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 testConstructionSorting(self):
""" Test that the coordinates elements and move vectors gets sorted """
# Set the input.
coordinates = [[0.0, 0.0, 0.0],
[3.0, 3.0, 3.0],
[1.0, 1.0, 1.0],
[1.1, 1.1, 1.1],
[1.5, 1.5, 1.5],
[2.5, 2.5, 2.5]]
elements_before = ["A", "B", "C", "P", "D", "E"]
elements_after = ["B", "C", "D", "P", "A", "E"]
basis_sites = [0]
rate_constant = 1.0
move_vectors = [(0, [ 1.5, 1.5, 1.5]),
(1, [-3.0,-3.0,-3.0]),
(2, [ 2.0, 2.0, 2.0]),
(4, [-0.5,-0.5,-0.5])]
# Construct.
p = KMCProcess(coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=1.0)
# Get the configurations out.
config_before = p.localConfigurations()[0]
config_after = p.localConfigurations()[1]
# Check that the coordinates, elements and move vectors
# have been sorted.
ref_coords = numpy.array([[ 0., 0., 0. ],
[ 1., 1., 1. ],
[ 1.1, 1.1, 1.1],
[ 1.5, 1.5, 1.5],
[ 2.5, 2.5, 2.5],
[ 3., 3., 3.]])
# Before move.
coords = config_before.coordinates()
norm = numpy.linalg.norm(ref_coords - coords)
self.assertAlmostEqual( norm, 0.0, 10 )
# After move.
coords = config_after.coordinates()
norm = numpy.linalg.norm(ref_coords - coords)
self.assertAlmostEqual( norm, 0.0, 10 )
# Check the elements before move.
ref_types = [[(1, "A")], [(1, "C")], [(1, "P")],
[(1, "D")], [(1, "E")], [(1, "B")]]
self.assertEqual( ref_types, config_before.types() )
# Check the elements after move.
ref_types = [[(1, "B")], [(1, "D")], [(1, "P")],
[(1, "A")], [(1, "E")], [(1, "C")]]
self.assertEqual( ref_types, config_after.types() )
ref_vectors = [(0, [ 1.5, 1.5, 1.5]),
(1, [ 2.0, 2.0, 2.0]),
(3, [-0.5,-0.5,-0.5]),
(5, [-3.0,-3.0,-3.0])]
ret_vectors = p.moveVectors()
for ref, ret in zip(ref_vectors, ret_vectors):
# Check the 'from' index.
self.assertEqual(ref[0], ret[0])
# Check the vector.
norm = numpy.linalg.norm(numpy.array(ref[1]) - numpy.array(ret[1]))
self.assertAlmostEqual( norm, 0.0, 10 )
def testConstructionSorting(self):
""" Test that the coordinates elements and move vectors gets sorted """
# Set the input.
coordinates = [[0.0, 0.0, 0.0], [3.0, 3.0, 3.0], [1.0, 1.0, 1.0],
[1.1, 1.1, 1.1], [1.5, 1.5, 1.5], [2.5, 2.5, 2.5]]
elements_before = ["A", "B", "C", "P", "D", "E"]
elements_after = ["B", "C", "D", "P", "A", "E"]
basis_sites = [0]
rate_constant = 1.0
move_vectors = [(0, [1.5, 1.5, 1.5]), (1, [-3.0, -3.0, -3.0]),
(2, [2.0, 2.0, 2.0]), (4, [-0.5, -0.5, -0.5])]
# Construct.
p = KMCProcess(coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=1.0)
# Get the configurations out.
config_before = p.localConfigurations()[0]
config_after = p.localConfigurations()[1]
# Check that the coordinates, elements and move vectors
# have been sorted.
ref_coords = numpy.array([[0., 0., 0.], [1., 1., 1.], [1.1, 1.1, 1.1],
[1.5, 1.5, 1.5], [2.5, 2.5, 2.5],
[3., 3., 3.]])
# Before move.
coords = config_before.coordinates()
norm = numpy.linalg.norm(ref_coords - coords)
self.assertAlmostEqual(norm, 0.0, 10)
# After move.
coords = config_after.coordinates()
norm = numpy.linalg.norm(ref_coords - coords)
self.assertAlmostEqual(norm, 0.0, 10)
# Check the elements before move.
ref_types = [[(1, "A")], [(1, "C")], [(1, "P")], [(1, "D")],
[(1, "E")], [(1, "B")]]
self.assertEqual(ref_types, config_before.types())
# Check the elements after move.
ref_types = [[(1, "B")], [(1, "D")], [(1, "P")], [(1, "A")],
[(1, "E")], [(1, "C")]]
self.assertEqual(ref_types, config_after.types())
ref_vectors = [(0, [1.5, 1.5, 1.5]), (1, [2.0, 2.0, 2.0]),
(3, [-0.5, -0.5, -0.5]), (5, [-3.0, -3.0, -3.0])]
ret_vectors = p.moveVectors()
for ref, ret in zip(ref_vectors, ret_vectors):
# Check the 'from' index.
self.assertEqual(ref[0], ret[0])
# Check the vector.
norm = numpy.linalg.norm(numpy.array(ref[1]) - numpy.array(ret[1]))
self.assertAlmostEqual(norm, 0.0, 10)
