins.3dmol.Py3DMolFormat` format.
`from_abacus_lcao_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_lcao_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_lcao_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_md`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusMDFormat` format.
`from_abacus_pw_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_relax`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`from_abacus_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSCFFormat` format.
`from_abacus_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_amber_md`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.AmberMDFormat` format.
`from_ase_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASEStructureFormat` format.
`from_ase_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.ase.ASETrajFormat` format.
`from_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_cp2k_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`from_cp2k_output`(file_name, **kwargs)	Read data from `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`from_deepmd`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_deepmd_comp`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_hdf5`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`from_deepmd_npy`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`from_deepmd_npy_mixed`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`from_deepmd_raw`(file_name, **kwargs)	Read data from `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`from_dftbplus`(file_name, **kwargs)	Read data from `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`from_dict`(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_n2p2`(file_name, **kwargs)	Read data from `dpdata.plugins.n2p2.N2P2Format` format.
`from_openmx_md`(file_name, **kwargs)	Read data from `dpdata.plugins.openmx.OPENMXFormat` format.
`from_orca_spout`(file_name, **kwargs)	Read data from `dpdata.plugins.orca.ORCASPOutFormat` format.
`from_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_psi4_inp`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4InputFormat` format.
`from_psi4_out`(file_name, **kwargs)	Read data from `dpdata.plugins.psi4.PSI4OutFormat` format.
`from_pwmat_atomconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_finalconfig`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`from_pwmat_mlmd`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_movement`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pwmat_output`(file_name, **kwargs)	Read data from `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`from_pymatgen_computedstructureentry`(...)	Read data from `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`from_pymatgen_molecule`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`from_pymatgen_structure`(file_name, **kwargs)	Read data from `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`from_qe_cp_traj`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPTrajFormat` format.
`from_qe_pw_scf`(file_name, **kwargs)	Read data from `dpdata.plugins.qe.QECPPWSCFFormat` format.
`from_quip_gap_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_quip_gap_xyz_file`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`from_sdf`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_sdf_file`(file_name, **kwargs)	Read data from `dpdata.plugins.rdkit.SdfFormat` format.
`from_siesta_aiMD_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_aimd_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`from_siesta_output`(file_name, **kwargs)	Read data from `dpdata.plugins.siesta.SiestaOutputFormat` format.
`from_sqm_in`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMINFormat` format.
`from_sqm_out`(file_name, **kwargs)	Read data from `dpdata.plugins.amber.SQMOutFormat` format.
`from_stru`(file_name, **kwargs)	Read data from `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`from_vasp_contcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_outcar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPOutcarFormat` format.
`from_vasp_poscar`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPPoscarFormat` format.
`from_vasp_string`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPStringFormat` format.
`from_vasp_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xml`(file_name, **kwargs)	Read data from `dpdata.plugins.vasp.VASPXMLFormat` format.
`from_xyz`(file_name, **kwargs)	Read data from `dpdata.plugins.xyz.XYZFormat` format.
`get_atom_names`()	Returns name of atoms.
`get_atom_numbs`()	Returns number of atoms.
`get_atom_types`()	Returns type of atoms.
`get_natoms`()	Returns total number of atoms in the system.
`get_nframes`()	Returns number of frames in the system.
`get_ntypes`()	Returns total number of atom types in the system.
`load`(filename)	Rebuild System obj.
`map_atom_types`([type_map])	Map the atom types of the system.
`minimize`(args, minimizer, *kwargs)	Minimize the geometry.
`perturb`(pert_num, cell_pert_fraction, ...[, ...])	Perturb each frame in the system randomly.
`pick_atom_idx`(idx[, nopbc])	Pick atom index.
`pick_by_amber_mask`(param, maskstr[, ...])	Pick atoms by amber mask.
`predict`(*args[, driver])	Predict energies and forces by a driver.
`register_data_type`(*data_type)	Register data type.
`remove_atom_names`(atom_names)	Remove atom names and all such atoms.
`remove_pbc`([protect_layer])	This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than protect_layer (2) translates the system such that the center-of-geometry of the system locates at the center of the cell.
`replicate`(ncopy)	Replicate the each frame in the system in 3 dimensions.
`shuffle`()	Shuffle frames randomly.
