def testBackendNoFailWrongBasisMatch(self):
""" Test for no failure when constructing backend with wrong n_basis """
# A first process.
coords = [[1.0, 2.0, 3.4], [1.1, 1.2, 1.3]]
types0 = ["A", "B"]
types1 = ["B", "A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=[0, 4],
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=[0, 1],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A": 13,
"D": 2,
"B": 3,
"J": 4,
"C": 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Get the backend - The [0,4] sites list for process_0 is simply ignored.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
self.assertEqual(len(cpp_interactions.processes()[0].basisSites()), 1)
self.assertEqual(cpp_interactions.processes()[0].basisSites()[0], 0)
self.assertEqual(len(cpp_interactions.processes()[1].basisSites()), 2)
self.assertEqual(cpp_interactions.processes()[1].basisSites()[0], 0)
self.assertEqual(cpp_interactions.processes()[1].basisSites()[1], 1)
def testBackendNoFailWrongBasisMatch(self):
""" Test for no failure when constructing backend with wrong n_basis """
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords, types0, types1, basis_sites=[0,4], 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=[0,1], rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A" : 13,
"D" : 2,
"B" : 3,
"J" : 4,
"C" : 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Get the backend - The [0,4] sites list for process_0 is simply ignored.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
self.assertEqual( len(cpp_interactions.processes()[0].basisSites()), 1 )
self.assertEqual( cpp_interactions.processes()[0].basisSites()[0], 0 )
self.assertEqual( len(cpp_interactions.processes()[1].basisSites()), 2 )
self.assertEqual( cpp_interactions.processes()[1].basisSites()[0], 0 )
self.assertEqual( cpp_interactions.processes()[1].basisSites()[1], 1 )
def testBackendWithCustomRates(self):
""" Test that we can construct the backend object with custom rates. """
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords, types0, types1, basis_sites=[0], 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=[0], rate_constant=rate_0_1)
processes = [process_0, process_1]
# Set the custom rates class to use.
custom_rates_class = CustomRateCalculator
# Set the rate function on the custom rates calculator for testing.
ref_rnd = numpy.random.uniform(0.0,1.0)
def testRateFunction(obj, coords, types_before, types_after, rate_const, process_number, global_coordinate):
return ref_rnd
# Store the original.
custom_rate_function = custom_rates_class.rate
try:
custom_rates_class.rate = testRateFunction
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=False)
# Setup a dict with the possible types.
possible_types = {
"A" : 13,
"D" : 2,
"B" : 3,
"J" : 4,
"C" : 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Test that it fails if the rate calculator is of wrong class.
kmc_interactions.setRateCalculator(rate_calculator=Error)
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
# Test that it fails if the rate calculator is the base class.
kmc_interactions.setRateCalculator(rate_calculator=KMCRateCalculatorPlugin)
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
# But this should work.
kmc_interactions.setRateCalculator(rate_calculator=custom_rates_class)
# Construct the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
# Test that the configuration on the custom rate class is the one given.
self.assertTrue(kmc_interactions._KMCInteractions__rate_calculator.configuration == config) # <- Check by reference.
# Get the rate calculator reference out of the C++ object and
# check that a call from C++ calls the Python extension.
cpp_coords = Backend.StdVectorDouble()
cpp_types1 = Backend.StdVectorString()
cpp_types2 = Backend.StdVectorString()
rate_constant = 543.2211
process_number = 33
coordinate = (1.2,3.4,5.6)
self.assertAlmostEqual( cpp_interactions.rateCalculator().backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), ref_rnd, 12 )
self.assertAlmostEqual( kmc_interactions._KMCInteractions__rate_calculator.backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), ref_rnd, 12 )
finally:
# Reset the class.
custom_rates_class.rate = custom_rate_function
# Construct a C++ RateCalculator object directly and check that this object
# returns the rate given to it.
cpp_rate_calculator = Backend.RateCalculator()
self.assertAlmostEqual( cpp_rate_calculator.backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), rate_constant, 12 )
def testBackendBuckets(self):
"""
Test that the backend behaves as expected with bucket processes.
