deepmd/raw format

deepmd/raw format#

Aliases#

deepmd, deepmd/raw

Implementation: DeePMDRawFormat

Overview#

DeePMD-kit raw text dataset directory.

DeePMD-kit is a deep learning package for training interatomic potentials. A raw dataset stores atom types in type.raw and frame properties in text files such as coord.raw, box.raw, energy.raw, and force.raw. It is human-readable and convenient for inspection, but deepmd/npy is usually smaller and faster for training.

Quick examples#

The examples use the preferred alias deepmd/raw; any alias listed above is equivalent.

import dpdata

# Geometry-only data
system = dpdata.System("input_file", fmt="deepmd/raw")

# Data with energies and forces
labeled_system = dpdata.LabeledSystem("input_file", fmt="deepmd/raw")

# Multiple compositions or calculation directories
systems = dpdata.MultiSystems.from_file("input_directory", fmt="deepmd/raw")

# Write geometry-only data
system.to("deepmd/raw", "output_path")

# Write multiple systems
systems.to("deepmd/raw", "output_path")

Conversions#

Convert from this format to System#

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

Load an unlabeled DeePMD raw dataset.

Parameters:
file_namestr or os.PathLike

DeePMD raw dataset directory.

type_maplist[str], optional

Element names used when type_map.raw is absent, or a requested ordering used to remap the stored atom types.

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:
System

converted system

Convert from System to this format#

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

Write a System or LabeledSystem as DeePMD raw text files.

Parameters:
file_namestr or os.PathLike

Destination dataset directory.

**kwargsdict

Additional format arguments accepted for API compatibility.

Convert from LabeledSystem to this format#

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

Write a System or LabeledSystem as DeePMD raw text files.

Parameters:
file_namestr or os.PathLike

Destination dataset directory.

**kwargsdict

Additional format arguments accepted for API compatibility.

Convert from this format to LabeledSystem#

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

Load a labeled DeePMD raw dataset.

Parameters:
file_namestr or os.PathLike

DeePMD raw dataset directory.

type_maplist[str], optional

Element names or requested type ordering used while loading.

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:
LabeledSystem

converted system

Convert from this format to MultiSystems#

dpdata.MultiSystems.from_deepmd(directory, **kwargs) → dpdata.system.MultiSystems
dpdata.MultiSystems.from_deepmd_raw(directory, **kwargs) → dpdata.system.MultiSystems

Convert this format to MultiSystems.

Parameters:
directorystr

directory of systems

Returns:
MultiSystems

converted system

Convert from MultiSystems to this format#

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

Convert MultiSystems to this format.

Parameters:
directorystr

directory to save systems

Returns:
MultiSystems

this system