def testConstruction(self):
""" Test the construction of the unitcell """
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.0, 0.0, 11.8]
basis_points = [[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5]]
cell_vectors = [vector_a,
vector_b,
vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Check the vectors stored on the class.
ref_vectors = numpy.array(cell_vectors)
check_vectors = cell._KMCUnitCell__cell_vectors
self.assertAlmostEqual( numpy.linalg.norm(ref_vectors - check_vectors), 0.0, 10)
# Check via the query function.
ret_vectors = cell.cellVectors()
self.assertAlmostEqual( numpy.linalg.norm(ref_vectors - ret_vectors), 0.0, 10)
# Check the basis points stored on the class.
ref_basis = numpy.array(basis_points)
check_basis = cell._KMCUnitCell__basis_points
self.assertAlmostEqual( numpy.linalg.norm(ref_basis - check_basis), 0.0, 10)
def testConstructionFailBasis2(self):
""" Make sure construction fails if there is a problem with the basis points. """
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.0, 0.0, 11.8]
basis_points = [
[0.0, 0.0, 1.1], # <- too large value
[0.5, 0.5, 0.5]
]
cell_vectors = [vector_a, vector_b, vector_c]
self.assertRaises(
Error, lambda: KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points))
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.0, 0.0, 11.8]
basis_points = [
[0.0, 0.0, 1.0], # <- too large value
[0.5, 0.5, 0.5]
]
cell_vectors = [vector_a, vector_b, vector_c]
self.assertRaises(
Error, lambda: KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points))
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.0, 0.0, 11.8]
basis_points = [[0.0, 0.0, 0.999999], [0.5, 0.5,
-0.01]] # <- too small value
cell_vectors = [vector_a, vector_b, vector_c]
self.assertRaises(
Error, lambda: KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points))
def testConstruction(self):
""" Test the construction of the unitcell """
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.0, 0.0, 11.8]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
cell_vectors = [vector_a, vector_b, vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Check the vectors stored on the class.
ref_vectors = numpy.array(cell_vectors)
check_vectors = cell._KMCUnitCell__cell_vectors
self.assertAlmostEqual(numpy.linalg.norm(ref_vectors - check_vectors),
0.0, 10)
# Check via the query function.
ret_vectors = cell.cellVectors()
self.assertAlmostEqual(numpy.linalg.norm(ref_vectors - ret_vectors),
0.0, 10)
# Check the basis points stored on the class.
ref_basis = numpy.array(basis_points)
check_basis = cell._KMCUnitCell__basis_points
self.assertAlmostEqual(numpy.linalg.norm(ref_basis - check_basis), 0.0,
10)
def testTransformToCartesian(self):
"""
Test the transformation from internal to cartesian coordinates.
"""
# Setup a simple reference system.
a = numpy.array([[1.0, 2.0, 3.0], [1.1, 0.4, 3.7], [1.2, 2.5, 0.8]])
r = numpy.array([[1.2, 2.5, 3.8], [3.2, 4.5, 5.8]])
ref_xyz = numpy.dot(r, a)
# Cell vectors.
vector_a = [1.0, 2.0, 3.0]
vector_b = [1.1, 0.4, 3.7]
vector_c = [1.2, 2.5, 0.8]
cell_vectors = [vector_a, vector_b, vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=[[0.0, 0.0, 0.0]])
# Transform r to cartesian coordinates.
xyz = cell.transformToCartesian(r)
diff = numpy.linalg.norm(xyz - ref_xyz)
self.assertAlmostEqual(diff, 0.0, 10)
def testTransformToCartesian(self):
"""
Test the transformation from internal to cartesian coordinates.
"""
# Setup a simple reference system.
a = numpy.array([[1.0, 2.0, 3.0],
[1.1, 0.4, 3.7],
[1.2, 2.5, 0.8]])
r = numpy.array([[1.2, 2.5, 3.8],
[3.2, 4.5, 5.8]])
ref_xyz = numpy.dot(r, a)
# Cell vectors.
vector_a = [1.0, 2.0, 3.0]
vector_b = [1.1, 0.4, 3.7]
vector_c = [1.2, 2.5, 0.8]
cell_vectors = [vector_a,
vector_b,
vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=[[0.0, 0.0, 0.0]])
# Transform r to cartesian coordinates.
xyz = cell.transformToCartesian(r)
diff = numpy.linalg.norm(xyz - ref_xyz)
self.assertAlmostEqual(diff, 0.0, 10)
def testGlobalIndex(self):
""" Test that the global index function returns correct values. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the repetitions.
nI = 2
nJ = 12
nK = 3
nB = 2
repetitions = (nI, nJ, nK)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Loop through all indices and check that the globalIndex function computes them correctly.
increment = 0
for i in range(nI):
for j in range(nJ):
for k in range(nK):
for b in range(nB):
index = lattice._globalIndex(i, j, k, b)
self.assertEqual(index, increment)
increment += 1
def testConstructionFailPeriodic(self):
""" Test that construction of the lattice fails if the periodic parameter is incorrect."""
# Setup a valid unitcell.
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
repetitions = (10, 12, 45)
# Fail because of not being a sequence.
periodic = True
self.assertRaises(
Error, lambda: KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic))
# Fail because of wrong length.
periodic = (True, True, True, True)
self.assertRaises(
Error, lambda: KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic))
# Fail because of wrong type.
periodic = (True, True, 1)
self.assertRaises(
Error, lambda: KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic))
def testLatticeQuery(self):
""" Test the query function for the lattice. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 1),
periodic=(True, True, False))
types = [
'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b',
'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a',
'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a',
'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a'
]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['a', 'c', 'b'])
# Query for the lattice.
ret_lattice = config.lattice()
# Check by reference.
self.assertTrue(lattice == ret_lattice)
def testLatticeMap(self):
""" Check that we can get a valid lattice map out. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the repetitions.
nI = 2
nJ = 12
nK = 3
nB = 2
repetitions = (nI, nJ, nK)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Get the lattice map.