"""
# A first process.
coords = [[1.0,2.0,3.4],[12.0,13.0,-1.0],[1.1,1.2,1.3]]
minimum_match = ["A","*","B"]
update = [[(-1,"A"), (1, "B")],[(0,"*")],[(1,"A"), (-1, "B")]]
rate_0_1 = 3.5
process_0 = KMCBucketProcess(coordinates=coords,
minimum_match=minimum_match,
update=update,
basis_sites=[0,1,3],
rate_constant=rate_0_1)
# A second process.
coords = [[1.0,2.0,3.4],[12.0,13.0,-1.0],[1.1,1.2,1.3]]
minimum_match = ["A","*","C"]
update = [[(-1,"A"), (1, "C")],[(0,"*")],[(1,"A"), (-1, "C")]]
rate_0_1 = 1.5
process_1 = KMCBucketProcess(coordinates=coords,
minimum_match=minimum_match,
update=update,
basis_sites=[0,1,3],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A" : 0,
"B" : 1,
"J" : 2,
"C" : 3,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Check that setting up the backend fails if we have types in the processes that do
# not corresponds to a type in the list of possible types.
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
possible_types = {
"A" : 0,
"B" : 1,
"D" : 2,
"J" : 3,
"C" : 4,
}
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
possible_types = {
"A" : 0,
"B" : 1,
"F" : 2,
"J" : 3,
"C" : 4,
}
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
# Both "D" and "F" must be present, and the widcard "*".
possible_types["D"] = 5
possible_types["*"] = 6
# Get the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
# Check the type.
self.assertTrue( isinstance(cpp_interactions, Backend.Interactions) )
# Get the processes out.
cpp_processes = cpp_interactions.processes()
# Check the length of the processes.
self.assertEqual(cpp_processes.size(), 2)
# Get the elements out of the second process.
update_types = cpp_processes[1].processMatchList()[0].update_types
# This is an "A"
match_types = cpp_processes[1].processMatchList()[0].match_types
self.assertEqual(match_types[0], 1)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 0)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 0)
# This is an "C"
match_types = cpp_processes[1].processMatchList()[1].match_types
self.assertEqual(match_types[0], 0)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 1)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 0)
# This is a "*"
match_types = cpp_processes[1].processMatchList()[2].match_types
self.assertEqual(match_types[0], 0)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 0)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 1)
def testBackend(self):
"""
Test that the generated backend object is what we expect.
"""
# A first process.
coords = [[1.0,2.0,3.4],[12.0,13.0,-1.0],[1.1,1.2,1.3]]
types0 = ["A","D","B"]
types1 = ["B","F","A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords, types0, types1, basis_sites=[0,1,3], rate_constant=rate_0_1)
# A second process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","C"]
types1 = ["C","A"]
rate_0_1 = 1.5
process_1 = KMCProcess(coords, types0, types1, basis_sites=[0,1,3], rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A" : 13,
"B" : 3,
"J" : 4,
"C" : 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Check that setting up the backend fails if we have types in the processes that do
# not corresponds to a type in the list of possible types.
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
possible_types = {
"A" : 13,
"B" : 3,
"D" : 2,
"J" : 4,
"C" : 5,
}
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
possible_types = {
"A" : 13,
"B" : 3,
"F" : 2,
"J" : 4,
"C" : 5,
}
self.assertRaises( Error, lambda : kmc_interactions._backend(possible_types, 2, config) )
# Both "D" and "F" must be present.
possible_types["D"] = 123
# Get the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
# Check the type.
self.assertTrue( isinstance(cpp_interactions, Backend.Interactions) )
# Get the processes out.
cpp_processes = cpp_interactions.processes()
# Check the length of the processes.
self.assertEqual(cpp_processes.size(), 2)
# Get the elements out of the second process.
match_types = cpp_processes[1].processMatchList()[0].match_types
update_types = cpp_processes[1].processMatchList()[0].update_types
# Match type should be "A" -> 15 and update type "C" -> 5
self.assertEqual( match_types[13], 1)
self.assertEqual( update_types[5], 1)
# Get the elements out of the second process.
match_types = cpp_processes[1].processMatchList()[1].match_types
update_types = cpp_processes[1].processMatchList()[1].update_types
# Match type should be "C" -> 5 and update type "A" -> 13
self.assertEqual( match_types[5], 1)
self.assertEqual( update_types[13], 1)
def testBackendWithCustomRates(self):
""" Test that we can construct the backend object with custom rates. """
# A first process.
coords = [[1.0, 2.0, 3.4], [1.1, 1.2, 1.3]]
types0 = ["A", "B"]
types1 = ["B", "A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=[0],
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=[0],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Set the custom rates class to use.
