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 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 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 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 testQueries(self):
""" Test the configuration's query functions. """
config = KMCConfiguration.__new__(KMCConfiguration)
c0_ref = numpy.random.random()
c1_ref = numpy.random.random()
c2_ref = numpy.random.random()
# Set the backend proxy.
class BackendProxy(object):
def __init__(self):
pass
def elements(self):
return ("B", "F", "A")
def atomIDElements(self):
return ("A", "B", "F")
def atomIDCoordinates(self):
return (Backend.Coordinate(c0_ref, c1_ref, c2_ref), )
config._KMCConfiguration__backend = BackendProxy()
# Query and check.
atom_id_types = config.atomIDTypes()
atom_id_coords = config.atomIDCoordinates()
lattice_types = config.types()
self.assertEqual(atom_id_types, ("A", "B", "F"))
self.assertEqual(lattice_types, ["B", "F", "A"])
self.assertAlmostEqual(atom_id_coords[0][0], c0_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][1], c1_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][2], c2_ref, 10)
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 testQueries(self):
""" Test the configuration's query functions. """
config = KMCConfiguration.__new__(KMCConfiguration)
c0_ref = numpy.random.random()
c1_ref = numpy.random.random()
c2_ref = numpy.random.random()
# Set the backend proxy.
class BackendProxy(object):
def __init__(self):
pass
def elements(self):
return ("B", "F", "A")
def atomIDElements(self):
return ("A", "B", "F")
def atomIDCoordinates(self):
return (Backend.Coordinate(c0_ref,c1_ref,c2_ref),)
config._KMCConfiguration__backend = BackendProxy()
# Query and check.
atom_id_types = config.atomIDTypes()
atom_id_coords = config.atomIDCoordinates()
lattice_types = config.types()
self.assertEqual(atom_id_types, ("A","B","F"))
self.assertEqual(lattice_types, ["B","F","A"])
self.assertAlmostEqual(atom_id_coords[0][0], c0_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][1], c1_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][2], c2_ref, 10)
def testQueries(self):
""" Test the configuration's query functions. """
config = KMCConfiguration.__new__(KMCConfiguration)
config._KMCConfiguration__use_buckets = False
c0_ref = numpy.random.random()
c1_ref = numpy.random.random()
c2_ref = numpy.random.random()
# Set the backend proxy.
class BackendProxy(object):
def __init__(self):
pass
def elements(self):
return ("B", "F", "A")
def atomIDElements(self):
return ("A", "B", "F")
def atomIDCoordinates(self):
return (Backend.Coordinate(c0_ref, c1_ref, c2_ref), )
def movedAtomIDs(self):
return (123, 234)
def latestEventProcess(self):
return 995976943
def latestEventSite(self):
return 556462676
def particlesPerType(self):
return (123, 467, 432)
config._KMCConfiguration__backend = BackendProxy()
# Query and check.
atom_id_types = config.atomIDTypes()
atom_id_coords = config.atomIDCoordinates()
lattice_types = config.types()
moved_atom_ids = config.movedAtomIDs()
latest_event_process = config.latestEventProcess()
latest_event_site = config.latestEventSite()
particles_per_type = config.particlesPerType()
self.assertEqual(atom_id_types, ("A", "B", "F"))
self.assertEqual(lattice_types, ["B", "F", "A"])
self.assertAlmostEqual(atom_id_coords[0][0], c0_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][1], c1_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][2], c2_ref, 10)
self.assertEqual(moved_atom_ids, (123, 234))
self.assertEqual(latest_event_process, 995976943)
self.assertEqual(latest_event_site, 556462676)
self.assertEqual(particles_per_type, (123, 467, 432))
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 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 testQueries(self):
""" Test the configuration's query functions. """
config = KMCConfiguration.__new__(KMCConfiguration)
config._KMCConfiguration__use_buckets = False
c0_ref = numpy.random.random()
c1_ref = numpy.random.random()
c2_ref = numpy.random.random()
# Set the backend proxy.
class BackendProxy(object):
def __init__(self):
pass
def elements(self):
return ("B", "F", "A")
def atomIDElements(self):
return ("A", "B", "F")
def atomIDCoordinates(self):
return (Backend.Coordinate(c0_ref,c1_ref,c2_ref),)
def movedAtomIDs(self):
return (123, 234)
def latestEventProcess(self):
return 995976943
def latestEventSite(self):
return 556462676
def particlesPerType(self):
return (123, 467, 432)
config._KMCConfiguration__backend = BackendProxy()