`sort_atom_names`([type_map])	Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names.
`sort_atom_types`()	Sort atom types.
`sub_system`(f_idx)	Construct a subsystem from the system.
`to`(fmt, args, *kwargs)	Dump systems to the specific format.
`to_3dmol`(args, *kwargs)	Dump data to `dpdata.plugins.3dmol.Py3DMolFormat` format.
`to_abacus_lcao_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_lcao_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_lcao_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_md`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusMDFormat` format.
`to_abacus_pw_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_relax`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusRelaxFormat` format.
`to_abacus_scf`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSCFFormat` format.
`to_abacus_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_amber_md`(args, *kwargs)	Dump data to `dpdata.plugins.amber.AmberMDFormat` format.
`to_ase_structure`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASEStructureFormat` format.
`to_ase_traj`(args, *kwargs)	Dump data to `dpdata.plugins.ase.ASETrajFormat` format.
`to_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_cp2k_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KAIMDOutputFormat` format.
`to_cp2k_output`(args, *kwargs)	Dump data to `dpdata.plugins.cp2k.CP2KOutputFormat` format.
`to_deepmd`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_deepmd_comp`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_hdf5`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDHDF5Format` format.
`to_deepmd_npy`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDCompFormat` format.
`to_deepmd_npy_mixed`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDMixedFormat` format.
`to_deepmd_raw`(args, *kwargs)	Dump data to `dpdata.plugins.deepmd.DeePMDRawFormat` format.
`to_dftbplus`(args, *kwargs)	Dump data to `dpdata.plugins.dftbplus.DFTBplusFormat` format.
`to_dump`(args, *kwargs)	Dump data to `dpdata.plugins.lammps.LAMMPSDumpFormat` format.
`to_fhi_aims_md`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_output`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiMDFormat` format.
`to_fhi_aims_scf`(args, *kwargs)	Dump data to `dpdata.plugins.fhi_aims.FhiSCFFormat` format.
`to_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_gaussian_gjf`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussiaGJFFormat` format.
`to_gaussian_log`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianLogFormat` format.
`to_gaussian_md`(args, *kwargs)	Dump data to `dpdata.plugins.gaussian.GaussianMDFormat` format.
`to_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_gromacs_gro`(args, *kwargs)	Dump data to `dpdata.plugins.gromacs.GromacsGroFormat` format.
`to_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_n2p2`(args, *kwargs)	Dump data to `dpdata.plugins.n2p2.N2P2Format` format.
`to_openmx_md`(args, *kwargs)	Dump data to `dpdata.plugins.openmx.OPENMXFormat` format.
`to_orca_spout`(args, *kwargs)	Dump data to `dpdata.plugins.orca.ORCASPOutFormat` format.
`to_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_psi4_inp`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4InputFormat` format.
`to_psi4_out`(args, *kwargs)	Dump data to `dpdata.plugins.psi4.PSI4OutFormat` format.
`to_pwmat_atomconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_finalconfig`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatAtomconfigFormat` format.
`to_pwmat_mlmd`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_movement`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pwmat_output`(args, *kwargs)	Dump data to `dpdata.plugins.pwmat.PwmatOutputFormat` format.
`to_pymatgen_ComputedStructureEntry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_computedstructureentry`(*args, ...)	Dump data to `dpdata.plugins.pymatgen.PyMatgenCSEFormat` format.
`to_pymatgen_molecule`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenMoleculeFormat` format.
`to_pymatgen_structure`(args, *kwargs)	Dump data to `dpdata.plugins.pymatgen.PyMatgenStructureFormat` format.
`to_qe_cp_traj`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPTrajFormat` format.
`to_qe_pw_scf`(args, *kwargs)	Dump data to `dpdata.plugins.qe.QECPPWSCFFormat` format.
`to_quip_gap_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_quip_gap_xyz_file`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.QuipGapXYZFormat` format.
`to_sdf`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_sdf_file`(args, *kwargs)	Dump data to `dpdata.plugins.rdkit.SdfFormat` format.
`to_siesta_aimd_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaAIMDOutputFormat` format.
`to_siesta_output`(args, *kwargs)	Dump data to `dpdata.plugins.siesta.SiestaOutputFormat` format.
`to_sqm_in`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMINFormat` format.
`to_sqm_out`(args, *kwargs)	Dump data to `dpdata.plugins.amber.SQMOutFormat` format.
`to_stru`(args, *kwargs)	Dump data to `dpdata.plugins.abacus.AbacusSTRUFormat` format.
`to_vasp_contcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_outcar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPOutcarFormat` format.
`to_vasp_poscar`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPPoscarFormat` format.
`to_vasp_string`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPStringFormat` format.
`to_vasp_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xml`(args, *kwargs)	Dump data to `dpdata.plugins.vasp.VASPXMLFormat` format.
`to_xyz`(args, *kwargs)	Dump data to `dpdata.plugins.xyz.XYZFormat` format.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