custom_rates_class = CustomRateCalculator
# Set the rate function on the custom rates calculator for testing.
ref_rnd = numpy.random.uniform(0.0, 1.0)
def testRateFunction(obj, coords, types_before, types_after,
rate_const, process_number, global_coordinate):
return ref_rnd
# Store the original.
custom_rate_function = custom_rates_class.rate
try:
custom_rates_class.rate = testRateFunction
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=False)
# Setup a dict with the possible types.
possible_types = {
"A": 13,
"D": 2,
"B": 3,
"J": 4,
"C": 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Test that it fails if the rate calculator is of wrong class.
kmc_interactions.setRateCalculator(rate_calculator=Error)
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
# Test that it fails if the rate calculator is the base class.
kmc_interactions.setRateCalculator(
rate_calculator=KMCRateCalculatorPlugin)
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
# But this should work.
kmc_interactions.setRateCalculator(
rate_calculator=custom_rates_class)
# Construct the backend.
cpp_interactions = kmc_interactions._backend(
possible_types, 2, config)
# Test that the configuration on the custom rate class is the one given.
self.assertTrue(
kmc_interactions._KMCInteractions__rate_calculator.
configuration == config) # <- Check by reference.
# Get the rate calculator reference out of the C++ object and
# check that a call from C++ calls the Python extension.
cpp_coords = Backend.StdVectorDouble()
cpp_types1 = Backend.StdVectorString()
cpp_types2 = Backend.StdVectorString()
rate_constant = 543.2211
process_number = 33
coordinate = (1.2, 3.4, 5.6)
self.assertAlmostEqual(
cpp_interactions.rateCalculator().backendRateCallback(
cpp_coords,
cpp_coords.size() / 3, cpp_types1, cpp_types2,
rate_constant, process_number, coordinate[0],
coordinate[1], coordinate[2]), ref_rnd, 12)
self.assertAlmostEqual(
kmc_interactions._KMCInteractions__rate_calculator.
backendRateCallback(cpp_coords,
cpp_coords.size() / 3, cpp_types1,
cpp_types2, rate_constant, process_number,
coordinate[0], coordinate[1],
coordinate[2]), ref_rnd, 12)
finally:
# Reset the class.
custom_rates_class.rate = custom_rate_function
# Construct a C++ RateCalculator object directly and check that this object
# returns the rate given to it.
cpp_rate_calculator = Backend.RateCalculator()
self.assertAlmostEqual(
cpp_rate_calculator.backendRateCallback(
cpp_coords,
cpp_coords.size() / 3, cpp_types1, cpp_types2, rate_constant,
process_number, coordinate[0], coordinate[1], coordinate[2]),
rate_constant, 12)
def testBackendBuckets(self):
"""
Test that the backend behaves as expected with bucket processes.
"""
# A first process.
coords = [[1.0, 2.0, 3.4], [12.0, 13.0, -1.0], [1.1, 1.2, 1.3]]
minimum_match = ["A", "*", "B"]
update = [[(-1, "A"), (1, "B")], [(0, "*")], [(1, "A"), (-1, "B")]]
rate_0_1 = 3.5
process_0 = KMCBucketProcess(coordinates=coords,
minimum_match=minimum_match,
update=update,
basis_sites=[0, 1, 3],
rate_constant=rate_0_1)
# A second process.
coords = [[1.0, 2.0, 3.4], [12.0, 13.0, -1.0], [1.1, 1.2, 1.3]]
minimum_match = ["A", "*", "C"]
update = [[(-1, "A"), (1, "C")], [(0, "*")], [(1, "A"), (-1, "C")]]
rate_0_1 = 1.5
process_1 = KMCBucketProcess(coordinates=coords,
minimum_match=minimum_match,
update=update,
basis_sites=[0, 1, 3],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A": 0,
"B": 1,
"J": 2,
"C": 3,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Check that setting up the backend fails if we have types in the processes that do