# Query and check.
atom_id_types = config.atomIDTypes()
atom_id_coords = config.atomIDCoordinates()
lattice_types = config.types()
moved_atom_ids = config.movedAtomIDs()
latest_event_process = config.latestEventProcess()
latest_event_site = config.latestEventSite()
particles_per_type = config.particlesPerType()
self.assertEqual(atom_id_types, ("A","B","F"))
self.assertEqual(lattice_types, ["B","F","A"])
self.assertAlmostEqual(atom_id_coords[0][0], c0_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][1], c1_ref, 10)
self.assertAlmostEqual(atom_id_coords[0][2], c2_ref, 10)
self.assertEqual(moved_atom_ids, (123, 234))
self.assertEqual(latest_event_process, 995976943)
self.assertEqual(latest_event_site, 556462676)
self.assertEqual(particles_per_type, (123, 467, 432))
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 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 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 testScript(self):
""" Test that we can generate a valid script. """
# 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 script.
script = config._script()
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 5.000000e-01, 5.000000e-01, 5.000000e-01],
[ 2.500000e-01, 2.500000e-01, 7.500000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# -----------------------------------------------------------------------------
# Configuration
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']
possible_types = ['a','c','b']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
"""
self.assertEqual(script, ref_script)
# Try another one.
# 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]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1,1,1),
periodic=(False,False,False))
types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']
possible_types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure', "A", "B", "CDEFGHI"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Get the script.
script = config._script(variable_name="config")
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(1,1,1),
periodic=(False, False, False))
# -----------------------------------------------------------------------------
# Configuration
types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']
possible_types = ['A','CDEFGHI','ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',
'B']
config = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
"""
self.assertEqual(script, ref_script)
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 testConstructionFailLongFormat(self):
""" Test everything that can go wrong when constructing with the long fomat. """
# 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)
# This fails because the lattice is of wrong type.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=unit_cell, types=types, default_type=default_type))
# This fails because no default type is given.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice, types=types))
# This fails because no default type is not a string.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types, default_type=['a']))
# This fails because the possible types are not set correctly.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice,
types=types,
default_type=default_type,
possible_types="agh"))
# This fails because there are types missing in the possible types.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice,
types=types,
default_type=default_type,
possible_types=['a', 'h']))
# This fails because there is a wildcard character in the possible types list.
self.assertRaises(
Error,
lambda: KMCConfiguration(lattice=lattice,
types=types,
default_type=default_type,
possible_types=['g', 'a', '*', 'h']))
types_1 = [123, 345]
# This fails because of wrong type in the types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (0, 0, 0, 'a')]
# This fails because of wrong type in the types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (0, 0, 0, 1, 'b', 3)]
# This fails because of wrong type in the types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [[0, 0, 0, 0, 'a'], [0, 0, 0, 1, 'b']]
# This fails because of wrong type in the types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (-1, 0, 0, 0, 'b')]
# This fails because of a negative first index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(100, 0, 0, 0, 'a'), (0, 0, 0, 0, 'b')]
# This fails because of a too large firs index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (0, -1, 0, 0, 'b')]
# This fails because of a negative second index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 100, 0, 0, 'a'), (0, 0, 0, 1, 'b')]
# This fails because of a too large second index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (0, 0, -1, 0, 'b')]
# This fails because of a negative third index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 100, 0, 'a'), (0, 0, 0, 0, 'b')]
# This fails because of a too large third index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 0, 'a'), (0, 0, 0, -1, 'b')]
# This fails because of a negative fourth index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
types_1 = [(0, 0, 0, 100, 'a'), (0, 0, 0, 1, 'b')]
# This fails because of a too large fourth index.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types_1, default_type=default_type))
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 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 testConstructionFailShort(self):
""" Test every thing that should fail when using the short 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 = [
'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'
]
default_type = 'a'
# This fails because the lattice is of wrong type.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=unit_cell, types=types))
# This fails because there is a default type given.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types, default_type=default_type))
# This fails becaulse of wrong length of the types.
types_1 = ['g', 'a', 'a']
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice, types=types_1))
types_1 = [
'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', 3, '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', 1
]
# This fails because of the wrong type of the types information.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice, types=types_1))
types_1 = "ABCDE"
# And this also.
self.assertRaises(
Error, lambda: KMCConfiguration(lattice=lattice, types=types_1))
# Use an incompatible possible types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types, possible_types=['a']))
# Use an incompatible possible types list.
self.assertRaises(
Error, lambda: KMCConfiguration(
lattice=lattice, types=types, possible_types="ABCD"))
# Use a possible types list with a wildcard.
self.assertRaises(
Error,
lambda: KMCConfiguration(lattice=lattice,
types=types,
possible_types=['g', 'a', 'h', '*']))
def testRunRngTypeDevice(self):
""" Test to use the PRNG DEVICE. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*16
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates,
['A'],
['B'],
basis_sites=[0],
rate_constant=4.0)
process_1 = KMCProcess(coordinates,
['B'],
['A'],
basis_sites=[0],
rate_constant=1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Setup the model.