affine_map
apply_type_map
from_fmt
from_fmt_obj
replace
rot_frame_lower_triangular
rot_lower_triangular
to_fmt_obj

DTYPES = (<dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>, <dpdata.data_type.DataType object>)

add_atom_names(atom_names)[source]: Add atom_names that do not exist.

affine_map(trans, f_idx=0)[source]

append(system)[source]

Append a system to this system.

Parameters:

systemSystem: The system to append

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

apply_type_map(type_map)[source]

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

check_data()[source]

Check if data is correct.

Raises:

DataError: if data is not correct

check_type_map(type_map)[source]

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

Parameters:

type_maplist: type_map

convert_to_mixed_type(type_map=None)[source]

Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms. Change the ‘atom_names’ to one placeholder type ‘MIXED_TOKEN’ and add ‘real_atom_types’ to store the real type vectors according to the given type_map.

Parameters:

type_maplist: type_map

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

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

extend(systems)[source]

Extend a system list to this system.

Parameters:

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

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

property formula_hash: str: Return the hash of the formula of this system.

from_3dmol(file_name, **kwargs): Read data from dpdata.plugins.3dmol.Py3DMolFormat format.

from_abacus_lcao_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_lcao_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_lcao_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_md(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusMDFormat format.

from_abacus_pw_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_relax(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusRelaxFormat format.

from_abacus_scf(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSCFFormat format.

from_abacus_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_amber_md(file_name, **kwargs): Read data from dpdata.plugins.amber.AmberMDFormat format.

from_ase_structure(file_name, **kwargs): Read data from dpdata.plugins.ase.ASEStructureFormat format.

from_ase_traj(file_name, **kwargs): Read data from dpdata.plugins.ase.ASETrajFormat format.

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

from_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_cp2k_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

from_cp2k_output(file_name, **kwargs): Read data from dpdata.plugins.cp2k.CP2KOutputFormat format.

from_deepmd(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_deepmd_comp(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_hdf5(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDHDF5Format format.

from_deepmd_npy(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDCompFormat format.

from_deepmd_npy_mixed(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDMixedFormat format.

from_deepmd_raw(file_name, **kwargs): Read data from dpdata.plugins.deepmd.DeePMDRawFormat format.

from_dftbplus(file_name, **kwargs): Read data from dpdata.plugins.dftbplus.DFTBplusFormat format.

from_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_fhi_aims_md(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_output(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiMDFormat format.

from_fhi_aims_scf(file_name, **kwargs): Read data from dpdata.plugins.fhi_aims.FhiSCFFormat format.

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

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

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

from_gaussian_gjf(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussiaGJFFormat format.

from_gaussian_log(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianLogFormat format.

from_gaussian_md(file_name, **kwargs): Read data from dpdata.plugins.gaussian.GaussianMDFormat format.

from_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_gromacs_gro(file_name, **kwargs): Read data from dpdata.plugins.gromacs.GromacsGroFormat format.

from_lammps_dump(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSDumpFormat format.

from_lammps_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_list(file_name, **kwargs): Read data from dpdata.plugins.list.ListFormat format.

from_lmp(file_name, **kwargs): Read data from dpdata.plugins.lammps.LAMMPSLmpFormat format.

from_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_mol(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_mol_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.MolFormat format.

from_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_n2p2(file_name, **kwargs): Read data from dpdata.plugins.n2p2.N2P2Format format.

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

from_orca_spout(file_name, **kwargs): Read data from dpdata.plugins.orca.ORCASPOutFormat format.

from_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_psi4_inp(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4InputFormat format.

from_psi4_out(file_name, **kwargs): Read data from dpdata.plugins.psi4.PSI4OutFormat format.