# not corresponds to a type in the list of possible types.
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
possible_types = {
"A": 0,
"B": 1,
"D": 2,
"J": 3,
"C": 4,
}
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
possible_types = {
"A": 0,
"B": 1,
"F": 2,
"J": 3,
"C": 4,
}
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
# Both "D" and "F" must be present, and the widcard "*".
possible_types["D"] = 5
possible_types["*"] = 6
# Get the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
# Check the type.
self.assertTrue(isinstance(cpp_interactions, Backend.Interactions))
# Get the processes out.
cpp_processes = cpp_interactions.processes()
# Check the length of the processes.
self.assertEqual(cpp_processes.size(), 2)
# Get the elements out of the second process.
update_types = cpp_processes[1].processMatchList()[0].update_types
# This is an "A"
match_types = cpp_processes[1].processMatchList()[0].match_types
self.assertEqual(match_types[0], 1)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 0)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 0)
# This is an "C"
match_types = cpp_processes[1].processMatchList()[1].match_types
self.assertEqual(match_types[0], 0)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 1)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 0)
# This is a "*"
match_types = cpp_processes[1].processMatchList()[2].match_types
self.assertEqual(match_types[0], 0)
self.assertEqual(match_types[1], 0)
self.assertEqual(match_types[2], 0)
self.assertEqual(match_types[3], 0)
self.assertEqual(match_types[4], 0)
self.assertEqual(match_types[5], 0)
self.assertEqual(match_types[6], 1)
def testBackend(self):
"""
Test that the generated backend object is what we expect.
"""
# A first process.
coords = [[1.0, 2.0, 3.4], [12.0, 13.0, -1.0], [1.1, 1.2, 1.3]]
types0 = ["A", "D", "B"]
types1 = ["B", "F", "A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=[0, 1, 3],
rate_constant=rate_0_1)
# A second process.
coords = [[1.0, 2.0, 3.4], [1.1, 1.2, 1.3]]
types0 = ["A", "C"]
types1 = ["C", "A"]
rate_0_1 = 1.5
process_1 = KMCProcess(coords,
types0,
types1,
basis_sites=[0, 1, 3],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes)
# Setup a dict with the possible types.
possible_types = {
"A": 13,
"B": 3,
"J": 4,
"C": 5,
}
# Use a dummy argument for the configuration.
config = "DummyConfig"
# Check that setting up the backend fails if we have types in the processes that do
# not corresponds to a type in the list of possible types.
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
possible_types = {
"A": 13,
"B": 3,
"D": 2,
"J": 4,
"C": 5,
}
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
possible_types = {
"A": 13,
"B": 3,
"F": 2,
"J": 4,
"C": 5,
}
self.assertRaises(
Error,
lambda: kmc_interactions._backend(possible_types, 2, config))
# Both "D" and "F" must be present.
possible_types["D"] = 123
# Get the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2, config)
# Check the type.
self.assertTrue(isinstance(cpp_interactions, Backend.Interactions))
# Get the processes out.
cpp_processes = cpp_interactions.processes()
# Check the length of the processes.
self.assertEqual(cpp_processes.size(), 2)
# Get the elements out of the second process.
match_types = cpp_processes[1].processMatchList()[0].match_types
update_types = cpp_processes[1].processMatchList()[0].update_types
# Match type should be "A" -> 15 and update type "C" -> 5
self.assertEqual(match_types[13], 1)
self.assertEqual(update_types[5], 1)
# Get the elements out of the second process.
match_types = cpp_processes[1].processMatchList()[1].match_types
update_types = cpp_processes[1].processMatchList()[1].update_types
# Match type should be "C" -> 5 and update type "A" -> 13
self.assertEqual(match_types[5], 1)
self.assertEqual(update_types[13], 1)
def testBackendWithCustomRates(self):
""" Test that we can construct the backend object with custom rates. """
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords, types0, types1, basis_sites=[0], 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=[0], rate_constant=rate_0_1)
processes = [process_0, process_1]