ab_flip_model_DEVICE = KMCLatticeModel(configuration, interactions)
support_device = False
if (not support_device):
# If DEVICE is not supported on your system this is the test you should run.
self.assertRaises( Error,
lambda: ab_flip_model_DEVICE.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="DEVICE")))
else:
# If DEVICE is supported the aboove test will fail, and you should run this tests instead.
# Run the model for 10000 steps with DEVICE.
ab_flip_model_DEVICE.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="DEVICE"))
# Get the simulation time out.
t_DEVICE = ab_flip_model_DEVICE._KMCLatticeModel__cpp_timer.simulationTime()
self.assertTrue(t_DEVICE < 410.0 and t_DEVICE > 370.0)
def testConstruction(self):
""" Test the construction of the lattice model """
# Setup a unitcell.
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'])
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
sites = [0,1,2]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# A second process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","C"]
types1 = ["C","A"]
sites = [0,1,2]
rate_0_1 = 1.5
process_1 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# Construct the interactions object.
processes = [process_0, process_1]
interactions = KMCInteractions(processes=processes)
# Construct the model.
model = KMCLatticeModel(config, interactions)
# Check that it has the attribute _backend which is None
self.assertTrue(hasattr(model,"_KMCLatticeModel__backend"))
self.assertTrue(model._KMCLatticeModel__backend is None)
# Check that it has the correct interactions stored.
self.assertTrue(model._KMCLatticeModel__interactions == interactions)
# Check that it has the correct configuration stored.
self.assertTrue(model._KMCLatticeModel__configuration == config)
def testRunTrajectory(self):
""" Test the run of an A-B flip model with trajectory output. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*16
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates,
['A'],
['B'],
basis_sites=[0],
rate_constant=4.0)
process_1 = KMCProcess(coordinates,
['B'],
['A'],
basis_sites=[0],
rate_constant=1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Setup the model.
ab_flip_model = KMCLatticeModel(configuration, interactions)
# Construct the trajectory fileames.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "TestUtilities", "Scratch")
lattice_trajectory_filename = os.path.join(name, "ab_flip_traj_lattice.py")
xyz_trajectory_filename = os.path.join(name, "ab_flip_traj_xyz.xyz")
self.__files_to_remove.append(lattice_trajectory_filename)
self.__files_to_remove.append(xyz_trajectory_filename)
# The control parameters.
control_parameters = KMCControlParameters(number_of_steps=1000,
dump_interval=500,
seed=2013)
# Run the model for 1000 steps with a lattice trajectory.
ab_flip_model.run(control_parameters,
trajectory_filename=lattice_trajectory_filename,
trajectory_type='lattice')
# Check the file content.
ref_lattice = """
sites=[[ 0.000000, 0.000000, 0.000000],
[ 0.000000, 1.000000, 0.000000],
[ 0.000000, 2.000000, 0.000000],
[ 0.000000, 3.000000, 0.000000],
[ 1.000000, 0.000000, 0.000000],
[ 1.000000, 1.000000, 0.000000],
[ 1.000000, 2.000000, 0.000000],
[ 1.000000, 3.000000, 0.000000],
[ 2.000000, 0.000000, 0.000000],
[ 2.000000, 1.000000, 0.000000],
[ 2.000000, 2.000000, 0.000000],
[ 2.000000, 3.000000, 0.000000],
[ 3.000000, 0.000000, 0.000000],
[ 3.000000, 1.000000, 0.000000],
[ 3.000000, 2.000000, 0.000000],
[ 3.000000, 3.000000, 0.000000]]
times=[]
steps=[]
types=[]
times.append( 0.0000000000e+00)
steps.append(0)
types.append(["B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B"])
times.append( 1.9093684175e+01)
steps.append(500)
types.append(["B","A","B","B","A","B","B","B","A","B","B","B","B","B","B","A"])
times.append( 4.0622006972e+01)
steps.append(1000)
types.append(["B","A","A","B","B","B","B","A","B","B","B","A","B","B","B","B"])
"""
with open(lattice_trajectory_filename, "r") as t:
lattice_data = t.read()
