mdsuite.file_io.lammps_trajectory_files module

MDSuite: A Zincwarecode package.

License

This program and the accompanying materials are made available under the terms of the Eclipse Public License v2.0 which accompanies this distribution, and is available at https://www.eclipse.org/legal/epl-v20.html

SPDX-License-Identifier: EPL-2.0

Copyright Contributors to the Zincwarecode Project.

Contact Information

email: zincwarecode@gmail.com github: https://github.com/zincware web: https://zincwarecode.com/

Citation

If you use this module please cite us with:

class mdsuite.file_io.lammps_trajectory_files.LAMMPSTrajectoryFile(file_path: Union[str, Path], trajectory_is_sorted_by_ids=False, custom_data_map: Optional[dict] = None)

Bases: TabularTextFileProcessor

Reader for LAMMPS files.

mdsuite.file_io.lammps_trajectory_files.extract_properties_from_header(header_property_names: list, database_correspondence_dict: dict) → dict

Takes the property names from a file header, sees if there is a corresponding mdsuite property in database_correspondence_dict. Returns a dict that links the mdsuite property names to the column indices at which they can be found in the file.

Parameters:

• header_property_names – The names of the columns in the data file

• database_correspondence_dict –

  The translation between mdsuite properties and the column names of the respective file format. lammps example: {“Positions”: [“x”, “y”, “z”],

  ”Unwrapped_Positions”: [“xu”, “yu”, “zu”],

Returns:

trajectory_properties – A dict of the form {‘MDSuite_Property_1’: [column_indices], ‘MDSuite_Property_2’: …} Example {‘Unwrapped_Positions’: [2,3,4], ‘Velocities’: [5,6,8]}

Return type:

dict