dpdata.plugins package

Submodules

dpdata.plugins.3dmol module

class dpdata.plugins.3dmol.Py3DMolFormat

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)

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

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)

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

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)

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

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)

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

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)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

to_system(data, file_name, frame_idx=0, **kwargs)

Dump the system into ABACUS STRU format file.

Parameters:

datadict

System data

file_namestr

The output file name

frame_idxint

The index of the frame to dump

pp_filelist of string, optional

List of pseudo potential files

numerical_orbitallist of string, optional

List of orbital files

masslist of float, optional

List of atomic masses

numerical_descriptorstr, optional

numerical descriptor file

**kwargsdict

other parameters

dpdata.plugins.amber module

class dpdata.plugins.amber.AmberMDFormat

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)

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)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

class dpdata.plugins.amber.SQMDriver(sqm_exec: str = 'sqm', **kwargs: dict)

Bases: Driver

AMBER sqm program driver.

Parameters:

sqm_execstr, default=sqm

path to sqm program

**kwargsdict

other arguments to make input files. See SQMINFormat

Examples

Use DFTB3 method to calculate potential energy:

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

Attributes:

ase_calculator

Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict

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

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)

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)

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

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

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)

Read from ambertools sqm.out.

from_system(fname, **kwargs)

Read from ambertools sqm.out.

dpdata.plugins.ase module

class dpdata.plugins.ase.ASEDriver(calculator: ase.calculators.calculator.Calculator)

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

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 = {})

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

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

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

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

Parameters:

atomsase.Atoms

an ASE Atoms, containing a structure

**kwargsdict

other parameters

Returns:

dict

data dict

Raises:

RuntimeError

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

from_multi_systems(file_name: str, begin: int | None = None, end: int | None = None, step: int | None = None, ase_fmt: str | None = None, **kwargs) → ase.Atoms

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

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)

Convert System to ASE Atoms object.

to_system(data, **kwargs)

Convert System to ASE Atom obj.

dpdata.plugins.cp2k module

class dpdata.plugins.cp2k.CP2KAIMDOutputFormat

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)

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

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)

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)

Bases: Driver

DeePMD-kit driver.

Parameters:

dpdeepmd.DeepPot or str

The deepmd-kit potential class or the filename of the model.

Examples

>>> DPDriver("frozen_model.pb")

Attributes:

ase_calculator

Returns an ase calculator based on this driver.

Methods

get_driver(key)	Get a driver plugin.
get_drivers()	Get all driver plugins.
label(data)	Label a system data by deepmd-kit.
register(key)	Register a driver plugin.

label(data: dict) → dict

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

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)

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)

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)

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

Bases: Format

HDF5 format for DeePMD-kit.

Examples

Dump a MultiSystems to a HDF5 file:

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

Methods

MultiModes()	File mode for MultiSystems.
from_bond_order_system(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
from_labeled_system(file_name[, type_map])	Convert HDF5 file to LabeledSystem data.
from_multi_systems(directory, **kwargs)	Generate HDF5 groups from a HDF5 file, which will be passed to from_system.
from_system(file_name[, type_map])	Convert HDF5 file to System data.
get_formats()	Get all registered formats.
get_from_methods()	Get all registered from methods.
get_to_methods()	Get all registered to methods.
mix_system(*system, type_map, **kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
post(func_name)	Register a post function for from method.
register(key)	Register a format plugin.
register_from(key)	Register a from method if the target method name is not default.
register_to(key)	Register a to method if the target method name is not default.
to_bond_order_system(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
to_labeled_system(data, *args, **kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
to_multi_systems(formulas, directory, **kwargs)	Generate HDF5 groups, which will be passed to to_system.
to_system(data, file_name[, set_size, comp_prec])	Convert System data to HDF5 file.

from_labeled_system(file_name: str | Group | File, type_map: List[str] | None = None, **kwargs) → dict

Convert HDF5 file to LabeledSystem data.

Parameters:

file_namestr or h5py.Group or h5py.File

file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group

type_mapdict[str]

type map

**kwargsdict

other parameters

Returns:

dict

LabeledSystem data

Raises:

TypeError

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

from_multi_systems(directory: str, **kwargs) → Group

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

Parameters:

directorystr

HDF5 file name

**kwargsdict

other parameters

Yields:

h5py.Group

a HDF5 group in the HDF5 file

from_system(file_name: str | Group | File, type_map: List[str] | None = None, **kwargs) → dict

Convert HDF5 file to System data.

Parameters:

file_namestr or h5py.Group or h5py.File

file name of the HDF5 file or HDF5 object. If it is a string, hashtag is used to split path to the HDF5 file and the HDF5 group

type_mapdict[str]

type map

**kwargsdict

other parameters

Returns:

dict

System data

Raises:

TypeError

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

to_multi_systems(formulas: List[str], directory: str, **kwargs) → Group

Generate HDF5 groups, which will be passed to to_system.

Parameters:

formulaslist[str]

formulas of MultiSystems

directorystr

HDF5 file name

**kwargsdict

other parameters

Yields:

h5py.Group

a HDF5 group with the name of formula

to_system(data: dict, file_name: str | ~h5py._hl.group.Group | ~h5py._hl.files.File, set_size: int = 5000, comp_prec: ~numpy.dtype = <class 'numpy.float64'>, **kwargs)

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

Bases: Format

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

Examples

Dump a MultiSystems into a mixed type numpy directory:

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

Load a mixed type data into a MultiSystems:

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

Methods

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

from_labeled_system_mix
from_system_mix

MultiMode = 1

from_labeled_system_mix(file_name, type_map=None, **kwargs)

from_multi_systems(directory, **kwargs)

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)

mix_system(*system, type_map, **kwargs)

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)

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

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)

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)

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)

Dump the system in deepmd raw format to directory file_name.

dpdata.plugins.dftbplus module

class dpdata.plugins.dftbplus.DFTBplusFormat

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)

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

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)

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

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)

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

Bases: Format

Gaussian input file.

