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 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 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 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 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 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 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 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) )