cpp_lattice_map = lattice._map()
# Check the type.
self.assertTrue(isinstance(cpp_lattice_map, Backend.LatticeMap))
# Get it again and check that we get the same instance.
cpp_lattice_map2 = lattice._map()
# Check the instance.
self.assertTrue(cpp_lattice_map == cpp_lattice_map2)
def testConstruction(self):
""" Test that the XYZTrajectory object can be constructed. """
filename = "abc123.xyz"
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
filename = os.path.join(name, filename)
if MPICommons.isMaster():
self.__files_to_remove.append(filename)
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, True, True),
repetitions=(4,4,4))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C","D"]*16)
t = XYZTrajectory(trajectory_filename=filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
# Check that the internal memory buffers have been initiated.
self.assertEqual(t._XYZTrajectory__atom_id_types, [])
self.assertEqual(t._XYZTrajectory__atom_id_coordinates, [])
self.assertEqual(t._XYZTrajectory__time, [])
self.assertEqual(t._XYZTrajectory__step, [])
def testLatticeMap(self):
""" Make sure the lattice map we get correspond to the lattice we give. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 1),
periodic=(True, True, False))
types = [
'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b',
'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a',
'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a',
'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a'
]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['a', 'c', 'b'])
# Get the lattice map.
cpp_lattice_map = config._latticeMap()
# Get the map from the lattice.
cpp_lattice_map_ref = lattice._map()
# Check that these two are references to the same underlying object.
self.assertTrue(cpp_lattice_map == cpp_lattice_map_ref)
def notestTypesBucketFormat(self):
""" Test that the configuration accepts the bucket input format. """
# Define the unit cell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.1, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]]),
basis_points=[[0.0, 0.0, 0.0]])
# And a lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(10, 1, 1),
periodic=(True, False, False))
# Populate the lattice with types.
types = [(2, "A"), "B", ["B", "B", "A"], ["B", (2, "A")], "B", "empty",
[(3, "A")], [(1, "B"), "A"], [(2, "A")], "empty"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['A', 'B', 'empty'])
# Retrieve the types information from the configuration backend.
# FXME: NEEDS IMPLEMENTATION
print config.types()
def testQueryUnitCell(self):
""" Test that the unitcell query function returns correctly. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the repetitions.
nI = 2
nJ = 12
nK = 3
nB = 2
repetitions = (nI, nJ, nK)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Query.
ret_unit_cell = lattice.unitCell()
# Test by reference.
self.assertTrue(unit_cell == ret_unit_cell)
def testConstructionLongFormat(self):
""" Test that the KMCConfiguration class can be constructed with the long types format. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 3, 2),
periodic=(True, True, False))
types = [(0, 0, 0, 0, 'g'), (3, 2, 1, 2, 'h')]
default_type = 'a'
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
default_type=default_type)
# Get the types information out.
ret_types = config.types()
ref_types = [
'g', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a',
'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a',
'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a',
'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a',
'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a',
'a', 'a', 'a', 'a', 'a', 'a', 'h'
]
# Check that they are what we inserted.
self.assertEqual(ref_types, ret_types)
# Check that the possible types are what we expect.
self.assertEqual(set(['a', 'g', 'h', '*']),
set(config._KMCConfiguration__possible_types))
# Check that the number of lattice sites corresponds
# to the lattice.
self.assertEqual(config._KMCConfiguration__n_lattice_sites,
len(lattice.sites()))
# Construct again, now with a list of possible types.
config = KMCConfiguration(lattice=lattice,
types=types,
default_type=default_type,
possible_types=['aa', 'a', 'h', 'g'])
# Check that the possible types are what we expect.
self.assertEqual(set(['aa', 'a', 'g', 'h', '*']),
set(config._KMCConfiguration__possible_types))
def testConstructionFailVectors(self):
""" Make sure construction fails if there is a problem with the unitcell vectors. """
vector_a = [2.3, 0.0, 0.0]
vector_b = [2.4, 3.0, 0.0, 1.3] # <- wrong shape
vector_c = [0.0, 0.0, 11.8]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
cell_vectors = [vector_a, vector_b, vector_c]
self.assertRaises(
Error, lambda: KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points))
def testConstructionShortFormat(self):
""" Test that the KMCConfiguration class can be constructed. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 1),
periodic=(True, True, False))
types = [
'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b',
'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a',
'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a',
'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a'
]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['a', 'c', 'b'])
# Get the types information out.
ret_types = config.types()
# Check that they are what we inserted.
self.assertEqual(types, ret_types)
# Check that the possible types are what we expect.
self.assertEqual(set(['a', 'c', 'b', '*']),
set(config._KMCConfiguration__possible_types.keys()))
# Check that the number of lattice sites corresponds to the lattice.
self.assertEqual(config._KMCConfiguration__n_lattice_sites,
len(lattice.sites()))
# Check that the lattice site can be returned from the configuration.
self.assertAlmostEqual(
numpy.linalg.norm(
numpy.array(config.sites()) - numpy.array(lattice.sites())),
0.0, 10)
# Construct without possible types and check that the list is set correctly
# from the given types.
config = KMCConfiguration(lattice=lattice, types=types)
self.assertEqual(set(['a', 'b', '*']),
set(config._KMCConfiguration__possible_types.keys()))
def testQueryLatticeSites(self):
""" Test that the returned lattice site data is coorect. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the other input.
repetitions = (2, 1, 1)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# These are all the sites in the lattice, given in
# the fractional coordinates of the original cell.
sites = lattice.sites()
ref_sites = numpy.array([[0., 0., 0.], [0.5, 0.5, 0.], [1., 0., 0.],
[1.5, 0.5, 0.]])
# Check against a hardcoded reference.
self.assertAlmostEqual(numpy.linalg.norm(sites - ref_sites), 0.0, 10)
# Test with another repetition.
repetitions = (2, 3, 4)
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
sites = lattice.sites()
ref_sites = numpy.array([[0., 0., 0.], [0.5, 0.5, 0.], [0., 0., 1.],
[0.5, 0.5, 1.], [0., 0., 2.], [0.5, 0.5, 2.],
[0., 0., 3.], [0.5, 0.5, 3.], [0., 1., 0.],
[0.5, 1.5, 0.], [0., 1., 1.], [0.5, 1.5, 1.],
[0., 1., 2.], [0.5, 1.5, 2.], [0., 1., 3.],
[0.5, 1.5, 3.], [0., 2., 0.], [0.5, 2.5, 0.],
[0., 2., 1.], [0.5, 2.5, 1.], [0., 2., 2.],
[0.5, 2.5, 2.], [0., 2., 3.], [0.5, 2.5, 3.],
[1., 0., 0.], [1.5, 0.5, 0.], [1., 0., 1.],
[1.5, 0.5, 1.], [1., 0., 2.], [1.5, 0.5, 2.],
[1., 0., 3.], [1.5, 0.5, 3.], [1., 1., 0.],
[1.5, 1.5, 0.], [1., 1., 1.], [1.5, 1.5, 1.],
[1., 1., 2.], [1.5, 1.5, 2.], [1., 1., 3.],
[1.5, 1.5, 3.], [1., 2., 0.], [1.5, 2.5, 0.],
[1., 2., 1.], [1.5, 2.5, 1.], [1., 2., 2.],
[1.5, 2.5, 2.], [1., 2., 3.], [1.5, 2.5, 3.]])
