MDMC.exporters.trajectories package

Submodules

MDMC.exporters.trajectories.H5MD_build module

A module for writing and saving a H5MD file.

MDMC.exporters.trajectories.H5MD_build.H5MD_DATA = {'creator_name': 'MDMC', 'creator_version': [0, 2], 'h5md_version': [1, 1], 'loc': 'h5md', 'module_name': ['units'], 'module_version': [[1, 0]]}

Generic H5MD information like, version of H5MD and any H5MD modules used.

MDMC.exporters.trajectories.H5MD_build.create_box_data(open_file: File, trajectory: CompactTrajectory)

Create the box group and add all attributes associated with this group.

Parameters:

• trajectory (CompactTrajectory) – The compact trajectory the file is being built from

• open_file (h5py.File) – A pre-opened file that the data is being written into

MDMC.exporters.trajectories.H5MD_build.create_empty_groups(open_file: File, groups: list[str])

Create all groups and subgroups that make up the main base structure of the file format.

Parameters:

• open_file (h5py.File) – A pre-opened file that is being written to

• groups (list[str]) – A list of groups that are being created

MDMC.exporters.trajectories.H5MD_build.create_metadata_group(open_file: File, *, creator_name: str, creator_email: str)

Create the H5MD group that contains all Metadata information.

Parameters:

• open_file (h5py.File) – A pre-opened file that the data is being written into

• creator_name (str) – Name of person running the MDMC simulation.

• creator_email (str) – Email of the person running the MDMC simulation.

MDMC.exporters.trajectories.H5MD_build.create_parameter_data(open_file: File, data: array)

Create and store the remaining parameter data in the H5MD file.

Parameters:

• open_file (h5py.File) – A pre-opened file that the data is being written into

• data (np.array) – The data being stored

MDMC.exporters.trajectories.H5MD_build.create_simulation_data(open_file: File, group_name: str, value: int | float | str | ndarray, unit: str = None, time_increment: int = None, step_increment: int = None, time_offset: int = None, step_offset: int = None)

Store data about the simulation.

Parameters:

• open_file (h5py.File) – A pre-opened file that the data is being written into

• group_name (str) – The group name for the data being stored

• value (int | float | str | np.ndarray) – The data being stored in the H5MD file

• unit (str, optional) – The units for the data being stored. Default is None.

• time_increment (int, optional) – The increment in time between each simulation step, by default None

• step_increment (int, optional) – The increment in between steps in a simulation, by default None

• time_offset (int, optional) – The offset that the time starts at, by default None

• step_offset (int, optional) – The offset what is where the steps start at, by default None

MDMC.exporters.trajectories.H5MD_build.write_H5MD(trajectory: CompactTrajectory, filename: str = 'trajectory.h5', *, timestamp: bool = True, file_loc: Path = PosixPath('.'), **settings)

Write a CompactTrajectory to a H5MD file.

In MDMC, an H5MD trajectory File is built from a CompactTrajectory. Once a CompactTrajectory is generated, an H5MD trajectory file can be created by passing it to the build_full() function. Once executed the a H5MD (.h5) file is created with the name “trajectory<timestamp>”

Parameters:

• trajectory (CompactTrajectory) – The compact trajectory the file is being built from.

• filename (str, optional) – The name of the H5MD file, standards suggest it ends with .h5, by default “trajectory.h5”.

• timestamp (bool, optional) – If true adds time timestamp to file name, by default True.

• file_loc (Path, optional) – The directory where the H5MD file should be stored, by default Path(‘.’).

Module contents