def setup(self, step, time, configuration):
"""
Recieves the setup call from the before the MC loop.
:param step: The step number of the simulation.
:type step: int
:param time: The time of the simulation.
:type time: float
:param configuration: The configuration of the simulation.
:type configuration: KMCConfiguration
"""
# Make sure the track type is one of the possible types.
if not self.__track_type in configuration.possibleTypes():
raise Error("The track type of the MSD calculator is not one of the valid types of the configuration.")
# Get the cell vectors out.
abc_to_xyz = numpy.array(configuration.lattice().unitCell().cellVectors()).transpose()
abc_to_xyz_cpp = numpy2DArrayToStdVectorCoordinate(abc_to_xyz)
# Setup the backend.
self.__backend = Backend.OnTheFlyMSD(configuration._backend(),
self.__history_steps,
self.__n_bins,
self.__t_max,
time,
self.__track_type,
abc_to_xyz_cpp,
self.__blocksize)