# Check against a hardcoded reference.
self.assertAlmostEqual(numpy.linalg.norm(sites - ref_sites), 0.0, 10)
def testScript(self):
""" Test that a valid script can be generated. """
# Setup a valid cell.
vector_a = [2.3, 1.0, 0.1]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.4, 0.3, 11.8]
basis_points = [[0.4, 0.3, 0.2], [0.2, 0.33, 0.11], [0.6, 0.5, 0.1]]
cell_vectors = [vector_a, vector_b, vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Get the script.
script = cell._script()
# Check against the known reference script.
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01],
[ 2.400000e+00, 3.000000e+00, 0.000000e+00],
[ 4.000000e-01, 3.000000e-01, 1.180000e+01]]
basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01],
[ 2.000000e-01, 3.300000e-01, 1.100000e-01],
[ 6.000000e-01, 5.000000e-01, 1.000000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
"""
self.assertEqual(script, ref_script)
# Setup another valid cell.
vector_a = [2.3, 1.0, 0.1]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.4, 0.3, 11.8]
basis_points = [[0.4, 0.3, 0.2]]
cell_vectors = [vector_a, vector_b, vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
script = cell._script(variable_name="CELL_NAME_HERE")
# Check against the known reference.
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01],
[ 2.400000e+00, 3.000000e+00, 0.000000e+00],
[ 4.000000e-01, 3.000000e-01, 1.180000e+01]]
basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01]]
CELL_NAME_HERE = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
"""
self.assertEqual(script, ref_script)
def testWriteHeader(self):
""" Test the header output. """
# Get a file name.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory.xyz")
if MPICommons.isMaster():
self.__files_to_remove.append(trajectory_filename)
# Setup the trajectory object.
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, True, True),
repetitions=(4,2,3))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C"]*8)
t = XYZTrajectory(trajectory_filename=trajectory_filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
if MPICommons.isMaster():
# Check that the header was written.
self.assertTrue(os.path.exists(trajectory_filename))
# Check the content of the header.
with open(trajectory_filename, "r") as f:
content = f.read()
ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15
CELL VECTORS
a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00
b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00
c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00
REPETITIONS 4 2 3
PERIODICITY True True True
"""
self.assertEqual( content, ref_content )
def testQueryRepetitionsAndPeriodic(self):
""" Test that the returned repetitions data is coorect. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the repetitions.
repetitions = (2, 1, 1)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Check that the repetitions are the same.
self.assertEqual(lattice.repetitions()[0], repetitions[0])
self.assertEqual(lattice.repetitions()[1], repetitions[1])
self.assertEqual(lattice.repetitions()[2], repetitions[2])
# Check that the periodic is the same.
self.assertTrue(lattice.periodic()[0])
self.assertTrue(lattice.periodic()[1])
self.assertFalse(lattice.periodic()[2])
# Setup again with different periodicity and check.
periodic = (True, False, True)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
self.assertTrue(lattice.periodic()[0])
self.assertFalse(lattice.periodic()[1])
self.assertTrue(lattice.periodic()[2])
# And again.
periodic = (False, True, True)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
self.assertFalse(lattice.periodic()[0])
self.assertTrue(lattice.periodic()[1])
self.assertTrue(lattice.periodic()[2])
def testGetScriptComponent(self):
""" Test the general get script component function. """
# Set the path to the file to read from.
module_path = os.path.abspath(os.path.dirname(__file__))
script_file_path = os.path.join(module_path, "..", "TestUtilities",
"Scripts")
script_file_path = os.path.join(script_file_path,
"kmc_configuration_script.py")
# Make sure the file exists.
self.assertTrue(os.path.exists(script_file_path))
# Get the KMCLattice out of this script.
lattice = getScriptComponent(script_file_path, KMCLattice)
# Check that it is the correct lattice by cheking its values
# against these known references.
unit_cell = KMCUnitCell(cell_vectors=[[2.8, 0.0, 0.0], [0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]],
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
ref_lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 1),
periodic=(True, True, False))
self.assertEqual(lattice.repetitions(), ref_lattice.repetitions())
self.assertEqual(lattice.periodic(), ref_lattice.periodic())
self.assertAlmostEqual(
numpy.linalg.norm(
numpy.array(lattice.sites()) -
numpy.array(ref_lattice.sites())), 0.0, 12)
self.assertEqual(
numpy.linalg.norm(
numpy.array(lattice.basis()) -
numpy.array(ref_lattice.basis())), 0.0, 12)
# Check that the function returns None if no component of the correct type is found.
self.assertTrue(
(getScriptComponent(script_file_path, numpy.ndarray) is None))
# Check that we fail in a controlled way if there is a problme with the file.
self.assertRaises(
Error, lambda: getScriptComponent("THIS IS NOT A VALID PATH", numpy
.ndarray))
def testConstruction(self):
""" Test the construction of the lattice """
# Setup a valid unitcell.
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the other input.
repetitions = (10, 12, 45)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Check that the unitcell object stored on the class
# is the same one as constructed here (checked by reference)
self.assertTrue(unit_cell == lattice._KMCLattice__unit_cell)
def testQueryBasis(self):
""" Test that the returned basis data is coorect. """
cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]]
basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the repetitions.
repetitions = (2, 1, 1)
periodic = (True, True, False)
# Construct the KMCLattice object.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=repetitions,
periodic=periodic)
# Check that the basis is the one from the unitcell.
self.assertAlmostEqual(
numpy.linalg.norm(lattice.basis() -
lattice._KMCLattice__unit_cell.basis()), 0.0, 10)
def testBackend(self):
""" Make sure the C++ backend is what we expect. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 1),
periodic=(True, True, False))
types = [
'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b',
'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a',
'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a',
'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a'
]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=['a', 'c', 'b'])
# Make sure that the backend stored on the config is None.
self.assertTrue(config._KMCConfiguration__backend is None)
# Query for the backend.
cpp_backend = config._backend()
# Check that the backend on the class is returned.
self.assertTrue(config._KMCConfiguration__backend == cpp_backend)
# Check the type of the cpp backend.
self.assertTrue(isinstance(cpp_backend, Backend.Configuration))
def testCalculation(self):
""" Test a calculation with the on-the-fly MSD analysis. """
# Setup a system, a periodic 10 atoms long 1D chain.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0],
[0.0,1.0,0.0],
[0.0,0.0,1.0]]),
basis_points=[[0.0,0.0,0.0]])
# And a lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(10,10,10),
periodic=(True,True,True))
# Setup an initial configuration with one B in a sea of A:s.
types = ["A"]*10*10*10
types[5] = "B"
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=["A","B"])