# Check with "in" to avoid comparing dates.
self.assertTrue(ref_lattice in lattice_data)
# Run the model for 1000 steps with an xyz trajectory.
ab_flip_model.run(control_parameters,
trajectory_filename=xyz_trajectory_filename,
trajectory_type='xyz')
ref_xyz = """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 1 1
PERIODICITY True True False
STEP 0
16
TIME 4.0622006972e+01
B 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0
A 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 1
A 0.0000000000e+00 2.0000000000e+00 0.0000000000e+00 2
B 0.0000000000e+00 3.0000000000e+00 0.0000000000e+00 3
B 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 4
B 1.0000000000e+00 1.0000000000e+00 0.0000000000e+00 5
B 1.0000000000e+00 2.0000000000e+00 0.0000000000e+00 6
A 1.0000000000e+00 3.0000000000e+00 0.0000000000e+00 7
B 2.0000000000e+00 0.0000000000e+00 0.0000000000e+00 8
B 2.0000000000e+00 1.0000000000e+00 0.0000000000e+00 9
B 2.0000000000e+00 2.0000000000e+00 0.0000000000e+00 10
A 2.0000000000e+00 3.0000000000e+00 0.0000000000e+00 11
B 3.0000000000e+00 0.0000000000e+00 0.0000000000e+00 12
B 3.0000000000e+00 1.0000000000e+00 0.0000000000e+00 13
B 3.0000000000e+00 2.0000000000e+00 0.0000000000e+00 14
B 3.0000000000e+00 3.0000000000e+00 0.0000000000e+00 15
STEP 500
16
TIME 5.9660935122e+01
B 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0
A 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 1
B 0.0000000000e+00 2.0000000000e+00 0.0000000000e+00 2
B 0.0000000000e+00 3.0000000000e+00 0.0000000000e+00 3
B 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 4
B 1.0000000000e+00 1.0000000000e+00 0.0000000000e+00 5
B 1.0000000000e+00 2.0000000000e+00 0.0000000000e+00 6
A 1.0000000000e+00 3.0000000000e+00 0.0000000000e+00 7
B 2.0000000000e+00 0.0000000000e+00 0.0000000000e+00 8
B 2.0000000000e+00 1.0000000000e+00 0.0000000000e+00 9
B 2.0000000000e+00 2.0000000000e+00 0.0000000000e+00 10
B 2.0000000000e+00 3.0000000000e+00 0.0000000000e+00 11
A 3.0000000000e+00 0.0000000000e+00 0.0000000000e+00 12
A 3.0000000000e+00 1.0000000000e+00 0.0000000000e+00 13
B 3.0000000000e+00 2.0000000000e+00 0.0000000000e+00 14
B 3.0000000000e+00 3.0000000000e+00 0.0000000000e+00 15
STEP 1000
16
TIME 8.1189257919e+01
A 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0
B 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 1
B 0.0000000000e+00 2.0000000000e+00 0.0000000000e+00 2
B 0.0000000000e+00 3.0000000000e+00 0.0000000000e+00 3
B 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 4
A 1.0000000000e+00 1.0000000000e+00 0.0000000000e+00 5
B 1.0000000000e+00 2.0000000000e+00 0.0000000000e+00 6
B 1.0000000000e+00 3.0000000000e+00 0.0000000000e+00 7
B 2.0000000000e+00 0.0000000000e+00 0.0000000000e+00 8
B 2.0000000000e+00 1.0000000000e+00 0.0000000000e+00 9
A 2.0000000000e+00 2.0000000000e+00 0.0000000000e+00 10
A 2.0000000000e+00 3.0000000000e+00 0.0000000000e+00 11
B 3.0000000000e+00 0.0000000000e+00 0.0000000000e+00 12
B 3.0000000000e+00 1.0000000000e+00 0.0000000000e+00 13
B 3.0000000000e+00 2.0000000000e+00 0.0000000000e+00 14
B 3.0000000000e+00 3.0000000000e+00 0.0000000000e+00 15
"""
with open(xyz_trajectory_filename, "r") as t:
xyz_data = t.read()
self.assertEqual(ref_xyz, xyz_data)