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

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

from_pwmat_mlmd(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_movement(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pwmat_output(file_name, **kwargs): Read data from dpdata.plugins.pwmat.PwmatOutputFormat format.

from_pymatgen_computedstructureentry(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

from_pymatgen_molecule(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

from_pymatgen_structure(file_name, **kwargs): Read data from dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

from_qe_cp_traj(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPTrajFormat format.

from_qe_pw_scf(file_name, **kwargs): Read data from dpdata.plugins.qe.QECPPWSCFFormat format.

from_quip_gap_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_quip_gap_xyz_file(file_name, **kwargs): Read data from dpdata.plugins.xyz.QuipGapXYZFormat format.

from_sdf(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_sdf_file(file_name, **kwargs): Read data from dpdata.plugins.rdkit.SdfFormat format.

from_siesta_aiMD_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_aimd_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

from_siesta_output(file_name, **kwargs): Read data from dpdata.plugins.siesta.SiestaOutputFormat format.

from_sqm_in(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMINFormat format.

from_sqm_out(file_name, **kwargs): Read data from dpdata.plugins.amber.SQMOutFormat format.

from_stru(file_name, **kwargs): Read data from dpdata.plugins.abacus.AbacusSTRUFormat format.

from_vasp_contcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_outcar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPOutcarFormat format.

from_vasp_poscar(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPPoscarFormat format.

from_vasp_string(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPStringFormat format.

from_vasp_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xml(file_name, **kwargs): Read data from dpdata.plugins.vasp.VASPXMLFormat format.

from_xyz(file_name, **kwargs): Read data from dpdata.plugins.xyz.XYZFormat format.

get_atom_names()[source]: Returns name of atoms.

get_atom_numbs()[source]: Returns number of atoms.

get_atom_types()[source]: Returns type of atoms.

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

get_nframes()[source]: Returns number of frames in the system.

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

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

map_atom_types(type_map=None) → ndarray[source]

Map the atom types of the system.

Parameters:

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

Returns:

new_atom_typesnp.ndarray: The mapped atom types

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

Minimize the geometry.

Parameters:

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

Returns:

labeled_sysLabeledSystem: A new labeled system.

property nopbc

perturb(pert_num, cell_pert_fraction, atom_pert_distance, atom_pert_style='normal')[source]

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

Parameters:

pert_numint

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

cell_pert_fractionfloat

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

atom_pert_distancefloat

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

atom_pert_stylestr

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

‘normal’: the distance will be object to chi-square distribution with 3 degrees of freedom after normalization.
The mean value of the distance is atom_pert_fraction*side_length

‘uniform’: will generate uniformly random points in a 3D-balls with radius as atom_pert_distance.
These points are treated as vector used by atoms to move. Obviously, the max length of the distance atoms move is atom_pert_distance.

‘const’: The distance atoms move will be a constant atom_pert_distance.

Returns:

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

pick_atom_idx(idx, nopbc=None)[source]

Pick atom index.

Parameters:

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

Returns:

new_sys: System: new system

pick_by_amber_mask(param, maskstr, pass_coords=False, nopbc=None)[source]

Pick atoms by amber mask.

Parameters:

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

post_funcs = <dpdata.plugin.Plugin object>

predict(*args: Any, driver: str = 'dp', **kwargs: Any) → LabeledSystem[source]

Predict energies and forces by a driver.

Parameters:

*argsiterable: Arguments passing to the driver
driverstr, default=dp: The assigned driver. For compatibility, default is dp
**kwargsdict: Other arguments passing to the driver

Returns:

labeled_sysLabeledSystem: A new labeled system.

Examples

The default driver is DP:

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

classmethod register_data_type(*data_type: Tuple[DataType])[source]

Register data type.

Parameters:

*data_typetuple[DataType]: data type to be regiestered

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

remove_pbc(protect_layer=9)[source]

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

Parameters:

protect_layerthe protect layer between the atoms and the cell: boundary

replace(initial_atom_type, end_atom_type, replace_num)[source]

replicate(ncopy)[source]

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

Parameters:

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

Returns:

tmpSystem: The system after replication.

rot_frame_lower_triangular(f_idx=0)[source]

rot_lower_triangular()[source]

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

property short_name: str

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

formula

short_formula

formula_hash.

