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)
def testNumpy2DArrayToStdVectorCoordinate(self):
""" Test the conversion of a Nx3 2D numpy array to a std::vector<Coordinate> representation. """
nI = 12;
nJ = 3;
array = numpy.random.rand(nI,nJ)
# Convert to c++
cpp_vector = numpy2DArrayToStdVectorCoordinate(array)
# Check the size.
self.assertEqual(cpp_vector.size(), nI)
# Check the type.
self.assertTrue( isinstance(cpp_vector, Backend.StdVectorCoordinate) )
# Convert back and check values.
converted = stdVectorCoordinateToNumpy2DArray(cpp_vector)
self.assertAlmostEqual(numpy.linalg.norm(array-converted), 0.0, 10)
def testNumpy2DArrayToStdVectorCoordinate(self):
""" Test the conversion of a Nx3 2D numpy array to a std::vector<Coordinate> representation. """
nI = 12
nJ = 3
array = numpy.random.rand(nI, nJ)
# Convert to c++
cpp_vector = numpy2DArrayToStdVectorCoordinate(array)
# Check the size.
self.assertEqual(cpp_vector.size(), nI)
# Check the type.
self.assertTrue(isinstance(cpp_vector, Backend.StdVectorCoordinate))
# Convert back and check values.
converted = stdVectorCoordinateToNumpy2DArray(cpp_vector)
self.assertAlmostEqual(numpy.linalg.norm(array - converted), 0.0, 10)