# Running with wrong trajectory_type input fails.
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
trajectory_filename=xyz_trajectory_filename,
trajectory_type='abc') )
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
trajectory_filename=xyz_trajectory_filename,
trajectory_type=123) )
def testCustomRatesRun(self):
""" Test the run of an A-B flip model with custom rates. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(10,10,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*100
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates, ['A'], ['B'], None, [0], 4.0)
process_1 = KMCProcess(coordinates, ['B'], ['A'], None, [0], 1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes,
implicit_wildcards=True)
# Custom rates.
rate_calculator = CustomRateCalculator
interactions.setRateCalculator(rate_calculator)
# Setup the model.
ab_flip_model = KMCLatticeModel(configuration, interactions)
# Run the model with a trajectory file.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "ab_flip_traj_custom.py")
self.__files_to_remove.append(trajectory_filename)
# The control parameters.
control_parameters = KMCControlParameters(number_of_steps=1000,
dump_interval=500,
seed=2013)
# Run the model for 1000 steps.
ab_flip_model.run(control_parameters,
trajectory_filename=trajectory_filename)
# Read the first last frames from the trajectory file and check that
# the fraction of A is close to 75% in the last, and 0 in the first.
if MPICommons.isMaster():
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Count the first frame.
elem = local_dict["types"][0]
nA = len([ ee for ee in elem if ee == "A" ])
nB = len([ ee for ee in elem if ee == "B" ])
self.assertEqual(nA, 0)
self.assertEqual(nB, 100)
# Count the last frame.
elem = local_dict["types"][-1]
nA = len([ ee for ee in elem if ee == "A" ])
nB = len([ ee for ee in elem if ee == "B" ])
# Note that the average over a long simulation should be
# 75% A using the modified rate function. In this particular
# step the A population is 74%.
value = 1.0 * nA / (nA + nB)
self.assertAlmostEqual(0.74, value, 2)
def testATKScript1(self):
""" Test that we can generate an ATK script from the configuration. """
# 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], [0.0, 0.5, 0.5],
[0.5, 0.75, 0.75]])
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1, 1, 1),
periodic=(False, False, False))
types = ['B', 'A', 'C']
possible_types = ['C', "A", "B", "D"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
types_mapping = {
'A': 'Copper',
'C': 'Iron',
'D': 'Vanadium',
}
# Get the ATK script.
atk_script = config._atkScript(types_mapping)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 2.80000000, 0.00000000, 0.00000000]*Angstrom
vector_b = [ 0.00000000, 3.20000000, 0.00000000]*Angstrom
vector_c = [ 0.00000000, 0.50000000, 3.00000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Copper, Iron]
# Define the coordinates.
coordinates = [[ 0.00000000e+00, 5.00000000e-01, 5.00000000e-01],
[ 5.00000000e-01, 7.50000000e-01, 7.50000000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
def testScript(self):
""" Test that we can generate a valid script. """
# 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 script.
script = config._script()
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 5.000000e-01, 5.000000e-01, 5.000000e-01],
[ 2.500000e-01, 2.500000e-01, 7.500000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# -----------------------------------------------------------------------------
# Configuration
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']
possible_types = ['a','c','b']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
"""
self.assertEqual(script, ref_script)
# Try another one.
# 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]])
# Setup the lattice.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1, 1, 1),
periodic=(False, False, False))
types = [
'ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure'
]
possible_types = [
'ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',
"A", "B", "CDEFGHI"
]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Get the script.
script = config._script(variable_name="config")
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(1,1,1),
periodic=(False, False, False))
# -----------------------------------------------------------------------------
# Configuration
types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']
possible_types = ['A','CDEFGHI','ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',
'B']
config = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
"""
self.assertEqual(script, ref_script)
def testRunRngType(self):
""" Test that it is possible to run with each of the supported PRNG:s. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*16
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates,
['A'],
['B'],
basis_sites=[0],
rate_constant=4.0)
process_1 = KMCProcess(coordinates,
['B'],
['A'],
basis_sites=[0],
rate_constant=1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Setup the models.