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

sort_atom_names(type_map=None)[source]

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

Parameters:

type_maplist: type_map

sort_atom_types() → ndarray[source]

Sort atom types.

Returns:

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

sub_system(f_idx)[source]

Construct a subsystem from the system.

Parameters:

f_idxint or index: Which frame to use in the subsystem

Returns:

sub_systemSystem: The subsystem

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

Dump systems to the specific format.

Parameters:

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

Returns:

System: self

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

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

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

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

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

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

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

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

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

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

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

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

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

to_ase_traj(*args, **kwargs): Dump data to dpdata.plugins.ase.ASETrajFormat format.

to_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_cp2k_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KAIMDOutputFormat format.

to_cp2k_output(*args, **kwargs): Dump data to dpdata.plugins.cp2k.CP2KOutputFormat format.

to_deepmd(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_deepmd_comp(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_hdf5(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDHDF5Format format.

to_deepmd_npy(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDCompFormat format.

to_deepmd_npy_mixed(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDMixedFormat format.

to_deepmd_raw(*args, **kwargs): Dump data to dpdata.plugins.deepmd.DeePMDRawFormat format.

to_dftbplus(*args, **kwargs): Dump data to dpdata.plugins.dftbplus.DFTBplusFormat format.

to_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_fhi_aims_md(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_output(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiMDFormat format.

to_fhi_aims_scf(*args, **kwargs): Dump data to dpdata.plugins.fhi_aims.FhiSCFFormat format.

to_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

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

to_gaussian_gjf(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussiaGJFFormat format.

to_gaussian_log(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianLogFormat format.

to_gaussian_md(*args, **kwargs): Dump data to dpdata.plugins.gaussian.GaussianMDFormat format.

to_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_gromacs_gro(*args, **kwargs): Dump data to dpdata.plugins.gromacs.GromacsGroFormat format.

to_lammps_dump(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSDumpFormat format.

to_lammps_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_list(*args, **kwargs): Dump data to dpdata.plugins.list.ListFormat format.

to_lmp(*args, **kwargs): Dump data to dpdata.plugins.lammps.LAMMPSLmpFormat format.

to_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_mol(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_mol_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.MolFormat format.

to_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_n2p2(*args, **kwargs): Dump data to dpdata.plugins.n2p2.N2P2Format format.

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

to_orca_spout(*args, **kwargs): Dump data to dpdata.plugins.orca.ORCASPOutFormat format.

to_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_psi4_inp(*args, **kwargs): Dump data to dpdata.plugins.psi4.PSI4InputFormat format.

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

to_pwmat_atomconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_finalconfig(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatAtomconfigFormat format.

to_pwmat_mlmd(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_movement(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pwmat_output(*args, **kwargs): Dump data to dpdata.plugins.pwmat.PwmatOutputFormat format.

to_pymatgen_ComputedStructureEntry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_computedstructureentry(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenCSEFormat format.

to_pymatgen_molecule(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenMoleculeFormat format.

to_pymatgen_structure(*args, **kwargs): Dump data to dpdata.plugins.pymatgen.PyMatgenStructureFormat format.

to_qe_cp_traj(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPTrajFormat format.

to_qe_pw_scf(*args, **kwargs): Dump data to dpdata.plugins.qe.QECPPWSCFFormat format.

to_quip_gap_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_quip_gap_xyz_file(*args, **kwargs): Dump data to dpdata.plugins.xyz.QuipGapXYZFormat format.

to_sdf(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_sdf_file(*args, **kwargs): Dump data to dpdata.plugins.rdkit.SdfFormat format.

to_siesta_aimd_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaAIMDOutputFormat format.

to_siesta_output(*args, **kwargs): Dump data to dpdata.plugins.siesta.SiestaOutputFormat format.

to_sqm_in(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMINFormat format.

to_sqm_out(*args, **kwargs): Dump data to dpdata.plugins.amber.SQMOutFormat format.

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

to_vasp_contcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_outcar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPOutcarFormat format.

to_vasp_poscar(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPPoscarFormat format.

to_vasp_string(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPStringFormat format.

to_vasp_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xml(*args, **kwargs): Dump data to dpdata.plugins.vasp.VASPXMLFormat format.

to_xyz(*args, **kwargs): Dump data to dpdata.plugins.xyz.XYZFormat format.