# Set the custom rates class to use.
custom_rates_class = CustomRateCalculator
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=False)
kmc_interactions.setRateCalculator(rate_calculator=custom_rates_class)
# Set the rate function on the custom rates calculator for testing.
ref_rnd = numpy.random.uniform(0.0,1.0)
def testRateFunction(coords, types_before, types_after, rate_const, process_number, global_coordinate):
return ref_rnd
kmc_interactions._KMCInteractions__rate_calculator.rate = testRateFunction
# Setup a dict with the possible types.
possible_types = {
"A" : 13,
"D" : 2,
"B" : 3,
"J" : 4,
"C" : 5,
}
# Construct the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2)
# Get the rate calculator reference out of the C++ object and
# check that a call from C++ calls the Python extension.
cpp_coords = Backend.StdVectorDouble()
cpp_types1 = Backend.StdVectorString()
cpp_types2 = Backend.StdVectorString()
rate_constant = 543.2211
process_number = 33
coordinate = (1.2,3.4,5.6)
self.assertAlmostEqual( cpp_interactions.rateCalculator().backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), ref_rnd, 12 )
self.assertAlmostEqual( kmc_interactions._KMCInteractions__rate_calculator.backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), ref_rnd, 12 )
# Construct a C++ RateCalculator object directly and check that this object
# returns the rate given to it.
cpp_rate_calculator = Backend.RateCalculator()
self.assertAlmostEqual( cpp_rate_calculator.backendRateCallback(cpp_coords,
cpp_coords.size()/3,
cpp_types1,
cpp_types2,
rate_constant,
process_number,
coordinate[0],
coordinate[1],
coordinate[2]), rate_constant, 12 )
def testBackendWithCustomRates(self):
""" Test that we can construct the backend object with custom rates. """
# A first process.
coords = [[1.0, 2.0, 3.4], [1.1, 1.2, 1.3]]
types0 = ["A", "B"]
types1 = ["B", "A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=[0],
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=[0],
rate_constant=rate_0_1)
processes = [process_0, process_1]
# Set the custom rates class to use.
custom_rates_class = CustomRateCalculator
# Construct the interactions object.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=False)
kmc_interactions.setRateCalculator(rate_calculator=custom_rates_class)
# Set the rate function on the custom rates calculator for testing.
ref_rnd = numpy.random.uniform(0.0, 1.0)
def testRateFunction(coords, types_before, types_after, rate_const,
process_number, global_coordinate):
return ref_rnd
kmc_interactions._KMCInteractions__rate_calculator.rate = testRateFunction
# Setup a dict with the possible types.
possible_types = {
"A": 13,
"D": 2,
"B": 3,
"J": 4,
"C": 5,
}
# Construct the backend.
cpp_interactions = kmc_interactions._backend(possible_types, 2)
# Get the rate calculator reference out of the C++ object and
# check that a call from C++ calls the Python extension.
cpp_coords = Backend.StdVectorDouble()
cpp_types1 = Backend.StdVectorString()
cpp_types2 = Backend.StdVectorString()
rate_constant = 543.2211
process_number = 33
coordinate = (1.2, 3.4, 5.6)
self.assertAlmostEqual(
cpp_interactions.rateCalculator().backendRateCallback(
cpp_coords,
cpp_coords.size() / 3, cpp_types1, cpp_types2, rate_constant,
process_number, coordinate[0], coordinate[1], coordinate[2]),
ref_rnd, 12)
self.assertAlmostEqual(
kmc_interactions._KMCInteractions__rate_calculator.
backendRateCallback(cpp_coords,
cpp_coords.size() / 3, cpp_types1, cpp_types2,
rate_constant, process_number, coordinate[0],
coordinate[1], coordinate[2]), ref_rnd, 12)
# Construct a C++ RateCalculator object directly and check that this object
# returns the rate given to it.
cpp_rate_calculator = Backend.RateCalculator()
self.assertAlmostEqual(
cpp_rate_calculator.backendRateCallback(
cpp_coords,
cpp_coords.size() / 3, cpp_types1, cpp_types2, rate_constant,
process_number, coordinate[0], coordinate[1], coordinate[2]),
rate_constant, 12)
