tcc_python_scripts.tcc package

Submodules

tcc_python_scripts.tcc.structures module

Information on clusters used by the TCC.

tcc_python_scripts.tcc.wrapper module

Python interface to the TCC executable.

class tcc_python_scripts.tcc.wrapper.TCCWrapper[source]

Bases: object

Python interface to the TCC executable. Runs the TCC on a single configuration.

The TCC accepts input parameters through a file IO system, so this wrapper acts as an intermediate layer to streamline the process of running the TCC from within python. All file operations are hidden from the user to create a more pythonic interface to the TCC.

On destruction of a wrapper object all of the file input/outputs are destroyed, so the user must be careful to extract all of the data they need (for e.g. postprocessing) and store this somewhere.

working_directory

The directory in which the TCC will run

tcc_executable_directory

The directory containing the TCC executable

tcc_executable_path

The full path of the TCC executable

input_parameters['Box']

TCC box paramaters used for TCC run

input_parameters['Run']

TCC run paramaters used for TCC run

input_parameters['Simulation']

TCC simulation paramaters used for TCC run

input_parameters['Output']

TCC output paramaters used for TCC run

input_parameters['Clusters_to_analyse']

List of clusters to include in the analysis, all are detected if list is empty

run(box, particle_coordinates, output_directory=None, particle_types='A', silent=True)[source]

Invoke the TCC using the provided coordinates and parameters.

Parameters:
  • box – box size for boundary conditions, list of [len_x, len_y, len_z]
  • particle_coordinates – a list of lists, one list for each frame containing coordinates of atoms
  • output_directory – If you want to save the output of the TCC specify a directory to store the output
  • particle_types – species of atoms individually (if given container) or collectively. This must be either length 1 (if specifying species of all atoms) or the same length as the number of particles.
  • silent – if set TCC executable console output will be suppressed
Returns:

pandas table containing the static cluster information
set_tcc_executable_directory(path)[source]

A method for setting the directory containing the compiled TCC executable.

Parameters:path – The directory containing the compiled TCC executable.