# Setup a diffusion process to the left.
coordinates_p0 = [[0.0, 0.0, 0.0],[-1.0, 0.0, 0.0]]
p0 = KMCProcess(coordinates=coordinates_p0,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p1 = [[0.0, 0.0, 0.0],[1.0, 0.0, 0.0]]
p1 = KMCProcess(coordinates=coordinates_p1,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p2 = [[0.0, 0.0, 0.0],[0.0,-1.0, 0.0]]
p2 = KMCProcess(coordinates=coordinates_p2,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p3 = [[0.0, 0.0, 0.0],[0.0, 1.0, 0.0]]
p3 = KMCProcess(coordinates=coordinates_p3,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p4 = [[0.0, 0.0, 0.0],[0.0, 0.0,-1.0]]
p4 = KMCProcess(coordinates=coordinates_p4,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p5 = [[0.0, 0.0, 0.0],[0.0, 0.0, 1.0]]
p5 = KMCProcess(coordinates=coordinates_p5,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
interactions = KMCInteractions(processes=[p0, p1, p2, p3, p4, p5],
implicit_wildcards=True)
model = KMCLatticeModel(configuration=config,
interactions=interactions)
# Setup the analysis.
msd = OnTheFlyMSD(history_steps=400,
n_bins=10,
t_max=25.0,
track_type="B")
# Setup the control parameters.
control_parameters = KMCControlParameters(number_of_steps=4000,
dump_interval=100,
analysis_interval=1,
seed=2013)
# Run the model.
model.run(control_parameters=control_parameters,
analysis=[msd])
# Get the results out.
results = msd.results()
time_steps = msd.timeSteps()
std_dev = msd.stdDev()
bin_counters = msd.binCounters()
# Compare against references.
ref_results = numpy.array([[ 2.77712331 , 8.22333156 , 14.21578638 , 21.11949845 , 27.57598537,
33.81520414, 40.5640313 , 47.35067074, 54.83134718, 63.0006103 ],
[ 2.80810946 , 8.48503234 , 13.7997313 , 17.62812205 , 22.37202018,
29.12157221, 35.40750463, 41.44944591, 48.94392653, 56.67111894],
[ 2.98786918 , 8.65022668 , 14.01808716 , 18.62678885 , 22.65708384,
26.03107861, 30.03937616, 35.1483 , 40.68319007, 47.21074474],
[ 5.58523277 , 16.70836389 , 28.01551768 , 38.74762049 , 49.94800555,
62.93677636, 75.97153593, 88.80011665, 103.77527371, 119.67172924],
[ 5.76499249 , 16.87355824 , 28.23387354 , 39.7462873 , 50.23306921,
59.84628275, 70.60340745, 82.49897073, 95.51453725, 110.21135504],
[ 5.79597864 , 17.13525902 , 27.81781846 , 36.2549109 , 45.02910402,
55.15265082, 65.44688079, 76.59774591, 89.62711659, 103.88186368],
[ 8.57310195 , 25.35859057 , 42.03360484 , 57.37440934 , 72.60508939,
88.96785497, 106.01091209, 123.94841665, 144.45846377, 166.88247398]])
diff = numpy.linalg.norm(ref_results - results)
self.assertAlmostEqual(diff, 0.0, 6)
ref_time_steps = numpy.array([ 1.25, 3.75, 6.25, 8.75, 11.25, 13.75, 16.25, 18.75, 21.25, 23.75])
diff = numpy.linalg.norm(ref_time_steps - time_steps)
self.assertAlmostEqual(diff, 0.0, 8)
ref_std_dev = numpy.array( [[ 0.14837207, 0.7305895 , 1.61912818, 2.84016862, 4.19935234,
5.69504607, 7.43238623, 9.31932103, 11.49445671, 13.97165319],
[ 0.15002755, 0.75383991, 1.57174096, 2.37064526, 3.40687718,
4.90455993, 6.48757634, 8.15787162, 10.26025939, 12.5679611 ],
[ 0.15963149, 0.76851636, 1.59661093, 2.50494685, 3.45028752,
4.38406911, 5.5039955 , 6.91771175, 8.52853689, 10.46993274],
[ 0.21100039, 1.04965011, 2.25628521, 3.68460183, 5.37841647,
7.49505328, 9.84289993, 12.35824143, 15.38290727, 18.76634124],
[ 0.2177914 , 1.06002792, 2.27387093, 3.77956739, 5.40911222,
7.12701069, 9.14740325, 11.48131598, 14.15839455, 17.28281115],
[ 0.218962 , 1.07646844, 2.24036311, 3.44756425, 4.84874766,
6.56805258, 8.47932177, 10.66004723, 13.28568526, 16.29025096],
[ 0.26444438, 1.30073885, 2.76405291, 4.45469653, 6.38348309,
8.65082886, 11.21442742, 14.08440462, 17.48404426, 21.36747194]])
diff = numpy.linalg.norm(ref_std_dev - std_dev)
self.assertAlmostEqual(diff, 0.0, 6)
ref_bin_counters = (59930, 59996, 59545, 59256, 59064, 59076, 58284, 58294, 57817, 57349)
self.assertEqual(bin_counters, ref_bin_counters)
def testFlush2(self):
""" Test the file output. """
# Get a file name.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory.xyz")
if MPICommons.isMaster():
self.__files_to_remove.append(trajectory_filename)
# Setup the trajectory object.
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, False, True),
repetitions=(4,4,4))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C","D"]*16)
t = XYZTrajectory(trajectory_filename=trajectory_filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
# Set data directly on the class.
t._XYZTrajectory__atom_id_types = [("A","B","C","D","E"),
("This","is","the","next","step")]
t._XYZTrajectory__atom_id_coordinates = [numpy.zeros((5,3)),
numpy.ones((5,3))*1.234]
t._XYZTrajectory__step = [0, 12]
t._XYZTrajectory__time = [12.123,75.43]
# Flush.
t.flush()
ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15
CELL VECTORS
a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00
b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00
c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00
REPETITIONS 4 4 4
PERIODICITY True False True
STEP 0
5
TIME 1.2123000000e+01
A 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0
B 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1
C 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 2
D 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 3
E 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 4
STEP 12
5
TIME 7.5430000000e+01
This 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 0
is 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 1
the 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 2
next 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 3
step 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 4
"""
if MPICommons.isMaster():
with open(trajectory_filename, "r") as f:
content = f.read()
self.assertEqual( content, ref_content )
# Check that the buffers are empty.
self.assertEqual(t._XYZTrajectory__atom_id_types, [])
self.assertEqual(t._XYZTrajectory__atom_id_coordinates, [])
self.assertEqual(t._XYZTrajectory__time, [])
self.assertEqual(t._XYZTrajectory__step, [])
def testBufferSize(self):
""" Test the buffer size function. """
# Get a file name.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory.xyz")
if MPICommons.isMaster():
self.__files_to_remove.append(trajectory_filename)
