polypy.read

Read functions of polypy. Herein contains classes to read DL_POLY HISTORY / CONFIG files and DL_MONTE ARCHIVE files. All of the data that is extracted from these files is stored in a trajectory class that is compatible with all three file types.

class polypy.read.Archive(file, atom_list)

Bases: object

The polypy.read.Trajectory class evaluates the positions of all atoms in a ARCHIVE.

Parameters:

• atom_list (list) – List of unique atom names in trajectory.
• datatype (str) – Datatype of the original dataset e.g. DL_MONTE ARCHIVE.

read_archive()

Read a DL_MONTE ARCHIVE file line by line and updates a polypy.read.Trajectory object.

class polypy.read.Config(file, atom_list)

Bases: object

The polypy.read.Trajectory class evaluates the positions of all atoms in a CONFIG.

Parameters:

• atom_list (list) – List of unique atom names in trajectory.
• datatype (str) – Datatype of the original dataset e.g. DL_POLY CONFIG.

read_config()

Read a DL_POLY HISTORY file line by line and updates a polypy.read.Trajectory object.

class polypy.read.History(file, atom_list)

Bases: object

The polypy.read.Trajectory class evaluates the positions of all atoms in the simulation.

Parameters:

• atom_list (list) – List of unique atom names in trajectory.
• datatype (str) – Datatype of the original dataset e.g. DL_POLY HISTORY.

read_history()

Reads a DL_POLY HISTORY file line by line and updates a polypy.read.Trajectory object.

class polypy.read.Trajectory(atom_list, datatype)

Bases: object

The polypy.read.Trajectory class evaluates the positions of all atoms in the simulation.

Parameters:

• atom_list (list) – List of unique atom names in trajectory.
• datatype (str) – Datatype of the original dataset
• DL_POLY HISTORY or CONFIG. (e.g.) –

get_atom(atom)

Isolates the trajectory for a specific atom type.

Parameters:atom (str) – Atom label. Returns:Trajectory object for desired atom. Return type:atom_trajectory (polypy.read.Trajectory)

get_config(timestep)

Isolates a specific DL_POLY CONFIG from a HISTORY file.

Parameters:timestep (int) – Timestep of desired CONFIG. Returns:Trajectory object for desired CONFIG. Return type:config_trajectory (polypy.read.Trajectory)

remove_final_timesteps(timesteps_to_exclude)

Removes timesteps from the end of a simulation

Parameters:timesteps_to_exclude (int) – Number of timesteps to exclude Returns:Trajectory object. Return type:new_trajectory (polypy.read.Trajectory)

remove_initial_timesteps(timesteps_to_exclude)

Removes timesteps from the beggining of a simulation

Parameters:timesteps_to_exclude (int) – Number of timesteps to exclude Returns:Trajectory object. Return type:new_trajectory (polypy.read.Trajectory)