pylammpstrj 1.0.2

Processing LAMMPS trajectory files.

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.