def testStdVectorBucketTypeToPython(self):
""" Test the buckets format conversion routine from C++ to Python. """
empty_py_vector = stdVectorTypeBucketToPython(
Backend.StdVectorTypeBucket(), Backend.StdVectorString())
self.assertEqual(empty_py_vector, [])
# Add a vector with content.
cpp_map = Backend.StdVectorString(3)
cpp_map[0] = "*"
cpp_map[1] = "A"
cpp_map[2] = "B"
cpp_vector = Backend.StdVectorTypeBucket(4, Backend.TypeBucket(3))
# [(1,"A")]
cpp_vector[0][0] = 0
cpp_vector[0][1] = 1
cpp_vector[0][2] = 0
# []
cpp_vector[1][0] = 0
cpp_vector[1][1] = 0
cpp_vector[1][2] = 0
# [(3,"A"), (1, "B")]
cpp_vector[2][0] = 0
cpp_vector[2][1] = 3
cpp_vector[2][2] = 1
# [(4,"A"), (5, "B")]
cpp_vector[3][0] = 1
cpp_vector[3][1] = 4
cpp_vector[3][2] = 5
# Translate to Python.
py_vector = stdVectorTypeBucketToPython(cpp_vector, cpp_map)
ref_py_vector = [[(1, "A")], [], [(3, "A"), (1, "B")],
[(4, "A"), (5, "B")]]
# Check.
self.assertEqual(py_vector, ref_py_vector)
def testStdVectorStringToStringList(self):
""" Test the conversion of a std::vector<std::string> to a string list. """
# Take a list of strings.
cpp_list = Backend.StdVectorString()
ref_list = ["AAA", "BB", "AbC", "def"]
for s in ref_list:
cpp_list.push_back(s)
# Convert.
py_repr = stdVectorStringToStringList(cpp_list)
# Check the type.
self.assertTrue(isinstance(py_repr, list))
# Check the result.
self.assertEqual(py_repr, ref_list)
def stringListToStdVectorString(string_list):
"""
Converts a list of strings to a std::vector<std::string> object.
:param string_list: The list of strings.
:returns: A corresponding std::vector<std::string> object.
"""
# Get the size.
size = len(string_list)
# Setup the c++ object.
cpp_list = Backend.StdVectorString()
# Copy values over.
for s in string_list:
cpp_list.push_back(s)
# Done.
return cpp_list
def _backend(self, possible_types):
"""
Query for the local configuration backend object.
:param possible_types: A dict with the global mapping of type strings
to integers.
:returns: The interactions object in C++
"""
if self.__backend is None:
# Construct the c++ backend object.
cpp_types = Backend.StdVectorString(self.__types)
cpp_coords = numpy2DArrayToStdVectorStdVectorDouble(self.__coordinates)
cpp_possible_types = Backend.StdMapStringInt(possible_types)
# Send in the coordinates and types to construct the backend configuration.
self.__backend = Backend.Configuration(cpp_coords,
cpp_types,
cpp_possible_types)
# Return the backend.
return self.__backend
def bucketListToStdVectorStdVectorString(bucket_list):
"""
Converts a list of the format [[(n,"A"), ...], ...]
to a std::vector< std::vector<std::string> > representation.
:param bucket_list: The list to convert.
:returns: A corresponding std::vector<std::vector<std::string> > object.
"""
cpp_list = Backend.StdVectorStdVectorString()
# For each site.
for ss in bucket_list:
# For all types at this site.
site_list = Backend.StdVectorString()
for s in ss:
# Add the number of types.
for i in range(s[0]):
site_list.push_back(s[1])
cpp_list.push_back(site_list)
# Done.
return cpp_list
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 testUsage(self):
""" Test that the KMCRateCalculatorPlugin can be used in a simulation. """
# To get the random numbers and process numbers returned.
ref_randoms = []
ref_process_numbers = []
ref_coordinates = []
# Define a derrived class.
class RateCalc(KMCRateCalculatorPlugin):
# Overload the initialize function.
def initialize(self):
# Save something on the class here.
self._times_called = 0
# Overload the rate function.
def rate(self, coords, types_befpre, types_after, rate_constant,
process_number, coordinate):
# Do some simple counting and return the random number.
self._times_called += 1
rnd = numpy.random.uniform(0.0, 1.0)
ref_randoms.append(rnd)
ref_process_numbers.append(process_number)
ref_coordinates.append(coordinate)
return rnd
# Overload the additive rate function.
def useAdditiveRate(self):
return False
# Construct.
calculator = RateCalc("DummyConfig")
# Send it to C++ to get the rate out, call it 4 times.
cpp_coords = Backend.StdVectorCoordinate()
cpp_coords.push_back(Backend.Coordinate(1.0, 2.9, 3.4))
cpp_types1 = Backend.StdVectorString()
cpp_types1.push_back("A")
cpp_types2 = Backend.StdVectorString()
cpp_types2.push_back("B")
rate_constant = 3.1415927
ret_randoms = []
process_numbers = [21, 12, 10, 2]
global_xyz = numpy.array([[0.2, 0.4, 0.5], [1.1, 1.3, 1.4],
[3.4, 4.3, 3.3], [4.2, 3.2, 1.9]])
ret_randoms.append(
Backend.getRate(calculator, cpp_coords, cpp_types1, cpp_types2,
rate_constant, process_numbers[0],
global_xyz[0, 0], global_xyz[0, 1], global_xyz[0,
2]))
ret_randoms.append(
Backend.getRate(calculator, cpp_coords, cpp_types1, cpp_types2,
rate_constant, process_numbers[1],
global_xyz[1, 0], global_xyz[1, 1], global_xyz[1,
2]))
ret_randoms.append(
Backend.getRate(calculator, cpp_coords, cpp_types1, cpp_types2,
rate_constant, process_numbers[2],
global_xyz[2, 0], global_xyz[2, 1], global_xyz[2,
2]))
ret_randoms.append(
Backend.getRate(calculator, cpp_coords, cpp_types1, cpp_types2,
rate_constant, process_numbers[3],
global_xyz[3, 0], global_xyz[3, 1], global_xyz[3,
2]))
# Check that it was called 4 times.
self.assertEqual(calculator._times_called, 4)
# Check the values.
self.assertAlmostEqual(ret_randoms, ref_randoms, 12)
# Check the reference process numbers.
self.assertEqual(ref_process_numbers[0], 21)
self.assertEqual(ref_process_numbers[1], 12)
self.assertEqual(ref_process_numbers[2], 10)
self.assertEqual(ref_process_numbers[3], 2)
# Check the reference coordinate.
self.assertAlmostEqual(
numpy.linalg.norm(global_xyz - numpy.array(ref_coordinates)), 0.0,
10)
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)
