def testConstructionWithCustomRates(self):
""" Test construction with custom rates. """
# A first process.
coords = [[1.0, 2.0, 3.4], [12.0, 13.0, -1.0], [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, 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]
# Test that it fails with the wrong rate calculator.
interactions = KMCInteractions(processes=processes,
implicit_wildcards=True)
# Test that it fails if the rate calculator is of wrong type.
self.assertRaises(
Error, lambda: interactions.setRateCalculator(
rate_calculator="CustomRateCalculator"))
# Test that it fails if the rate calculator is instantiated.
self.assertRaises(
Error, lambda: interactions.setRateCalculator(
rate_calculator=CustomRateCalculator("DummyConfig")))
# Construct the interactions object with a custom rate calculator class.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=True)
kmc_interactions.setRateCalculator(
rate_calculator=CustomRateCalculator)
# Test the stored name.
self.assertEqual(
kmc_interactions._KMCInteractions__rate_calculator_str,
"CustomRateCalculator")
# Test the stored rate calculator class.
self.assertTrue(
kmc_interactions._KMCInteractions__rate_calculator_class ==
CustomRateCalculator)
def testConstructionWithCustomRates(self):
""" Test construction with custom rates. """
# A first process.
coords = [[1.0,2.0,3.4],[12.0,13.0,-1.0],[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=[0,1,3], 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]
# Test that it fails with the wrong rate calculator.
interactions = KMCInteractions(processes=processes,
implicit_wildcards=True)
# Test that it fails if the rate calculator is of wrong type.
self.assertRaises( Error, lambda : interactions.setRateCalculator(rate_calculator="CustomRateCalculator") )
# Test that it fails if the rate calculator is instantiated.
self.assertRaises( Error, lambda : interactions.setRateCalculator(rate_calculator=CustomRateCalculator("DummyConfig")) )
# Construct the interactions object with a custom rate calculator class.
kmc_interactions = KMCInteractions(processes=processes,
implicit_wildcards=True)
kmc_interactions.setRateCalculator(rate_calculator=CustomRateCalculator)
# Test the stored name.
self.assertEqual(kmc_interactions._KMCInteractions__rate_calculator_str, "CustomRateCalculator")
# Test the stored rate calculator class.
self.assertTrue(kmc_interactions._KMCInteractions__rate_calculator_class == CustomRateCalculator)
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 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 testCustomRatesRun(self):
""" Test the run of an A-B flip model with custom rates. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(10,10,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*100
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates, ['A'], ['B'], None, [0], 4.0)
process_1 = KMCProcess(coordinates, ['B'], ['A'], None, [0], 1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes,
implicit_wildcards=True)
# Custom rates.
rate_calculator = CustomRateCalculator
interactions.setRateCalculator(rate_calculator)
# Setup the model.
ab_flip_model = KMCLatticeModel(configuration, interactions)
# Run the model with a trajectory file.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "ab_flip_traj_custom.py")
self.__files_to_remove.append(trajectory_filename)
# The control parameters.
control_parameters = KMCControlParameters(number_of_steps=1000,
dump_interval=500,
seed=2013)
# Run the model for 1000 steps.
ab_flip_model.run(control_parameters,
trajectory_filename=trajectory_filename)
# Read the first last frames from the trajectory file and check that
# the fraction of A is close to 75% in the last, and 0 in the first.
if MPICommons.isMaster():
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Count the first frame.
elem = local_dict["types"][0]
nA = len([ ee for ee in elem if ee == "A" ])
nB = len([ ee for ee in elem if ee == "B" ])
self.assertEqual(nA, 0)
self.assertEqual(nB, 100)
# Count the last frame.
elem = local_dict["types"][-1]
nA = len([ ee for ee in elem if ee == "A" ])
nB = len([ ee for ee in elem if ee == "B" ])
# Note that the average over a long simulation should be
# 75% A using the modified rate function. In this particular
# step the A population is 74%.
value = 1.0 * nA / (nA + nB)
self.assertAlmostEqual(0.74, value, 2)
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)