ab_flip_model_MT = KMCLatticeModel(configuration, interactions)
ab_flip_model_RANLUX24 = KMCLatticeModel(configuration, interactions)
ab_flip_model_RANLUX48 = KMCLatticeModel(configuration, interactions)
ab_flip_model_MINSTD = KMCLatticeModel(configuration, interactions)
ab_flip_model_DEVICE = KMCLatticeModel(configuration, interactions)
# Run the model for 10000 steps with MT.
ab_flip_model_MT.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="MT"))
# Get the simulation time out.
t_MT = ab_flip_model_MT._KMCLatticeModel__cpp_timer.simulationTime()
# Run the model for 10000 steps with RANLUX24.
ab_flip_model_RANLUX24.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="RANLUX24"))
# Get the simulation time out.
t_RANLUX24 = ab_flip_model_RANLUX24._KMCLatticeModel__cpp_timer.simulationTime()
# Run the model for 10000 steps with RANLUX48.
ab_flip_model_RANLUX48.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="RANLUX48"))
# Get the simulation time out.
t_RANLUX48 = ab_flip_model_RANLUX48._KMCLatticeModel__cpp_timer.simulationTime()
# Run the model for 10000 steps with MINSTD.
ab_flip_model_MINSTD.run(KMCControlParameters(number_of_steps=10000,
dump_interval=5000,
seed=2013,
rng_type="MINSTD"))
# Get the simulation time out.
t_MINSTD = ab_flip_model_MINSTD._KMCLatticeModel__cpp_timer.simulationTime()
# These values should be simillar but not equal. Check against hardcoded values.
self.assertAlmostEqual(t_MT, 394.569398158, 5)
self.assertAlmostEqual(t_RANLUX24, 389.712162523, 5)
self.assertAlmostEqual(t_RANLUX48, 390.544423280, 5)
self.assertAlmostEqual(t_MINSTD, 384.712302086, 5)
def testRunFailAnalysis(self):
""" Test that the analyis plugins get called correctly. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(10,10,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*100
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates,
['A'],
['B'],
basis_sites=[0],
rate_constant=4.0)
process_1 = KMCProcess(coordinates,
['B'],
['A'],
basis_sites=[0],
rate_constant=1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Setup the model.
ab_flip_model = KMCLatticeModel(configuration, interactions)
# The control parameters.
control_parameters = KMCControlParameters(number_of_steps=1000,
dump_interval=500)
# Setup a valid minimal analysis object.
class AnalysisProxy1(KMCAnalysisPlugin):
def __init__(self):
pass
# Fail because of not instantitated analysis.
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
analysis=[AnalysisProxy1]) )
# Fail because of empty analyis list.
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
analysis=[]) )
# Fail because of not list.
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
analysis=AnalysisProxy1()) )
# Fail because of wrong type.
self.assertRaises( Error,
lambda : ab_flip_model.run(control_parameters,
analysis=[AnalysisProxy1(), "AP3"]) )
def testATKScript2(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
cell_vectors = [[ 5.640000e+00, 0.330000e+00, 0.120000e+00],
[ 0.110000e+00, 5.460000e+00, 0.100000e+00],
[ 0.500000e+00, 0.430000e+00, 5.410000e+00]]
basis_points = [[ 0.200000e+00, 0.300000e+00, 0.400000e+00],
[ 5.200000e-01, 5.400000e-01, 5.010000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the lattice and types.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,4),
periodic=(True, True, True))
types = ['Ce3','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','Vacancy','Ce','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Empty','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce3','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Ce','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce','O','Empty','O','Ce','O','Empty','O']
possible_types = ['Ce3','Empty','O','Ce','Vacancy']
# Setup the configuration.
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
type_map = {
"Ce3" : "Vanadium",
"Ce" : "Cerium",
"O" : "Oxygen",
}
# Get the ATK script.
atk_script = configuration._atkScript(type_map)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 22.56000000, 1.32000000, 0.48000000]*Angstrom
vector_b = [ 0.44000000, 21.84000000, 0.40000000]*Angstrom
vector_c = [ 2.00000000, 1.72000000, 21.64000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Vanadium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Oxygen, Cerium, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Vanadium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen]
# Define the coordinates.
coordinates = [[ 5.00000000e-02, 7.50000000e-02, 1.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 7.50000000e-02, 6.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 1.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 6.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 1.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 6.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 1.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 6.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 8.75250000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_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)
def testBackend(self):
""" Test that the backend object is correctly constructed. """
# Setup a unitcell.
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'])
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
sites = [0,1,2,3,4]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# A second process.
types0 = ["A","C"]
types1 = ["C","A"]
rate_0_1 = 1.5
process_1 = KMCProcess(coords,
types0,
types1,
basis_sites=sites,
rate_constant=rate_0_1)
# Construct the interactions object.
processes = [process_0, process_1]
interactions = KMCInteractions(processes=processes)
# Construct the model.
model = KMCLatticeModel(config, interactions)
# Get the c++ backend out.
cpp_model = model._backend()
# Check that this backend object is stored on the class.
self.assertTrue(model._KMCLatticeModel__backend == cpp_model)
def testRunWithAnalysis(self):
""" Test that the analyis plugins get called correctly. """
# Cell.
cell_vectors = [[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 1.000000e+00, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Lattice.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(10,10,1),
periodic=(True, True, False))
# Configuration.
types = ['B']*100
possible_types = ['A','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Interactions.
