postprocess package¶

Submodules¶

postprocess.extract module¶

Module for post-process in lammps

class postprocess.extract.Extraction(path='.')[source]¶

Bases: object

Extraction class. We can extract either scalars, vector or per-particle magnitudes

box(fname, idx=0)[source]¶

Extract the boxes that are in a lammps dump file that matches the parameters.

Parameters:	fname : str LAMMPS dump filename idx : datatype, optional Index of the timestep to look for [not the timestep itself]
Returns:	output : list A list of numpy arrays with the boxes that match all parameters.

entries(parameters)[source]¶

Return all the entries from the database that match the parameters.

Parameters:	parameters : dict A dictionary of parameters to look for in the database
Returns:	ret : list A list of the entries (directories) in the database.

particle(cols, fname, dtype=<type 'numpy.float64'>, idx=0)[source]¶

Extract a ‘per particle’ magnitude that is the given lammps dump file.

Parameters:	cols : tuple Columns to extract fname : str LAMMPS dump filename dtype : datatype, optional Datatype of the array idx : datatype, optional Index of the timestep to look for [not the timestep itself]
Returns:	output : list A list of numpy arrays with the requested data that match all parameters.

t(fname, idx=0)[source]¶

Extract the types that are in a lammps dump file that matches the parameters.

Parameters:	fname : str LAMMPS dump filename idx : datatype, optional Index of the timestep to look for [not the timestep itself]
Returns:	t : list A list of numpy arrays with the types that match all parameters.

v(fname, idx=0)[source]¶

Extract the velocities that are in a lammps dump file that matches the parameters.

Parameters:	fname : str LAMMPS dump filename idx : datatype, optional Index of the timestep to look for [not the timestep itself]
Returns:	v : list A list of numpy arrays with the velocities that match all parameters.

x(fname, idx=0)[source]¶

Extract the positions that are in a lammps dump file that matches the parameters.

Parameters:	fname : str LAMMPS dump filename idx : datatype, optional Index of the timestep to look for [not the timestep itself]
Returns:	x : list A list of numpy arrays with the positions that match all parameters.

postprocess.tools module¶

postprocess.tools.replicate(x, t, box, nrep=1)[source]¶

Replicate positions of particles in a box according to periodic boundary conditions.

Parameters:	x : numpy array Positions of the particles t : numpy array Types of the particles box : iterable Simulation box nrep : int, optional Number of repetitions to consider. Default value is 1.
Returns:	x, t, box : numpy array, numpy array, box Positions, type and box of the repeated values.

Module contents¶