mixed format

Class: DeePMDMixedFormat

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

Examples

Dump a MultiSystems into a mixed type numpy directory:

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

Load a mixed type data into a MultiSystems:

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

Conversions

Convert from System to this format

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

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

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

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

Parameters:

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

Convert from LabeledSystem to this format

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

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

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

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

Parameters:

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

Convert from this format to MultiSystems

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

Convert this format to MultiSystems.

Parameters:

directorystr: directory of systems

Returns:

MultiSystems: converted system

Convert from MultiSystems to this format

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

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

Convert MultiSystems to this format.

Parameters:

directorystr: directory to save systems

Returns:

MultiSystems: this system