# Setup the trajectory object.
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, True, True),
repetitions=(4,4,4))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C","D"]*16)
t = XYZTrajectory(trajectory_filename=trajectory_filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
# Store a bunch of data.
simulation_time = 1.234
step = 123
t._storeData(simulation_time, step, config)
buffer_size = t._bufferSize()
# Check the size again.
ref_size = sys.getsizeof(t._XYZTrajectory__atom_id_coordinates)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_coordinates[0])*len(t._XYZTrajectory__atom_id_coordinates)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types[0])*len(t._XYZTrajectory__atom_id_types)
ref_size += sys.getsizeof(t._XYZTrajectory__time)
ref_size += sys.getsizeof(t._XYZTrajectory__time[0])*len(t._XYZTrajectory__time)
ref_size += sys.getsizeof(t._XYZTrajectory__step)
ref_size += sys.getsizeof(t._XYZTrajectory__step[0])*len(t._XYZTrajectory__step)
self.assertEqual(buffer_size, ref_size)
# Store more data.
t._storeData(simulation_time, step, config)
# Check the size again.
t._storeData(simulation_time, step, config)
t._storeData(simulation_time, step, config)
t._storeData(simulation_time, step, config)
t._storeData(simulation_time, step, config)
t._storeData(simulation_time, step, config)
ref_size = sys.getsizeof(t._XYZTrajectory__atom_id_coordinates)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_coordinates[0])*len(t._XYZTrajectory__atom_id_coordinates)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types)
ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types[0])*len(t._XYZTrajectory__atom_id_types)
ref_size += sys.getsizeof(t._XYZTrajectory__time)
ref_size += sys.getsizeof(t._XYZTrajectory__time[0])*len(t._XYZTrajectory__time)
ref_size += sys.getsizeof(t._XYZTrajectory__step)
ref_size += sys.getsizeof(t._XYZTrajectory__step[0])*len(t._XYZTrajectory__step)
buffer_size = t._bufferSize()
self.assertEqual(buffer_size, ref_size)
def testFlush(self):
""" Test the file output. """
# Get a file name.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory.xyz")
if MPICommons.isMaster():
self.__files_to_remove.append(trajectory_filename)
# Setup the trajectory object.
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, False, True),
repetitions=(4,4,4))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C","D"]*16)
t = XYZTrajectory(trajectory_filename=trajectory_filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
# Store data.
simulation_time = 1.234
step = 123
t._storeData(simulation_time, step, config)
# Flush.
t.flush()
# Check the file.
ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15
CELL VECTORS
a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00
b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00
c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00
REPETITIONS 4 4 4
PERIODICITY True False True
STEP 123
64
TIME 1.2340000000e+00
A 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0
B 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 1
C 0.0000000000e+00 0.0000000000e+00 2.0000000000e+00 2
D 0.0000000000e+00 0.0000000000e+00 3.0000000000e+00 3
A 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 4
B 0.0000000000e+00 1.0000000000e+00 1.0000000000e+00 5
C 0.0000000000e+00 1.0000000000e+00 2.0000000000e+00 6
D 0.0000000000e+00 1.0000000000e+00 3.0000000000e+00 7
A 0.0000000000e+00 2.0000000000e+00 0.0000000000e+00 8
B 0.0000000000e+00 2.0000000000e+00 1.0000000000e+00 9
C 0.0000000000e+00 2.0000000000e+00 2.0000000000e+00 10
D 0.0000000000e+00 2.0000000000e+00 3.0000000000e+00 11
A 0.0000000000e+00 3.0000000000e+00 0.0000000000e+00 12
B 0.0000000000e+00 3.0000000000e+00 1.0000000000e+00 13
C 0.0000000000e+00 3.0000000000e+00 2.0000000000e+00 14
D 0.0000000000e+00 3.0000000000e+00 3.0000000000e+00 15
A 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 16
B 1.0000000000e+00 0.0000000000e+00 1.0000000000e+00 17
C 1.0000000000e+00 0.0000000000e+00 2.0000000000e+00 18
D 1.0000000000e+00 0.0000000000e+00 3.0000000000e+00 19
A 1.0000000000e+00 1.0000000000e+00 0.0000000000e+00 20
B 1.0000000000e+00 1.0000000000e+00 1.0000000000e+00 21
C 1.0000000000e+00 1.0000000000e+00 2.0000000000e+00 22
D 1.0000000000e+00 1.0000000000e+00 3.0000000000e+00 23
A 1.0000000000e+00 2.0000000000e+00 0.0000000000e+00 24
B 1.0000000000e+00 2.0000000000e+00 1.0000000000e+00 25
C 1.0000000000e+00 2.0000000000e+00 2.0000000000e+00 26
D 1.0000000000e+00 2.0000000000e+00 3.0000000000e+00 27
A 1.0000000000e+00 3.0000000000e+00 0.0000000000e+00 28
B 1.0000000000e+00 3.0000000000e+00 1.0000000000e+00 29
C 1.0000000000e+00 3.0000000000e+00 2.0000000000e+00 30
D 1.0000000000e+00 3.0000000000e+00 3.0000000000e+00 31
A 2.0000000000e+00 0.0000000000e+00 0.0000000000e+00 32
B 2.0000000000e+00 0.0000000000e+00 1.0000000000e+00 33
C 2.0000000000e+00 0.0000000000e+00 2.0000000000e+00 34
D 2.0000000000e+00 0.0000000000e+00 3.0000000000e+00 35
A 2.0000000000e+00 1.0000000000e+00 0.0000000000e+00 36
B 2.0000000000e+00 1.0000000000e+00 1.0000000000e+00 37
C 2.0000000000e+00 1.0000000000e+00 2.0000000000e+00 38
D 2.0000000000e+00 1.0000000000e+00 3.0000000000e+00 39
A 2.0000000000e+00 2.0000000000e+00 0.0000000000e+00 40
B 2.0000000000e+00 2.0000000000e+00 1.0000000000e+00 41
C 2.0000000000e+00 2.0000000000e+00 2.0000000000e+00 42
D 2.0000000000e+00 2.0000000000e+00 3.0000000000e+00 43
A 2.0000000000e+00 3.0000000000e+00 0.0000000000e+00 44
B 2.0000000000e+00 3.0000000000e+00 1.0000000000e+00 45
C 2.0000000000e+00 3.0000000000e+00 2.0000000000e+00 46
D 2.0000000000e+00 3.0000000000e+00 3.0000000000e+00 47
A 3.0000000000e+00 0.0000000000e+00 0.0000000000e+00 48
B 3.0000000000e+00 0.0000000000e+00 1.0000000000e+00 49
C 3.0000000000e+00 0.0000000000e+00 2.0000000000e+00 50
D 3.0000000000e+00 0.0000000000e+00 3.0000000000e+00 51
A 3.0000000000e+00 1.0000000000e+00 0.0000000000e+00 52
B 3.0000000000e+00 1.0000000000e+00 1.0000000000e+00 53
C 3.0000000000e+00 1.0000000000e+00 2.0000000000e+00 54
D 3.0000000000e+00 1.0000000000e+00 3.0000000000e+00 55
A 3.0000000000e+00 2.0000000000e+00 0.0000000000e+00 56
B 3.0000000000e+00 2.0000000000e+00 1.0000000000e+00 57
C 3.0000000000e+00 2.0000000000e+00 2.0000000000e+00 58
D 3.0000000000e+00 2.0000000000e+00 3.0000000000e+00 59
A 3.0000000000e+00 3.0000000000e+00 0.0000000000e+00 60
B 3.0000000000e+00 3.0000000000e+00 1.0000000000e+00 61
C 3.0000000000e+00 3.0000000000e+00 2.0000000000e+00 62
D 3.0000000000e+00 3.0000000000e+00 3.0000000000e+00 63
"""
if MPICommons.isMaster():
with open(trajectory_filename, "r") as f:
content = f.read()
self.assertEqual( content, ref_content )
