def testLocalConfigurations(self):
""" Test that the local configurations are correctly set up """
coordinates = numpy.array([[1.0,2.0,3.0], [2.3,5.5,3.2]])
elements1 = ["First", "Second"]
elements2 = ["Second", "First"]
# Construct the process.
process = KMCProcess(coordinates,
elements1,
elements2,
basis_sites=[9],
rate_constant=1.0)
# Get the local configurations out.
c1 = process.localConfigurations()[0]
c2 = process.localConfigurations()[1]
# Construct the two reference local configurations.
ref_c1 = KMCLocalConfiguration(coordinates, elements1, center=0)
ref_c2 = KMCLocalConfiguration(coordinates, elements2, center=0)
# Check coordinates.
self.assertAlmostEqual( numpy.linalg.norm(c1.coordinates() - ref_c1.coordinates()), 0.0, 12 )
self.assertAlmostEqual( numpy.linalg.norm(c2.coordinates() - ref_c2.coordinates()), 0.0, 12 )
# Check types.
self.assertAlmostEqual( c1.types(), ref_c1.types() )
self.assertAlmostEqual( c2.types(), ref_c2.types() )
def testLocalConfigurations(self):
""" Test that the local configurations are correctly set up """
coordinates = numpy.array([[1.0, 2.0, 3.0], [2.3, 5.5, 3.2]])
elements1 = ["First", "Second"]
elements2 = ["Second", "First"]
# Construct the process.
process = KMCProcess(coordinates,
elements1,
elements2,
basis_sites=[9],
rate_constant=1.0)
# Get the local configurations out.
c1 = process.localConfigurations()[0]
c2 = process.localConfigurations()[1]
# Construct the two reference local configurations.
ref_c1 = KMCLocalConfiguration(coordinates, elements1, center=0)
ref_c2 = KMCLocalConfiguration(coordinates, elements2, center=0)
# Check coordinates.
self.assertAlmostEqual(
numpy.linalg.norm(c1.coordinates() - ref_c1.coordinates()), 0.0,
12)
self.assertAlmostEqual(
numpy.linalg.norm(c2.coordinates() - ref_c2.coordinates()), 0.0,
12)
# Check types.
self.assertAlmostEqual(c1.types(), ref_c1.types())
self.assertAlmostEqual(c2.types(), ref_c2.types())
def testBackend(self):
""" Test that we can get a valid backend object out. """
# Construct with coordinate list.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types = ["A","B"]
local_config = KMCLocalConfiguration(coordinates=coords,
types=types,
center=1)
# Setup a possible types dict.
possible_types = {
"A" : 0,
"B" : 1,
"C" : 2,
}
# Get the backend.
backend = local_config._backend(possible_types)
# Check its type.
self.assertTrue( isinstance(backend, Backend.Configuration) )
# Get the coordinates back out and check.
cpp_coords = backend.coordinates()
py_coords = local_config.coordinates()
self.assertAlmostEqual( cpp_coords[0][0], py_coords[0][0], 10 )
self.assertAlmostEqual( cpp_coords[0][1], py_coords[0][1], 10 )
self.assertAlmostEqual( cpp_coords[0][2], py_coords[0][2], 10 )
# Get the types back out.
cpp_types = list(backend.elements())
py_types = local_config.types()
self.assertEqual(py_types, cpp_types)
def testMemberDataQuery(self):
""" Check that the correct member data is stored and returned. """
# Setup the configuration.
coords = [[1.0, 2.0, 3.0], [1.0, 1.0, 3.0], [3.0, 8.0, 9.0]]
types = ["C", "B", "A"]
local_config = KMCLocalConfiguration(coordinates=coords,
types=types,
center=1)
# Define the reference data.
ref_coords = numpy.array([[0.0, 1.0, 0.0], [0.0, 0.0, 0.0],
[2.0, 7.0, 6.0]])
ref_types = [[(1, "C")], [(1, "B")], [(1, "A")]]
# Check the coordinates.
self.assertAlmostEqual(
numpy.linalg.norm(
local_config._KMCLocalConfiguration__coordinates - ref_coords),
0.0, 10)
#
self.assertAlmostEqual(
numpy.linalg.norm(local_config.coordinates() - ref_coords), 0.0,
10)
# Check the types.
self.assertEqual(local_config._KMCLocalConfiguration__types, ref_types)
#
self.assertEqual(local_config.types(), ref_types)
def testBackend(self):
""" Test that we can get a valid backend object out. """
# Construct with coordinate list.
coords = [[1.0, 2.0, 3.4], [1.1, 1.2, 1.3]]
types = ["A", "B"]
local_config = KMCLocalConfiguration(coordinates=coords,
types=types,
center=1)
# Setup a possible types dict.
possible_types = {
"A": 0,
"B": 1,
"C": 2,
}
# Get the backend.
backend = local_config._backend(possible_types)
# Check its type.
self.assertTrue(isinstance(backend, Backend.Configuration))
# Get the coordinates back out and check.
cpp_coords = backend.coordinates()
py_coords = local_config.coordinates()
self.assertAlmostEqual(cpp_coords[0][0], py_coords[0][0], 10)
self.assertAlmostEqual(cpp_coords[0][1], py_coords[0][1], 10)
self.assertAlmostEqual(cpp_coords[0][2], py_coords[0][2], 10)
# Get the types back out.
cpp_types = list(backend.elements())
py_types = local_config.types()
self.assertEqual(py_types, cpp_types)
def testMemberDataQuery(self):
""" Check that the correct member data is stored and returned. """
# Setup the configuration.
coords = [[1.0,2.0,3.0],[1.0,1.0,3.0],[3.0,8.0,9.0]]
types = ["C","B","A"]
local_config = KMCLocalConfiguration(coordinates=coords,
types=types,
center=1)
# Define the reference data.
ref_coords = numpy.array([[0.0,1.0,0.0],[0.0,0.0,0.0],[2.0,7.0,6.0]])
ref_types = ["C","B","A"]
# Check the coordinates.
self.assertAlmostEqual(numpy.linalg.norm(local_config._KMCLocalConfiguration__coordinates - ref_coords), 0.0, 10)
#
self.assertAlmostEqual(numpy.linalg.norm(local_config.coordinates() - ref_coords), 0.0, 10)
# Check the types.
self.assertEqual(local_config._KMCLocalConfiguration__types, ref_types)
#
self.assertEqual(local_config.types(), ref_types)