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]
process_0 = KMCProcess(coordinates,
['A'],
['B'],
basis_sites=[0],
rate_constant=4.0)
process_1 = KMCProcess(coordinates,
['B'],
['A'],
basis_sites=[0],
rate_constant=1.0)
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Setup the model.
ab_flip_model = KMCLatticeModel(configuration, interactions)
# Run the model with a trajectory file.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "ab_flip_traj.py")
self.__files_to_remove.append(trajectory_filename)
# The control parameters.
control_parameters = KMCControlParameters(number_of_steps=1000,
dump_interval=500,
analysis_interval=300)
# Setup a valid minimal analysis object.
class AnalysisProxy1(KMCAnalysisPlugin):
def __init__(self):
pass
# Setup a slightly larger analyis object.
class AnalysisProxy2(KMCAnalysisPlugin):
def __init__(self):
self.setup_called = False
self.finalize_called = False
self.register_step_counts = 0
def setup(self, step, time, configuration):
self.setup_called = True
def registerStep(self, step, time, configuration):
self.register_step_counts += 1
def finalize(self):
self.finalize_called = True
ap2 = AnalysisProxy2()
analysis = [ AnalysisProxy1(), ap2 ]
# Run the model for 1000 steps with the analysis objects.
# With dump interval 500 the analysis objects should be
# called on startup, the at step 300, 600 and step 900 and
# a finalization after that.
ab_flip_model.run(control_parameters,
trajectory_filename=trajectory_filename,
analysis=analysis)
self.assertTrue(ap2.setup_called)
self.assertTrue(ap2.finalize_called)
self.assertEqual(ap2.register_step_counts, 3)
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 testATKScript1(self):
""" Test that we can generate an ATK script from the configuration. """
# 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],
[0.0, 0.5, 0.5],
[0.5,0.75,0.75]])
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1,1,1),
periodic=(False,False,False))
types = ['B','A','C']
possible_types = ['C', "A", "B", "D"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
types_mapping = { 'A' : 'Copper',
'C' : 'Iron',
'D' : 'Vanadium',
}
# Get the ATK script.
atk_script = config._atkScript(types_mapping)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 2.80000000, 0.00000000, 0.00000000]*Angstrom
vector_b = [ 0.00000000, 3.20000000, 0.00000000]*Angstrom
vector_c = [ 0.00000000, 0.50000000, 3.00000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Copper, Iron]
# Define the coordinates.
coordinates = [[ 0.00000000e+00, 5.00000000e-01, 5.00000000e-01],
[ 5.00000000e-01, 7.50000000e-01, 7.50000000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
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 testATKScript2(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
cell_vectors = [[5.640000e+00, 0.330000e+00, 0.120000e+00],
[0.110000e+00, 5.460000e+00, 0.100000e+00],
[0.500000e+00, 0.430000e+00, 5.410000e+00]]
basis_points = [[0.200000e+00, 0.300000e+00, 0.400000e+00],
[5.200000e-01, 5.400000e-01, 5.010000e-01]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 4),
periodic=(True, True, True))
types = [
'Ce3', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'Vacancy', 'Ce', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce3',
'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce',
'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O'
]
possible_types = ['Ce3', 'Empty', 'O', 'Ce', 'Vacancy']
# Setup the configuration.
configuration = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
type_map = {
"Ce3": "Vanadium",
"Ce": "Cerium",
"O": "Oxygen",
}
# Get the ATK script.
atk_script = configuration._atkScript(type_map)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 22.56000000, 1.32000000, 0.48000000]*Angstrom
vector_b = [ 0.44000000, 21.84000000, 0.40000000]*Angstrom
vector_c = [ 2.00000000, 1.72000000, 21.64000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Vanadium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Oxygen, Cerium, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Vanadium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen]
# Define the coordinates.
coordinates = [[ 5.00000000e-02, 7.50000000e-02, 1.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 7.50000000e-02, 6.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 1.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 6.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 1.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 6.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 1.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 6.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 8.75250000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
def testScript(self):
""" Test that a script can be created. """