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.

dpdata.system.add_format_methods()[source]

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

Notes

Ensure all plugins have been loaded before execuating this function!

dpdata.system.get_atom_perturb_vector(atom_pert_distance, atom_pert_style='normal')[source]

dpdata.system.get_cell_perturb_matrix(cell_pert_fraction)[source]

dpdata.system.get_cls_name(cls: object) → str[source]

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

Parameters:

clsobject: the class

Returns:

str: the fully qualified name of a class

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

dpdata.unit module

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

Bases: ABC

Methods

set_value
value

set_value(value)[source]

value()[source]

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

Bases: Conversion

Methods

set_value
value

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

Bases: Conversion

Methods

set_value
value

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

Bases: Conversion

Methods

set_value
value

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

Bases: Conversion

Methods

set_value
value

dpdata.unit.check_unit(unit)[source]

dpdata.utils module

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

dpdata.utils.elements_index_map(elements, standard=False, inverse=False)[source]

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

dpdata.utils.sort_atom_names(data, 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:

datadict: system data
type_maplist: type_map

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

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

Parameters:

datadict: data dict of System, LabeledSystem

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

Authors

A bot of @njzjz
AngelJia
AnguseZhang
1. Thang Nguyen
Chen Tao
Chentao168
Chenxing Luo
Duo
Ericwang6
Feifei Tian
Han Wang
Haruka
Hedley
Hedley Dong
HuangJiameng
Jia-Xin Zhu
Jingchao Zhang
Jinzhe Zeng
Junhan Chang
L-RuiHao
Levi Zhou
LiangWenshuo1118
Linfeng Zhang
Liu Renxi
Liu-RX
LiuGroupHNU
LiuHanyu
LiuLiping
Logan Ward
Marián Rynik
PKUfjh
Pan Xiang
Peng Xingliang
Shigetomo Yanase
Silvia-liu
Wanrun Jiang
Wenxin Zhang
Yifan Li李一帆
Yingze Wang
Yixiao Chen
Yongbin Zhuang
Yu Liu
Yuan Fengbo
Zezhong Zhang
deepmodeling
ericwang6
felix5572
haidi
hl2500
hongriTianqi
jameswind
kiwi
link89
liuliping
pee8379
pre-commit-ci[bot]
pxlxingliang
repo-ranger[bot]
robinzhuang
robinzyb
tianhongzhen
tuoping
wang laosi
xfanak
yuzhi
zezhong-zhang

dpdata

dpdata is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian. dpdata only works with python 3.7 or above.

Installation

One can download the source code of dpdata by

git clone https://github.com/deepmodeling/dpdata.git dpdata

then use pip to install the module from source

cd dpdata
pip install .

dpdata can also by install via pip without source

pip install dpdata

Quick start

This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.

import dpdata

The typicall workflow of dpdata is

Load data from vasp or lammps or deepmd-kit data files.
Manipulate data
Dump data to in a desired format

Load data

d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")

or let dpdata infer the format (vasp/poscar) of the file from the file name extension

d_poscar = dpdata.System("my.POSCAR")

The number of atoms, atom types, coordinates are loaded from the POSCAR and stored to a data System called d_poscar. A data System (a concept used by deepmd-kit) contains frames 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. It is noted that POSCAR only contains one frame. If the multiple frames stored in, for example, a OUTCAR is wanted,

d_outcar = dpdata.LabeledSystem("OUTCAR")

The labels provided in the OUTCAR, i.e. energies, forces and virials (if any), are loaded by LabeledSystem. It is noted that the forces of atoms are always assumed to exist. LabeledSystem is a derived class of System.

The System or LabeledSystem can be constructed from the following file formats with the format key in the table passed to argument fmt:

