def __init__(self, cell_vectors=None, basis_points=None):
"""
Constructor for the KMCUnitCell class.
:param cell_vectors: A 3x3 matrix, nested lists or numpy array with
rows corresponding to the a, b and c vectors in
cartesian coordinates.
:param basis_points: A Nx3 matrix, nested lists or numpy array with
each row corresponding to the fractional coordinates
of a basis point.
"""
# Check the cell vectors.
self.__cell_vectors = checkCellVectors(cell_vectors)
# Check the basis points are of correct format.
basis_points = checkCoordinateList(basis_points,
varname="basis_points")
# Check that the basis points are given in fractional coordinates.
for point in basis_points:
if not all([b < 1.0 and b >= 0.0 for b in point]):
raise Error(
"All basis points must be given in fractional coordinates in the range 0.0 <= basis_point < 1.0."
)
self.__basis_points = basis_points
def __init__(self,
cell_vectors=None,
basis_points=None):
"""
Constructor for the KMCUnitCell class.
:param cell_vectors: A 3x3 matrix, nested lists or numpy array with
rows corresponding to the a, b and c vectors in
cartesian coordinates.
:param basis_points: A Nx3 matrix, nested lists or numpy array with
each row corresponding to the fractional coordinates
of a basis point.
"""
# Check the cell vectors.
self.__cell_vectors = checkCellVectors(cell_vectors)
# Check the basis points are of correct format.
basis_points = checkCoordinateList(basis_points, varname="basis_points")
# Check that the basis points are given in fractional coordinates.
for point in basis_points:
if not all([b < 1.0 and b >= 0.0 for b in point]):
raise Error("All basis points must be given in fractional coordinates in the range 0.0 <= basis_point < 1.0.")
self.__basis_points = basis_points
def testCheckCoordinateList(self):
""" Test the coordinate list checking function. """
# Setup some valid coordinates.
valid_coordinates = [[1.0,2.0,3.4],[3.0,3.0,3.5]]
# Make sure they pass the check.
checked_coords = checkCoordinateList(valid_coordinates)
self.assertAlmostEqual( numpy.linalg.norm(valid_coordinates-checked_coords), 0.0, 10)
# Again, with numpy.
valid_coordinates = numpy.array(valid_coordinates)
checked_coords = checkCoordinateList(valid_coordinates)
self.assertAlmostEqual( numpy.linalg.norm(valid_coordinates-checked_coords), 0.0, 10)
# Test some things that fails.
# Wrong type.
invalid_coordinates = [[1.0,1.0,1.0],[1.0,1.0,1]]
self.assertRaises(Error, lambda: checkCoordinateList(invalid_coordinates))
# Wrong type.
invalid_coordinates = "[[1.0,1.0,1.0],[1.0,1.0,1]]"
self.assertRaises(Error, lambda: checkCoordinateList(invalid_coordinates))
# Wrong size.
invalid_coordinates = [[1.0,2.0,3.4],[3.0,3.0],[3.0,3.0,3.5]]
self.assertRaises(Error, lambda: checkCoordinateList(invalid_coordinates))
invalid_coordinates = [[1.0,2.0,3.4],[3.0,3.0,1.2],[3.0,3.0,3.5,32.3]]
self.assertRaises(Error, lambda: checkCoordinateList(invalid_coordinates))
def __init__(self,
coordinates=None,
basis_sites=None,
rate_constant=None):
"""
Constructor for the KMCBaseProcess.
:param coordinates: The local coordinates, corresponding to the lattice
positions of the surrounding of the center where
the process will be preformed.
:param basis_sites: The basis sites in the lattice at which the process
can possibly be applied. Only if the length of this
list is 1 can implicit wildcards be used for the
matching.
:param rate_constant: The rate constant associated with this process.
:type rate_constant: float
"""
# Check the coordinates.
coordinates = checkCoordinateList(coordinates)
# Center the coordinates on the first entry.
center = 0
self._coordinates = centerCoordinates(coordinates, center)
# Check the list of basis sites.
basis_sites = checkSequenceOfPositiveIntegers(basis_sites,
msg="The basis_sites must be given as a list of positive integers.")
if len(basis_sites) == 0:
msg = "The list of available basis sites for a process may not be empty."
# Passed the tests.
self._basis_sites = basis_sites
# Check the rate constant.
self._rate_constant = checkPositiveFloat(rate_constant,
default_parameter=None,
parameter_name="rate_constant")
# To be updated by the derrived classes.
self._elements_before = None
self._elements_after = None
self._move_vectors = None
self._all_present_types = None
self._local_configurations = None
def __init__(self, coordinates=None, basis_sites=None, rate_constant=None):
"""
Constructor for the KMCBaseProcess.
:param coordinates: The local coordinates, corresponding to the lattice
positions of the surrounding of the center where
the process will be preformed.
:param basis_sites: The basis sites in the lattice at which the process
can possibly be applied. Only if the length of this
list is 1 can implicit wildcards be used for the
matching.
:param rate_constant: The rate constant associated with this process.
:type rate_constant: float
"""
# Check the coordinates.
coordinates = checkCoordinateList(coordinates)
# Center the coordinates on the first entry.
center = 0
self._coordinates = centerCoordinates(coordinates, center)
# Check the list of basis sites.
basis_sites = checkSequenceOfPositiveIntegers(
basis_sites,
msg="The basis_sites must be given as a list of positive integers."
)
if len(basis_sites) == 0:
msg = "The list of available basis sites for a process may not be empty."