# Setup a unitcell.
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'])
# A first process.
coords = [[1.0,2.0,3.4],[1.1,1.2,1.3]]
types0 = ["A","B"]
types1 = ["B","A"]
rate_0_1 = 3.5
process_0 = KMCProcess(coords,
types0,
types1,
basis_sites=[0],
rate_constant=rate_0_1)
# A second process.
types0 = ["A","C"]
types1 = ["C","A"]
rate_0_1 = 1.5
process_1 = KMCProcess(coords,
types0,
types1,
basis_sites=[0],
rate_constant=rate_0_1)
# Construct the interactions object.
processes = [process_0, process_1]
interactions = KMCInteractions(processes)
# Construct the model.
model = KMCLatticeModel(config, interactions)
# Get the script.
script = model._script()
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 5.000000e-01, 5.000000e-01, 5.000000e-01],
[ 2.500000e-01, 2.500000e-01, 7.500000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# -----------------------------------------------------------------------------
# Configuration
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']
possible_types = ['A','C','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# -----------------------------------------------------------------------------
# Interactions
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 1.000000e-01, -8.000000e-01, -2.100000e+00]]
elements_before = ['A','B']
elements_after = ['B','A']
move_vectors = [( 0,[ 1.000000e-01, -8.000000e-01, -2.100000e+00]),
( 1,[ -1.000000e-01, 8.000000e-01, 2.100000e+00])]
basis_sites = [0]
rate_constant = 3.500000e+00
process_0 = KMCProcess(
coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=rate_constant)
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 1.000000e-01, -8.000000e-01, -2.100000e+00]]
elements_before = ['A','C']
elements_after = ['C','A']
move_vectors = [( 0,[ 1.000000e-01, -8.000000e-01, -2.100000e+00]),
( 1,[ -1.000000e-01, 8.000000e-01, 2.100000e+00])]
basis_sites = [0]
rate_constant = 1.500000e+00
process_1 = KMCProcess(
coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=rate_constant)
processes = [process_0,
process_1]
interactions = KMCInteractions(
processes=processes,
implicit_wildcards=True)
# -----------------------------------------------------------------------------
# Lattice model
model = KMCLatticeModel(
configuration=configuration,
interactions=interactions)
"""
self.assertEqual(script, ref_script)
# Get the script again, with a different variable name.
script = model._script(variable_name="my_model")
ref_script = """
# -----------------------------------------------------------------------------
# Unit cell
cell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 3.200000e+00, 0.000000e+00],
[ 0.000000e+00, 5.000000e-01, 3.000000e+00]]
basis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 5.000000e-01, 5.000000e-01, 5.000000e-01],
[ 2.500000e-01, 2.500000e-01, 7.500000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# -----------------------------------------------------------------------------
# Lattice
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,1),
periodic=(True, True, False))
# -----------------------------------------------------------------------------
# Configuration
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']
possible_types = ['A','C','B']
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# -----------------------------------------------------------------------------
# Interactions
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 1.000000e-01, -8.000000e-01, -2.100000e+00]]
elements_before = ['A','B']
elements_after = ['B','A']
move_vectors = [( 0,[ 1.000000e-01, -8.000000e-01, -2.100000e+00]),
( 1,[ -1.000000e-01, 8.000000e-01, 2.100000e+00])]
basis_sites = [0]
rate_constant = 3.500000e+00
process_0 = KMCProcess(
coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=rate_constant)
coordinates = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00],
[ 1.000000e-01, -8.000000e-01, -2.100000e+00]]
elements_before = ['A','C']
elements_after = ['C','A']
move_vectors = [( 0,[ 1.000000e-01, -8.000000e-01, -2.100000e+00]),
( 1,[ -1.000000e-01, 8.000000e-01, 2.100000e+00])]
basis_sites = [0]
rate_constant = 1.500000e+00
process_1 = KMCProcess(
coordinates=coordinates,
elements_before=elements_before,
elements_after=elements_after,
move_vectors=move_vectors,
basis_sites=basis_sites,
rate_constant=rate_constant)
processes = [process_0,
process_1]
interactions = KMCInteractions(
processes=processes,
implicit_wildcards=True)
# -----------------------------------------------------------------------------
# Lattice model
my_model = KMCLatticeModel(
configuration=configuration,
interactions=interactions)
"""
# Check.
self.assertEqual(script, ref_script)