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 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 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 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()))