# Check that the buffers are empty.
self.assertEqual(t._XYZTrajectory__atom_id_types, [])
self.assertEqual(t._XYZTrajectory__atom_id_coordinates, [])
self.assertEqual(t._XYZTrajectory__time, [])
self.assertEqual(t._XYZTrajectory__step, [])
def testStoreData(self):
""" Test the data storage function. """
# Get a file name.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory.xyz")
if MPICommons.isMaster():
self.__files_to_remove.append(trajectory_filename)
# Setup the trajectory object.
unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]],
basis_points=[[0.0, 0.0, 0.0]])
lattice = KMCLattice(unit_cell=unit_cell,
periodic=(True, True, True),
repetitions=(4,4,4))
config = KMCConfiguration(lattice=lattice,
types=["A","B","C","D"]*16)
t = XYZTrajectory(trajectory_filename=trajectory_filename,
configuration=config,
max_buffer_size=12345,
max_buffer_time=123.0)
# Construct data to store.
simulation_time = 1.234
step = 123
configuration = config
# Store.
t._storeData(simulation_time, step, configuration)
# Check that the member data was updated.
self.assertEqual(len(t._XYZTrajectory__atom_id_types), 1)
self.assertEqual(len(t._XYZTrajectory__atom_id_coordinates), 1)
self.assertEqual(len(t._XYZTrajectory__time), 1)
self.assertEqual(len(t._XYZTrajectory__step), 1)
# store again.
simulation_time = 1.999
step = 4444
t._storeData(simulation_time, step, configuration)
# Check that the member data was updated.
self.assertEqual(len(t._XYZTrajectory__atom_id_types), 2)
self.assertEqual(len(t._XYZTrajectory__atom_id_coordinates), 2)
self.assertEqual(len(t._XYZTrajectory__time), 2)
self.assertEqual(len(t._XYZTrajectory__step), 2)
# Check the values of the stored data.
self.assertAlmostEqual(t._XYZTrajectory__time[0], 1.234, 10)
self.assertAlmostEqual(t._XYZTrajectory__time[1], 1.999, 10)
self.assertEqual(t._XYZTrajectory__step[0], 123)
self.assertEqual(t._XYZTrajectory__step[1], 4444)
diff = numpy.linalg.norm(config.atomIDCoordinates() - t._XYZTrajectory__atom_id_coordinates[0])
self.assertAlmostEqual(diff, 0.0, 10)
diff = numpy.linalg.norm(config.atomIDCoordinates() - t._XYZTrajectory__atom_id_coordinates[1])
self.assertAlmostEqual(diff, 0.0, 10)
self.assertEqual(t._XYZTrajectory__atom_id_types[0], config.atomIDTypes())
self.assertEqual(t._XYZTrajectory__atom_id_types[1], config.atomIDTypes())
def testFinalizeWithCoordinateTransform(self):
""" Test finalization. """
msd = OnTheFlyMSD.__new__(OnTheFlyMSD)
# Replace the getBackendResults function.
def dummy():
pass
msd._OnTheFlyMSD__getBackendResults = dummy
# Set a unitcell on the class.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0],
[0.0,1.0,0.0],
[0.0,0.0,1.0]]),
basis_points=[[0.0,0.0,0.0]])
msd._OnTheFlyMSD__unit_cell = unit_cell
# Set the values.
msd._OnTheFlyMSD__raw_histogram = numpy.array([[ 171144., 173906., 188389.],
[ 516721., 497558., 536213.],
[ 851961., 810151., 836426.],
[ 1195930., 1046238., 1111184.],
[ 1507650., 1366678., 1434213.],
[ 1780731., 1743443., 1719186.],
[ 2155426., 2154562., 1980822.],
[ 2554205., 2604757., 2354967.],
[ 2954351., 3032799., 2698023.],
[ 3372070., 3443433., 3158002.]])
bin_counters = (60283, 60628, 60461, 59779, 59683, 59178, 58856, 58752, 58162, 57881)
msd._OnTheFlyMSD__bin_counters = bin_counters
msd._OnTheFlyMSD__n_bins = 10
msd._OnTheFlyMSD__binsize = 2.5
hstep_counts = [8919,8918,8917,8916,8915,8914,8913,8912,8911,8910,8099,8908,8907,8906,8905,8904,8903,8902,8901]
msd._OnTheFlyMSD__hstep_counts = hstep_counts
history_bin_counters = [(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
(0, 0, 0, 0, 0, 1, 87, 58752, 58162, 57881)]
msd._OnTheFlyMSD__history_bin_counters = history_bin_counters
msd._OnTheFlyMSD__n_eff = [1.12, 2.24, 3.36, 4.48, 5.60, 6.72, 7.84, 8.96, 9.0, 10.12]
# Call the finalize function.
msd.finalize()
