deepmd/hdf5/mixed format

deepmd/hdf5/mixed format#

Class: DeePMDHDF5MixedFormat

Mixed type HDF5 format for DeePMD-kit.

Mixed type data stores frames with the same atom count in one dataset even when their formulas differ. The placeholder type.raw contains only the mixed token type, while set.*/real_atom_types.npy stores the real atom type layout for each frame. Loading reconstructs regular Systems by splitting frames with different real_atom_types rows.

The HDF5 layout mirrors deepmd/npy/mixed inside HDF5 groups. For dpdata.MultiSystems, each top-level mixed group is keyed by the number of atoms after optional padding, such as "4" or "8". A string path may include "#group/path" to read or write mixed data under a nested HDF5 group.

Examples

Dump a dpdata.MultiSystems object to a mixed HDF5 file:

>>> systems.to_deepmd_hdf5_mixed("mixed.hdf5")

Dump with atom-count padding:

>>> systems.to_deepmd_hdf5_mixed("mixed.hdf5", atom_numb_pad=8)

Load a mixed HDF5 file into dpdata.MultiSystems:

>>> dpdata.MultiSystems().from_deepmd_hdf5_mixed("mixed.hdf5")

Conversions#

Convert from System to this format#

dpdata.System.to(fmt: Literal['deepmd/hdf5/mixed'], file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>, comp_prec=None)
dpdata.System.to_deepmd_hdf5_mixed(file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>, comp_prec=None)

Dump a System data dict in mixed HDF5 format.

Parameters:
file_namestr or h5py.Group or h5py.File

HDF5 file, HDF5 group, or string in "file.hdf5#group" form. Strings open the target file in write mode. HDF5 objects are written in place.

set_sizeint, default=2000

Maximum number of frames per set.* group.

precnumpy.dtype, default=numpy.float64

Floating point precision for dumped frame data. Kept for consistency with deepmd/npy/mixed.

comp_precnumpy.dtype, optional

Explicit floating point precision. When provided, this overrides prec.

Raises:
TypeError

If file_name is not a string, HDF5 group, or HDF5 file.

Convert from LabeledSystem to this format#

dpdata.LabeledSystem.to(fmt: Literal['deepmd/hdf5/mixed'], file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>, comp_prec=None)
dpdata.LabeledSystem.to_deepmd_hdf5_mixed(file_name, set_size: 'int' = 2000, prec=<class 'numpy.float64'>, comp_prec=None)

Dump a System data dict in mixed HDF5 format.

Parameters:
file_namestr or h5py.Group or h5py.File

HDF5 file, HDF5 group, or string in "file.hdf5#group" form. Strings open the target file in write mode. HDF5 objects are written in place.

set_sizeint, default=2000

Maximum number of frames per set.* group.

precnumpy.dtype, default=numpy.float64

Floating point precision for dumped frame data. Kept for consistency with deepmd/npy/mixed.

comp_precnumpy.dtype, optional

Explicit floating point precision. When provided, this overrides prec.

Raises:
TypeError

If file_name is not a string, HDF5 group, or HDF5 file.

Convert from this format to MultiSystems#

dpdata.MultiSystems.from_deepmd_hdf5_mixed(directory) → dpdata.system.MultiSystems

Generate mixed HDF5 groups for MultiSystems loading.

Parameters:
directorystr or h5py.Group or h5py.File

HDF5 file, HDF5 group, or string in "file.hdf5#group" form. The selected object may be either one mixed system group or a container of mixed groups.

Returns:
MultiSystems

converted system

Raises:
TypeError

If directory is not a string, HDF5 group, or HDF5 file.

Convert from MultiSystems to this format#

dpdata.MultiSystems.to(fmt: Literal['deepmd/hdf5/mixed'], directory) → dpdata.system.MultiSystems
dpdata.MultiSystems.to_deepmd_hdf5_mixed(directory) → dpdata.system.MultiSystems

Generate HDF5 groups for MultiSystems mixed dumping.

Parameters:
directorystr or h5py.Group or h5py.File

HDF5 file, HDF5 group, or string in "file.hdf5#group" form. Strings open the target file in write mode.

Returns:
MultiSystems

this system

Raises:
TypeError

If directory is not a string, HDF5 group, or HDF5 file.