dpdata.plugins package

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: FileType, 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
**kwargsdict: other parameters

dpdata.plugins.abacus.register_mag_data(data)[source]#

dpdata.plugins.abacus.register_move_data(data)[source]#

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)[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

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.

Examples

Use DFTB3 method to calculate potential energy:

>>> labeled_system = system.predict(theory="DFTB3", driver="sqm")
>>> labeled_system['energies'][0]
-15.41111246

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) → Generator[ase.Atoms, None, None][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) → list[ase.Atoms][source]#: Convert System to ASE Atoms object.

to_system(data, **kwargs) → list[ase.Atoms][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[, file_name])	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[, file_name])	Convert System to ASE Atoms object.

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

to_labeled_system(data, file_name: str = 'labeled_confs.traj', *args, **kwargs) → None[source]#

Convert System to ASE Atoms object.

Parameters:

file_namestr: path to file

to_system(data, file_name: str = 'confs.traj', **kwargs) → None[source]#

Convert System to ASE Atoms object.

Parameters:

file_namestr: path to file

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.

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.

Examples

>>> DPDriver("frozen_model.pb")

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.

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.

Examples

Dump a MultiSystems to a HDF5 file:

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

from_labeled_system(file_name: str | h5py.Group | h5py.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) → h5py.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 | h5py.Group | h5py.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) → h5py.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.Group | h5py.File), set_size: int = 5000, comp_prec: np.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.

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

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")

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.deepmd.register_spin()[source]#

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: FileType, **kwargs)[source]#

Read Gaussian input file.

Parameters:

file_namestr: file name
**kwargsdict: keyword arguments

to_system(data: dict, file_name: FileType, **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)[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()

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.

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

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: FileType, 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: FileType, **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: FileType | None = 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, ...])	Read the data from a lammps dump 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, args, *kwargs)	Implement System.to that converts from System to this format.

from_system(file_name: str, type_map: list[str] = None, begin: int = 0, step: int = 1, unwrap: bool = False, input_file: str = None, **kwargs)[source]#

Read the data from a lammps dump file.

Parameters:

file_namestr: The dump file name
type_mapList[str], optional: The atom type list
beginint, optional: The begin step
stepint, optional: The step
unwrapbool, optional: Whether to unwrap the coordinates
input_filestr, optional: The input file name

Returns:

dict: The system data

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: FileType, 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: FileType, 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.lammps.register_spin(data)[source]#

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: FileType, **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: FileType, **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: FileType, **kwargs) → dict[source]#

Read from ORCA single point energy output.

Parameters:

file_nameFileType: 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: FileType, 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: FileType, **kwargs) → dict[source]#

Read from Psi4 output.

Parameters:

file_nameFileType: 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: FileType, **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: FileType, 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`(structure, **kwargs)	Convert pymatgen.core.Structure 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.

from_system(structure, **kwargs) → dict[source]#

Convert pymatgen.core.Structure to System.

Parameters:

structurepymatgen.core.Structure: a Pymatgen Structure, containing a structure
**kwargsdict: other parameters

Returns:

dict: data dict

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: FileType, **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: FileType, 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.vasp.register_move_data(data)[source]#

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.

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.

Examples

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

from_system(file_name: FileType, **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: FileType, **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.plugins package

Contents

dpdata.plugins package#

Submodules#

dpdata.plugins.3dmol module#

dpdata.plugins.abacus module#

dpdata.plugins.amber module#

dpdata.plugins.ase module#

dpdata.plugins.cp2k module#

dpdata.plugins.deepmd module#

dpdata.plugins.dftbplus module#

dpdata.plugins.fhi_aims module#

dpdata.plugins.gaussian module#

dpdata.plugins.gromacs module#

dpdata.plugins.lammps module#

dpdata.plugins.list module#

dpdata.plugins.n2p2 module#

dpdata.plugins.openmx module#

dpdata.plugins.orca module#

dpdata.plugins.psi4 module#

dpdata.plugins.pwmat module#

dpdata.plugins.pymatgen module#

dpdata.plugins.qe module#

dpdata.plugins.rdkit module#

dpdata.plugins.siesta module#

dpdata.plugins.vasp module#

dpdata.plugins.xyz module#