# Check a few results.
result_0_3 = 1195930. / 59779.0
self.assertAlmostEqual(result_0_3, msd._OnTheFlyMSD__results[0][3], 10)
result_1_7 = 2604757.0 / 58752.0
self.assertAlmostEqual(result_1_7, msd._OnTheFlyMSD__results[1][7], 10)
result_2_0 = 188389.0 / 60283.0
self.assertAlmostEqual(result_2_0, msd._OnTheFlyMSD__results[2][0], 10)
result_3_4 = ( 1507650.0 + 1366678.0) / 59683.0
self.assertAlmostEqual(result_3_4, msd._OnTheFlyMSD__results[3][4], 10)
result_4_4 = ( 1507650.0 + 1434213.0) / 59683.0
self.assertAlmostEqual(result_4_4, msd._OnTheFlyMSD__results[4][4], 10)
result_5_6 = ( 2154562.0 + 1980822.0) / 58856.0
self.assertAlmostEqual(result_5_6, msd._OnTheFlyMSD__results[5][6], 10)
result_6_5 = ( 1780731.0 + 1743443.0 + 1719186.0)/ 59178.0
self.assertAlmostEqual(result_6_5, msd._OnTheFlyMSD__results[6][5], 10)
# Check the corresponding standard deviation against hardcoded values.
std_0_3 = 42.291401180595834
std_1_7 = 0.813230156401512
std_2_0 = 6.634050132990601
std_3_4 = 71.931090096615776
std_4_4 = 73.621177716983027
std_5_6 = 7.877909031669120
std_6_5 = 62.119638306131414
self.assertAlmostEqual(std_0_3, msd._OnTheFlyMSD__std_dev[0][3], 10)
self.assertAlmostEqual(std_1_7, msd._OnTheFlyMSD__std_dev[1][7], 10)
self.assertAlmostEqual(std_2_0, msd._OnTheFlyMSD__std_dev[2][0], 10)
self.assertAlmostEqual(std_3_4, msd._OnTheFlyMSD__std_dev[3][4], 10)
self.assertAlmostEqual(std_4_4, msd._OnTheFlyMSD__std_dev[4][4], 10)
self.assertAlmostEqual(std_5_6, msd._OnTheFlyMSD__std_dev[5][6], 10)
self.assertAlmostEqual(std_6_5, msd._OnTheFlyMSD__std_dev[6][5], 10)
def testFinalizeNoCoordinateTransform(self):
""" Test finalization. """
msd = OnTheFlyMSD.__new__(OnTheFlyMSD)
# Replace the getBackendResults function.
def dummy():
pass
msd._OnTheFlyMSD__getBackendResults = dummy
# Set a unitcell on the class.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0],
[0.0,1.0,0.0],
[0.0,0.0,1.0]]),
basis_points=[[0.0,0.0,0.0]])
msd._OnTheFlyMSD__unit_cell = unit_cell
# Set the values.
msd._OnTheFlyMSD__raw_histogram = numpy.array([[ 171144., 173906., 188389.],
[ 516721., 497558., 536213.],
[ 851961., 810151., 836426.],
[ 1195930., 1046238., 1111184.],
[ 1507650., 1366678., 1434213.],
[ 1780731., 1743443., 1719186.],
[ 2155426., 2154562., 1980822.],
[ 2554205., 2604757., 2354967.],
[ 2954351., 3032799., 2698023.],
[ 3372070., 3443433., 3158002.]])
bin_counters = (60283, 60628, 60461, 59779, 59683, 59178, 58856, 58752, 58162, 57881)
msd._OnTheFlyMSD__bin_counters = bin_counters
msd._OnTheFlyMSD__n_bins = 10
msd._OnTheFlyMSD__binsize = 2.5
hstep_counts = [8919,8918,8917,8916,8915,8914,8913,8912,8911,8910,8099,8908,8907,8906,8905,8904,8903,8902,8901]
msd._OnTheFlyMSD__hstep_counts = hstep_counts
history_bin_counters = [(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
(0, 0, 0, 0, 0, 1, 87, 58752, 58162, 57881)]
msd._OnTheFlyMSD__history_bin_counters = history_bin_counters
msd._OnTheFlyMSD__n_eff = [1.12, 2.24, 3.36, 4.48, 5.60, 6.72, 7.84, 8.96, 9.0, 10.12]
# Call the finalize function.
msd.finalize()
# Check a few results.
result_0_3 = 1195930. / 59779.0
self.assertAlmostEqual(result_0_3, msd._OnTheFlyMSD__results[0][3], 10)
result_1_7 = 2604757.0 / 58752.0
self.assertAlmostEqual(result_1_7, msd._OnTheFlyMSD__results[1][7], 10)
result_2_0 = 188389.0 / 60283.0
self.assertAlmostEqual(result_2_0, msd._OnTheFlyMSD__results[2][0], 10)
# Check the corresponding standard deviation.
n_eff = numpy.zeros(10)
for i in range(len(n_eff)):
for b in range(len(history_bin_counters)):
fraction = float(history_bin_counters[b][i]) / float(bin_counters[i])
n_eff[i] += fraction * (b+1.0)
K1 = hstep_counts[int(n_eff[3]+1)]
K2 = K1*K1
std_0_3 = result_0_3 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[3]*n_eff[3]*K1 + 2*K1 + n_eff[3] - n_eff[3]*n_eff[3]*n_eff[3])/(n_eff[3]*6*K2))
self.assertAlmostEqual(std_0_3, msd._OnTheFlyMSD__std_dev[0][3], 10)
K1 = hstep_counts[int(n_eff[7]+1)]
K2 = K1*K1
std_1_7 = result_1_7 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[7]*n_eff[7]*K1 + 2*K1 + n_eff[7] - n_eff[7]*n_eff[7]*n_eff[7])/(n_eff[7]*6*K2))
self.assertAlmostEqual(std_1_7, msd._OnTheFlyMSD__std_dev[1][7], 10)
K1 = hstep_counts[int(n_eff[0]+1)]
K2 = K1*K1
std_2_0 = result_2_0 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[0]*n_eff[0]*K1 + 2*K1 + n_eff[0] - n_eff[0]*n_eff[0]*n_eff[0])/(n_eff[0]*6*K2))
self.assertAlmostEqual(std_2_0, msd._OnTheFlyMSD__std_dev[2][0], 10)
def testScript(self):
""" Test that a valid script can be generated. """
# Setup a valid cell.
vector_a = [2.3, 1.0, 0.1]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.4, 0.3, 11.8]
basis_points = [[0.4, 0.3, 0.2],
[0.2, 0.33, 0.11],
[0.6, 0.5, 0.1]]
cell_vectors = [vector_a,
vector_b,
vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Get the script.