# Passed the tests.
self._basis_sites = basis_sites
# Check the rate constant.
self._rate_constant = checkPositiveFloat(
rate_constant,
default_parameter=None,
parameter_name="rate_constant")
# To be updated by the derrived classes.
self._elements_before = None
self._elements_after = None
self._move_vectors = None
self._all_present_types = None
self._local_configurations = None
def __init__(self,
coordinates=None,
types=None,
center=None):
"""
Constructor for the KMCLocalConfiguration.
:param coordinates: The coordinates of the configuration given as
a 3xN sequence of floating point numbers, where
N is the number of local sites.
:param types: The lattice site types at the specified coordinates given
as a sequence of strings of length N.
:param center: The coordinate in the list to treat as the central site
indexed from zero. If not given it will default to the
first coordinate (i.e. center == 0).
:type center: int
"""
# ML:
# FIXME: Must support bucket types information.
# Check the coordinates.
coordinates = checkCoordinateList(coordinates)
# Set the center coordinate if not given.
if center is None:
center = 0
# Check the bounds of the center coordinate.
center = checkIndexWithinBounds(center,
coordinates,
msg="The 'center' index paramter must be one in the coordinate list.")
# Center the coordinates.
self.__coordinates = centerCoordinates(coordinates, center)
# Check the types.
if len(types) != len(coordinates):
raise Error("The length of the types must match the coordinates.")
self.__types = [checkAndNormaliseBucketEntry(t) for t in types]
# Set the backend to None, to generate it at first query.
self.__backend = None
def testCheckCoordinateList(self):
""" Test the coordinate list checking function. """
# Setup some valid coordinates.
valid_coordinates = [[1.0, 2.0, 3.4], [3.0, 3.0, 3.5]]
# Make sure they pass the check.
checked_coords = checkCoordinateList(valid_coordinates)
self.assertAlmostEqual(
numpy.linalg.norm(valid_coordinates - checked_coords), 0.0, 10)
# Again, with numpy.
valid_coordinates = numpy.array(valid_coordinates)
checked_coords = checkCoordinateList(valid_coordinates)
self.assertAlmostEqual(
numpy.linalg.norm(valid_coordinates - checked_coords), 0.0, 10)
# Test some things that fails.
# Wrong type.
invalid_coordinates = [[1.0, 1.0, 1.0], [1.0, 1.0, 1]]
self.assertRaises(Error,
lambda: checkCoordinateList(invalid_coordinates))
# Wrong type.
invalid_coordinates = "[[1.0,1.0,1.0],[1.0,1.0,1]]"
self.assertRaises(Error,
lambda: checkCoordinateList(invalid_coordinates))
# Wrong size.
invalid_coordinates = [[1.0, 2.0, 3.4], [3.0, 3.0], [3.0, 3.0, 3.5]]
self.assertRaises(Error,
lambda: checkCoordinateList(invalid_coordinates))
invalid_coordinates = [[1.0, 2.0, 3.4], [3.0, 3.0, 1.2],
[3.0, 3.0, 3.5, 32.3]]
self.assertRaises(Error,
lambda: checkCoordinateList(invalid_coordinates))
def __init__(self,
coordinates=None,
elements_before=None,
elements_after=None,
move_vectors=None,
basis_sites=None,
rate_constant=None):
"""
Constructor for the KMCProcess.
:param coordinates: The local coordinates, corresponding to the lattice
positions of the surrounding of the center where
the process will be preformed.
:param elements_before: The elements, as a list of strings,
before the process is preformed.
This list of elements will be used to match the
local surroundings of each center in the
simulation, to determine at which sites the
process can be performed.
:param elements_after: The elements, as a list of strings,
after the process is preformed.
This list of elements will be used to update the
local surrounding of the site where the process
is performed.
:param move_vectors: A set of vectors in the local coordinates that define
which elements are moved to which place in the move.
The vectors are given as a list of tuples, where the first
element in each tuple indicates which index is moved and
the second element in the tuple is a vector in local coordinates
indicating where the move is to.
:param basis_sites: The basis sites in the lattice at which the process
can possibly be applied. Only if the length of this
list is 1 can implicit wildcards be used for the
matching.
:param rate_constant: The rate constant associated with this process.
:type rate_constant: float
"""
# Check the coordinates.
coordinates = checkCoordinateList(coordinates)
# Center the coordinates on the first entry.
center = 0
self.__coordinates = centerCoordinates(coordinates, center)
# Check the types.
elements_before = checkTypes(elements_before, len(coordinates))
elements_after = checkTypes(elements_after, len(coordinates))
# Check that the elements represents a valid move.
self.__checkValidMoveElements(elements_before, elements_after)
# All types checking done.
self.__elements_before = elements_before
self.__elements_after = elements_after
# Check that the move vectors are compatible with the elements.
self.__move_vectors = self.__checkValidMoveVectors(move_vectors)
# Sort the coordinates and co-sort the elements and move vectors.
self.__sortCoordinatesElementsAndMoveVectors()
# Check the list of basis sites.
basis_sites = checkSequenceOfPositiveIntegers(basis_sites,
msg="The basis_sites must be given as a list of positive integers.")
if len(basis_sites) == 0:
msg = "The list of available basis sites for a process may not be empty."
# Passed the tests.
self.__basis_sites = basis_sites
# Check the rate constant.
self.__rate_constant = checkPositiveFloat(rate_constant,
default_parameter=None,
parameter_name="rate_constant")
# Setup the local configurations.
c1 = KMCLocalConfiguration(self.__coordinates, self.__elements_before, center)
c2 = KMCLocalConfiguration(self.__coordinates, self.__elements_after, center)
self.__local_configurations = (c1, c2)
