PyLammpstrj

This module gives several utilities for LAMMPS trajectory files (i.e. files output with the dump command) processing.

Usage example

The first module method to use is pylammpstrj.read to generate a pylammpstrj.PyTrajectory object. A start step can optionally be given to skip configurations until start.

This trajectory object holds the informations about: the atoms (as a list of lists of pylammpstrj.PyAtom objects), the simulation boxes (as a list of pylammpstrj.PyBox objects), the dump_format of the file, the fields_names of the file, the additional_fields (see details below), the number of atoms in each configurations (N_atoms), the number of configurations (N_configurations).

Then, processings can be issued on this trajectory:

• atoms can be selected with the PyTrajectory.select_atoms method, when the selection is provided as three arguments: a str matching a field name, a comparison operator (one of pylammpstrj.LESS_THAN, pylammpstrj.LESS_THAN_EQUAL_TO, ..., pylammpstrj.GREATER_THAN), and a value (either a float, int, or str depending on the target field).
  By default, this method returns a new pylammpstrj.PyTrajectory, but this behavior can be changed with the inplace boolean argument) in which case the method returns None.
• an atom property can also be averaged over the atoms at each configuration with PyTrajectory.average_property. This method takes only a field name (as str) to return a list of float of length PyTrajectory.N_configurations representing the average of the property at each configuration.

Copyright

Copyright 2024 Heiarii Lou Chao.