Methods

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

from_system(file_name: str, **kwargs)

Read Gaussian input file.

Parameters:

file_namestr

file name

**kwargsdict

keyword arguments

to_system(data: dict, file_name: str, **kwargs)

Generate Gaussian input file.

Parameters:

datadict

system data

file_namestr

file name

**kwargsdict

Other parameters to make input files. See dpdata.gaussian.gjf.make_gaussian_input()

class dpdata.plugins.gaussian.GaussianDriver(gaussian_exec: str = 'g16', **kwargs: dict)

Bases: Driver

Gaussian driver.

Note that “force” keyword must be added. If the number of atoms is large, “Geom=PrintInputOrient” should be added.

Parameters:

gaussian_execstr, default=g16

path to gaussian program

**kwargsdict

other arguments to make input files. See dpdata.gaussian.gjf.make_gaussian_input()

Examples

Use B3LYP method to calculate potential energy of a methane molecule:

>>> labeled_system = system.predict(keywords="force b3lyp/6-31g**", driver="gaussian")
>>> labeled_system['energies'][0]
-1102.714590995794

Attributes:

ase_calculator

Returns an ase calculator based on this driver.

Methods

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

label(data: dict) → dict

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

Bases: Format

Methods

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

from_labeled_system(file_name, md=False, **kwargs)

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

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)

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

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)

Load gromacs .gro file.

Parameters:

file_namestr

The input file name

format_atom_namebool

Whether to format the atom name

**kwargsdict

other parameters

to_system(data, file_name=None, frame_idx=-1, **kwargs)

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

Bases: Format

Methods

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

from_system(file_name, type_map=None, begin=0, step=1, unwrap=False, **kwargs)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

class dpdata.plugins.lammps.LAMMPSLmpFormat

Bases: Format

Methods

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

from_system(file_name, type_map=None, **kwargs)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

to_system(data, file_name, frame_idx=0, **kwargs)

Dump the system in lammps data format.

Parameters:

datadict

System data

file_namestr

The output file name

frame_idxint

The index of the frame to dump

**kwargsdict

other parameters

dpdata.plugins.list module

class dpdata.plugins.list.ListFormat

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)

Convert system to list, usefull for data collection.

dpdata.plugins.psi4 module

class dpdata.plugins.psi4.PSI4OutFormat

Bases: Format

Psi4 output.

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

Methods

MultiModes()	File mode for MultiSystems.
from_bond_order_system(file_name, **kwargs)	Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
from_labeled_system(file_name, **kwargs)	Read from Psi4 output.
from_multi_systems(directory, **kwargs)	Implement MultiSystems.from that converts from this format to MultiSystems.
from_system(file_name, **kwargs)	Implement System.from that converts from this format to System.
get_formats()	Get all registered formats.
get_from_methods()	Get all registered from methods.
get_to_methods()	Get all registered to methods.
mix_system(*system, type_map, **kwargs)	Mix the systems into mixed_type ones according to the unified given type_map.
post(func_name)	Register a post function for from method.
register(key)	Register a format plugin.
register_from(key)	Register a from method if the target method name is not default.
register_to(key)	Register a to method if the target method name is not default.
to_bond_order_system(data, rdkit_mol, *args, ...)	Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
to_labeled_system(data, *args, **kwargs)	Implement LabeledSystem.to that converts from LabeledSystem to this format.
to_multi_systems(formulas, directory, **kwargs)	Implement MultiSystems.to that converts from MultiSystems to this format.
to_system(data, *args, **kwargs)	Implement System.to that converts from System to this format.

from_labeled_system(file_name: str, **kwargs) → dict

Read from Psi4 output.

Parameters:

file_namestr

file name

**kwargs

keyword arguments

Returns:

dict

system data

dpdata.plugins.pwmat module

class dpdata.plugins.pwmat.PwmatAtomconfigFormat

Bases: Format

Methods

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

from_system(file_name, **kwargs)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

to_system(data, file_name, frame_idx=0, *args, **kwargs)

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

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)

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

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)

Convert System to Pymagen ComputedStructureEntry obj.

class dpdata.plugins.pymatgen.PyMatgenMoleculeFormat

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)

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)

Convert System to Pymatgen Molecule obj.

class dpdata.plugins.pymatgen.PyMatgenStructureFormat

Bases: Format

Methods

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

to_system(data, **kwargs)

Convert System to Pymatgen Structure obj.

dpdata.plugins.qe module

class dpdata.plugins.qe.QECPPWSCFFormat

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)

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

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)

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)

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

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)

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)

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

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)

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)

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

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)

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)

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

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)

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)

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

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)

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

Bases: Format

Methods

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

from_system(file_name, **kwargs)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in System.DTYPES

to_system(data, file_name, frame_idx=0, **kwargs)

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

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)

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

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)

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

Parameters:

file_namestr

file name, i.e. the first argument

**kwargsdict

keyword arguments that will be passed from the method

Returns:

datadict

system data, whose keys are defined in LabeledSystem.DTYPES

dpdata.plugins.xyz module

class dpdata.plugins.xyz.QuipGapXYZFormat

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)

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)

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

Bases: Format

XYZ foramt.

Examples

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

Methods

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

from_system(file_name, **kwargs)

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)

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