Software	format	multi frames	labeled	class	format key
vasp	poscar	False	False	System	‘vasp/poscar’
vasp	outcar	True	True	LabeledSystem	‘vasp/outcar’
vasp	xml	True	True	LabeledSystem	‘vasp/xml’
lammps	lmp	False	False	System	‘lammps/lmp’
lammps	dump	True	False	System	‘lammps/dump’
deepmd	raw	True	False	System	‘deepmd/raw’
deepmd	npy	True	False	System	‘deepmd/npy’
deepmd	raw	True	True	LabeledSystem	‘deepmd/raw’
deepmd	npy	True	True	LabeledSystem	‘deepmd/npy’
deepmd	npy	True	True	MultiSystems	‘deepmd/npy/mixed’
deepmd	npy	True	False	MultiSystems	‘deepmd/npy/mixed’
gaussian	log	False	True	LabeledSystem	‘gaussian/log’
gaussian	log	True	True	LabeledSystem	‘gaussian/md’
siesta	output	False	True	LabeledSystem	‘siesta/output’
siesta	aimd_output	True	True	LabeledSystem	‘siesta/aimd_output’
cp2k(deprecated in future)	output	False	True	LabeledSystem	‘cp2k/output’
cp2k(deprecated in future)	aimd_output	True	True	LabeledSystem	‘cp2k/aimd_output’
cp2k(plug-in)	stdout	False	True	LabeledSystem	‘cp2kdata/e_f’
cp2k(plug-in)	stdout	True	True	LabeledSystem	‘cp2kdata/md’
QE	log	False	True	LabeledSystem	‘qe/pw/scf’
QE	log	True	False	System	‘qe/cp/traj’
QE	log	True	True	LabeledSystem	‘qe/cp/traj’
Fhi-aims	output	True	True	LabeledSystem	‘fhi_aims/md’
Fhi-aims	output	False	True	LabeledSystem	‘fhi_aims/scf’
quip/gap	xyz	True	True	MultiSystems	‘quip/gap/xyz’
PWmat	atom.config	False	False	System	‘pwmat/atom.config’
PWmat	movement	True	True	LabeledSystem	‘pwmat/movement’
PWmat	OUT.MLMD	True	True	LabeledSystem	‘pwmat/out.mlmd’
Amber	multi	True	True	LabeledSystem	‘amber/md’
Amber/sqm	sqm.out	False	False	System	‘sqm/out’
Gromacs	gro	True	False	System	‘gromacs/gro’
ABACUS	STRU	False	False	System	‘abacus/stru’
ABACUS	STRU	False	True	LabeledSystem	‘abacus/scf’
ABACUS	cif	True	True	LabeledSystem	‘abacus/md’
ABACUS	STRU	True	True	LabeledSystem	‘abacus/relax’
ase	structure	True	True	MultiSystems	‘ase/structure’
DFTB+	dftbplus	False	True	LabeledSystem	‘dftbplus’
n2p2	n2p2	True	True	LabeledSystem	‘n2p2’

The Class dpdata.MultiSystems can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

Use dpdata.MultiSystems.from_dir to read from a directory, dpdata.MultiSystems will walk in the directory Recursively and find all file with specific file_name. Supports all the file formats that dpdata.LabeledSystem supports.

Use dpdata.MultiSystems.from_file to read from single file. Single-file support is available for the quip/gap/xyz and ase/structure formats.

For example, for quip/gap xyz files, single .xyz file may contain many different configurations with different atom numbers and atom type.

The following commands relating to Class dpdata.MultiSystems may be useful.

# load data

xyz_multi_systems = dpdata.MultiSystems.from_file(
    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
)
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
)

# use wildcard
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
)

# print the multi_system infomation
print(xyz_multi_systems)
print(xyz_multi_systems.systems)  # return a dictionaries

# print the system infomation
print(xyz_multi_systems.systems["B1C9"].data)

# dump a system's data to ./my_work_dir/B1C9_raw folder
xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")

# dump all systems
xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")

You may also use the following code to parse muti-system:

from dpdata import LabeledSystem, MultiSystems
from glob import glob

"""
process multi systems
"""
fs = glob("./*/OUTCAR")  # remeber to change here !!!
ms = MultiSystems()
for f in fs:
    try:
        ls = LabeledSystem(f)
    except:
        print(f)
    if len(ls) > 0:
        ms.append(ls)

ms.to_deepmd_raw("deepmd")
ms.to_deepmd_npy("deepmd")

Access data

These properties stored in System and LabeledSystem can be accessed by operator [] with the key of the property supplied, for example

coords = d_outcar["coords"]

Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)

key	type	dimension	are labels	description
‘atom_names’	list of str	ntypes	False	The name of each atom type
‘atom_numbs’	list of int	ntypes	False	The number of atoms of each atom type
‘atom_types’	np.ndarray	natoms	False	Array assigning type to each atom
‘cells’	np.ndarray	nframes x 3 x 3	False	The cell tensor of each frame
‘coords’	np.ndarray	nframes x natoms x 3	False	The atom coordinates
‘energies’	np.ndarray	nframes	True	The frame energies
‘forces’	np.ndarray	nframes x natoms x 3	True	The atom forces
‘virials’	np.ndarray	nframes x 3 x 3	True	The virial tensor of each frame

Dump data

The data stored in System or LabeledSystem can be dumped in ‘lammps/lmp’ or ‘vasp/poscar’ format, for example:

d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)

The first frames of d_outcar will be dumped to ‘conf.lmp’

d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)

The last frames of d_outcar will be dumped to ‘POSCAR’.

The data stored in LabeledSystem can be dumped to deepmd-kit raw format, for example

d_outcar.to("deepmd/raw", "dpmd_raw")

Or a simpler command:

dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")

Frame selection can be implemented by

dpdata.LabeledSystem("OUTCAR").sub_system([0, -1]).to("deepmd/raw", "dpmd_raw")

by which only the first and last frames are dumped to dpmd_raw.

replicate

dpdata will create a super cell of the current atom configuration.

dpdata.System("./POSCAR").replicate(
    (
        1,
        2,
        3,
    )
)

tuple(1,2,3) means don’t copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.

perturb

By the following example, each frame of the original system (dpdata.System('./POSCAR')) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. atom_pert_style indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to atom_pert_style areuniform (uniform in a ball), and const (uniform on a sphere).

perturbed_system = dpdata.System("./POSCAR").perturb(
    pert_num=3,
    cell_pert_fraction=0.05,
    atom_pert_distance=0.6,
    atom_pert_style="normal",
)
print(perturbed_system.data)

replace

By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.

s = dpdata.System("tests/poscars/POSCAR.P42nmc", fmt="vasp/poscar")
s.replace("Hf", "Zr", 8)
s.to_vasp_poscar("POSCAR.P42nmc.replace")

BondOrderSystem

A new class BondOrderSystem which inherits from class System is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in BondOrderSystem.data['bonds'], BondOrderSystem.data['formal_charges']). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).

import dpdata

system_1 = dpdata.BondOrderSystem(
    "tests/bond_order/CH3OH.mol", fmt="mol"
)  # read from .mol file
system_2 = dpdata.BondOrderSystem(
    "tests/bond_order/methane.sdf", fmt="sdf"
)  # read from .sdf file

In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration). BondOrderSystem also supports initialize from a rdkit.Chem.rdchem.Mol object directly.

from rdkit import Chem
from rdkit.Chem import AllChem
import dpdata

mol = Chem.MolFromSmiles("CC")
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)

Bond Order Assignment

The BondOrderSystem implements a more robust sanitize procedure for rdkit Mol, as defined in dpdata.rdkit.santizie.Sanitizer. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).

low: use rdkit.Chem.SanitizeMol() function to sanitize molecule.
medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call obabel to pre-process the mol and repeat the sanitization procedure. That is to say, if you wan’t to use this level of sanitization, please ensure ``obabel`` is installed in the environment. According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use obabel xxx -O xxx -h to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.

import dpdata

for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
    syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)

Formal Charge Assignment

BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As

import dpdata

syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
print(syst.get_formal_charges())  # return the formal charge on each atom
print(syst.get_charge())  # return the total charge of the system

If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.

Mixed Type Format

The format deepmd/npy/mixed is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class dpdata.MultiSystems.

Under this format, systems with the same number of atoms but different formula can be put together for a larger system, especially when the frame numbers in systems are sparse.

This also helps to mixture the type information together for model training with type embedding network.

Here are examples using deepmd/npy/mixed format:

Dump a MultiSystems into a mixed type numpy directory: ```python import dpdata

dpdata.MultiSystems(*systems).to_deepmd_npy_mixed(“mixed_dir”)

- Load a mixed type data into a MultiSystems:
```python
import dpdata

dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")

Plugins

One can follow a simple example to add their own format by creating and installing plugins. It’s critical to add the Format class to entry_points['dpdata.plugins'] in ``pyproject.toml` <plugin_example/pyproject.toml>`_:

[project.entry-points.'dpdata.plugins']
random = "dpdata_random:RandomFormat"