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 testCheckCellVectors(self):
""" Test the cell vector checking function. """
# The simplest possible vectors.
trial_vectors = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
numpy_vectors = numpy.array(trial_vectors)
# This must pass.
checked_vectors = checkCellVectors(trial_vectors)
self.assertAlmostEqual(
numpy.linalg.norm(checked_vectors - numpy_vectors), 0.0, 10)
# This should also pass.
checked_vectors = checkCellVectors(numpy_vectors)
self.assertAlmostEqual(
numpy.linalg.norm(checked_vectors - numpy_vectors), 0.0, 10)
# This should fail because of wrong format / shape.
trial_vectors = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 1.0]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# As well as this.
trial_vectors = [1.0, 0.0, 0.0, 0.0, 1.0]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# This should also fail, because of wrong shape.
trial_vectors = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0],
[0.0, 1.0]])
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# This should fail because of wrong type.
trial_vectors = "ABC"
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# These should fail because of linear dependencies.
trial_vectors = [[1.0, 0.0, 0.0], [0.0, 1.0, 2.0],
[0.5, 0.5, 1.000001]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
trial_vectors = [[1.0, 0.0, 0.0], [0.5, 0.5, 1.0], [0.0, 1.0, 2.0]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
def testCheckCellVectors(self):
""" Test the cell vector checking function. """
# The simplest possible vectors.
trial_vectors = [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0]]
numpy_vectors = numpy.array(trial_vectors)
# This must pass.
checked_vectors = checkCellVectors(trial_vectors)
self.assertAlmostEqual(numpy.linalg.norm(checked_vectors - numpy_vectors), 0.0, 10)
# This should also pass.
checked_vectors = checkCellVectors(numpy_vectors)
self.assertAlmostEqual(numpy.linalg.norm(checked_vectors - numpy_vectors), 0.0, 10)
# This should fail because of wrong format / shape.
trial_vectors = [[1.0,0.0,0.0],[0.0,1.0,0.0,0.0],[0.0,1.0]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# As well as this.
trial_vectors = [1.0,0.0,0.0,0.0,1.0]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# This should also fail, because of wrong shape.
trial_vectors = numpy.array([[1.0,0.0,0.0],[0.0,1.0,0.0,0.0],[0.0,1.0]])
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# This should fail because of wrong type.
trial_vectors = "ABC"
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
# These should fail because of linear dependencies.
trial_vectors = [[1.0,0.0,0.0],[0.0,1.0,2.0],[0.5,0.5,1.000001]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
trial_vectors = [[1.0,0.0,0.0],[0.5,0.5,1.0],[0.0,1.0,2.0]]
self.assertRaises(Error, lambda: checkCellVectors(trial_vectors))