script = cell._script()
# Check against the known reference script.
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01],
[ 2.400000e+00, 3.000000e+00, 0.000000e+00],
[ 4.000000e-01, 3.000000e-01, 1.180000e+01]]
basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01],
[ 2.000000e-01, 3.300000e-01, 1.100000e-01],
[ 6.000000e-01, 5.000000e-01, 1.000000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
"""
self.assertEqual(script, ref_script)
# Setup another valid cell.
vector_a = [2.3, 1.0, 0.1]
vector_b = [2.4, 3.0, 0.0]
vector_c = [0.4, 0.3, 11.8]
basis_points = [[0.4, 0.3, 0.2]]
cell_vectors = [vector_a,
vector_b,
vector_c]
cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
script = cell._script(variable_name="CELL_NAME_HERE")
# Check against the known reference.
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01],
[ 2.400000e+00, 3.000000e+00, 0.000000e+00],
[ 4.000000e-01, 3.000000e-01, 1.180000e+01]]
basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01]]
CELL_NAME_HERE = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
"""
self.assertEqual(script, ref_script)
def testCalculationNonOrthogonal(self):
""" Test a calculation with the on-the-fly MSD analysis. """
# Setup a system, a periodic 10 atoms long 1D chain.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.0,1.0,0.0],
[0.0,1.0,0.0],
[0.0,2.0,1.0]]),
basis_points=[[0.0,0.0,0.0]])
# And a lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(10,10,10),
periodic=(True,True,True))
# Setup an initial configuration with one B in a sea of A:s.
types = ["A"]*10*10*10
types[5] = "B"
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=["A","B"])
# Setup a diffusion process to the left.
coordinates_p0 = [[0.0, 0.0, 0.0],[-1.0, 0.0, 0.0]]
p0 = KMCProcess(coordinates=coordinates_p0,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p1 = [[0.0, 0.0, 0.0],[1.0, 0.0, 0.0]]
p1 = KMCProcess(coordinates=coordinates_p1,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p2 = [[0.0, 0.0, 0.0],[0.0,-1.0, 0.0]]
p2 = KMCProcess(coordinates=coordinates_p2,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p3 = [[0.0, 0.0, 0.0],[0.0, 1.0, 0.0]]
p3 = KMCProcess(coordinates=coordinates_p3,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p4 = [[0.0, 0.0, 0.0],[0.0, 0.0,-1.0]]
p4 = KMCProcess(coordinates=coordinates_p4,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
coordinates_p5 = [[0.0, 0.0, 0.0],[0.0, 0.0, 1.0]]
p5 = KMCProcess(coordinates=coordinates_p5,
elements_before=["B","A"],
elements_after=["A","B"],
move_vectors=None,
basis_sites=[0],
rate_constant=1.0)
interactions = KMCInteractions(processes=[p0, p1, p2, p3, p4, p5],
implicit_wildcards=True)
model = KMCLatticeModel(configuration=config,
interactions=interactions)
# Setup the analysis.
msd = OnTheFlyMSD(history_steps=400,
n_bins=10,
t_max=25.0,
track_type="B")
# Setup the control parameters.
control_parameters = KMCControlParameters(number_of_steps=4000,
dump_interval=100,
analysis_interval=1,
seed=2013)
# Run the model.
model.run(control_parameters=control_parameters,
analysis=[msd])
# Get the results out.
results = msd.results()
time_steps = msd.timeSteps()
std_dev = msd.stdDev()
bin_counters = msd.binCounters()
# Compare against references.
ref_results = numpy.array([[ 11.10849324 , 32.89332622 , 56.86314552 , 84.47799379 , 110.30394149,
135.26081658, 162.25612518, 189.40268295, 219.32538873, 252.00244119],
[ 17.33153679 , 50.69982999 , 82.74958435 , 111.33382274 , 136.44824258,
164.84499628, 193.94367236, 234.25340515, 272.64453361, 302.94924061],
[ 2.98786918 , 8.65022668 , 14.01808716 , 18.62678885 , 22.65708384,
26.03107861, 30.03937616, 35.1483 , 40.68319007, 47.21074474],
[ 28.44003004 , 83.59315621 , 139.61272987 , 195.81181652 , 246.75218407,
300.10581285, 356.19979754, 423.65608811, 491.96992234, 554.95168181],
[ 14.09636242 , 41.5435529 , 70.88123268 , 103.10478264 , 132.96102533,
161.29189519, 192.29550134, 224.55098295, 260.00857879, 299.21318593],
[ 20.31940597 , 59.35005667 , 96.76767151 , 129.96061158 , 159.10532643,
190.87607489, 223.98304852, 269.40170515, 313.32772368, 350.15998535],
[ 31.42789922 , 92.24338289 , 153.63081703 , 214.43860537 , 269.40926791,
326.13689146, 386.2391737 , 458.8043881 , 532.65311241, 602.16242655]])
diff = numpy.linalg.norm(ref_results - results)
self.assertAlmostEqual(diff, 0.0, 6)
ref_time_steps = numpy.array([ 1.25, 3.75, 6.25, 8.75, 11.25, 13.75, 16.25, 18.75, 21.25, 23.75])
diff = numpy.linalg.norm(ref_time_steps - time_steps)
self.assertAlmostEqual(diff, 0.0, 8)
ref_std_dev = numpy.array([[ 0.59348826 , 2.92235801 , 6.47651272 , 11.36067446 , 16.79740936,
22.78018427, 29.72954492, 37.27728411, 45.97782684, 55.88661276],
[ 0.92596389 , 4.50435001 , 9.42488725 , 14.97226982 , 20.7787406,
27.76265504, 35.53552825, 46.10457783, 57.15527613, 67.18509081],
[ 0.15963149 , 0.76851636 , 1.59661093 , 2.50494685 , 3.45028752,
4.38406911 , 5.5039955 , 6.91771175 , 8.52853689 , 10.46993274],
[ 1.07441492 , 5.2514756 , 11.24398775 , 18.62020347 , 26.57035045,
35.73918442, 46.14937581, 58.95988 , 72.92611647, 87.02483617],
[ 0.53253608 , 2.60984229 , 5.70856048 , 9.80447485 , 14.31728377,
19.20802777, 24.91387536, 31.25058126, 38.54181941, 46.9211633 ],
[ 0.76763185 , 3.72847956 , 7.7933761 , 12.35825842 , 17.13251009,
22.73116664, 29.01932554, 37.49242051, 46.4454696 , 54.91039375],
[ 0.96941939 , 4.731515 , 10.1024813 , 16.6495642 , 23.68662473,
31.71206536, 40.85854085, 52.13448317, 64.46787783, 77.10029967]])
diff = numpy.linalg.norm(ref_std_dev - std_dev)
self.assertAlmostEqual(diff, 0.0, 6)
ref_bin_counters = (59930, 59996, 59545, 59256, 59064, 59076, 58284, 58294, 57817, 57349)
self.assertEqual(bin_counters, ref_bin_counters)
