def testBackend(self):
""" Test that the backend object is correctly constructed. """
# Setup a unitcell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8,0.0,0.0],
[0.0,3.2,0.0],
[0.0,0.5,3.0]]),
basis_points=[[0.0,0.0,0.0],
[0.5,0.5,0.5],
[0.25,0.25,0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True,True,False))
types = ['A','A','A','A','B','B',
'A','A','A','B','B','B',
'B','B','A','A','B','A',
'B','B','B','A','B','A',
'B','A','A','A','B','B',
'B','B','B','B','B','B',
'A','A','A','A','B','B',
'B','B','A','B','B','A']
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['A','C','B'])
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
sites = [0,1,2,3,4]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# A second process.
types0 = ["A","C"]
types1 = ["C","A"]
rate_0_1 = 1.5
process_1 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# Construct the interactions object.
processes = [process_0, process_1]
interactions = KMCInteractions(processes=processes)
# Construct the model.
model = KMCLatticeModel(config, interactions)
# Get the c++ backend out.
cpp_model = model._backend()
# Check that this backend object is stored on the class.
self.assertTrue(model._KMCLatticeModel__backend == cpp_model)
def testRunImplicitWildcards(self):
""" Test that ta valid model can run for a few steps. """
# Setup a unitcell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0],
[0.0,1.0,0.0],
[0.0,0.0,1.0]]),
basis_points=[[0.0,0.0,0.0]])
# And a lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(10,10,1),
periodic=(True,True,False))
# Set the stating configuration types.
types = ['B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'A', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'A', 'B', 'B', 'B', 'B', 'B', 'A', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'A', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'A', 'B', 'B',
'A', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'A']
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=["A","B"])
# Generate the interactions with a distance so large that we get a
# layer of implicite wildcards in the C++ matchlists.
sites = [0]
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ -1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, -1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 2.000000e+00, 2.000000e+00, 0.000000e+00]]
types0 = ['A', 'B', 'B', 'B', 'B', 'A']
types1 = ['B', 'B', 'A', 'B', 'B', 'A']
process_0 = KMCProcess(coordinates, types0, types1, None, sites, 1.0)
types0 = ['A', 'B', 'B', 'B', 'B', 'B']
types1 = ['B', 'B', 'A', 'B', 'B', 'B']
process_1 = KMCProcess(coordinates, types0, types1, None, sites, 1.0)
types0 = ['A', 'B', 'B', 'B', 'B', 'B']
types1 = ['B', 'B', 'B', 'A', 'B', 'B']
process_2 = KMCProcess(coordinates, types0, types1, None, sites, 1.0)
types0 = ['A', 'B', 'B', 'B', 'B', 'B']
types1 = ['B', 'B', 'B', 'B', 'A', 'B']
process_3 = KMCProcess(coordinates, types0, types1, None, sites, 1.0)
# Processes.
processes = [process_0,
process_1,
process_2,
process_3]
# No implicit wildcards.
interactions = KMCInteractions(processes=processes,
implicit_wildcards=False)
# Create the model.
model = KMCLatticeModel(config, interactions)
# Get the match types out.
match_types = [ l.match_type for l in model._backend().interactions().processes()[0].minimalMatchList() ]
# This does not have wildcards added.
ref_match_types = [1, 2, 2, 2, 2, 1]
self.assertEqual( match_types, ref_match_types )
# Create with implicit wildcards - this is default behavior.
interactions = KMCInteractions(processes=processes)
# Create the model.
model = KMCLatticeModel(config, interactions)
# Check the process matchlists again.
match_types = [ l.match_type for l in model._backend().interactions().processes()[0].minimalMatchList() ]
ref_match_types = [1, 2, 2, 2, 2,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 1]
# This one has the wildcards (zeroes) added.
self.assertEqual( match_types, ref_match_types )
# Setup the run paramters.
control_parameters = KMCControlParameters(number_of_steps=10,
dump_interval=1)
model.run(control_parameters)
