def testCheckSequence(self):
""" Test that the sequence checking works. """
# This is a sequence.
sequence = [1, 2, 3, 'a', 12.3, "ABC"]
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
# This also.
sequence = numpy.array([[12.0, 1.3], [1., 4.3]])
checked_sequence = checkSequence(sequence)
self.assertAlmostEqual(numpy.linalg.norm(checked_sequence - sequence),
0.0, 10)
# And these.
sequence = "A"
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
sequence = []
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
# But this is not.
sequence = 1
self.assertRaises(Error, lambda: checkSequence(sequence))
def __checkPeriodic(self, periodic):
""" """
"""
Private helper routine to check the periodic input.
"""
# Handle the default case.
if periodic is None:
periodic = (True, True, True)
# Check that it is a sequence.
periodic = checkSequence(
periodic,
"The 'periodic' input parametr is not given as a sequence of bools."
)
# Check its length.
if len(periodic) != 3:
raise Error(
"The 'periodic' input parameter must have length == 3.")
# Check the values.
for val in periodic:
if not isinstance(val, bool):
raise Error(
"The 'periodic' input paramter must be given as a list or tuple of three bools, e.g. (True,True,False)."
)
# Done.
return periodic
def __checkPeriodic(self, periodic):
""" """
"""
Private helper routine to check the periodic input.
"""
# Handle the default case.
if periodic is None:
periodic = (True, True, True)
# Check that it is a sequence.
periodic = checkSequence(periodic, "The 'periodic' input parametr is not given as a sequence of bools.")
# Check its length.
if len(periodic) != 3:
raise Error("The 'periodic' input parameter must have length == 3.")
# Check the values.
for val in periodic:
if not isinstance(val, bool):
raise Error(
"The 'periodic' input paramter must be given as a list or tuple of three bools, e.g. (True,True,False)."
)
# Done.
return periodic
def __checkRepetitions(self, repetitions):
""" """
"""
Private helper routine to check the repetitions input.
"""
# Handle the default case.
if repetitions is None:
repetitions = (1, 1, 1)
# Check that it is a sequence.
repetitions = checkSequence(
repetitions, "The 'repetitions' input parametr is not given as a sequence of numbers."
)
# Check its length.
if len(repetitions) != 3:
raise Error("The 'repetitions' input parameter must have length == 3.")
# Check the values.
for val in repetitions:
if not isinstance(val, int):
raise Error(
"The 'repetitions' input paramter must be given as a list or tuple of three integers, e.g. (5,5,6)"
)
# Check for the occurance of too small values.
for val in repetitions:
if val < 1:
raise Error("The all elements in the 'repetitions' parameter must be larger than zero.")
# Done.
return repetitions
def testCheckSequence(self):
""" Test that the sequence checking works. """
# This is a sequence.
sequence = [1,2,3,'a',12.3, "ABC"]
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
# This also.
sequence = numpy.array([[12.0,1.3],[1.,4.3]])
checked_sequence = checkSequence(sequence)
self.assertAlmostEqual( numpy.linalg.norm(checked_sequence-sequence), 0.0, 10)
# And these.
sequence = "A"
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
sequence = []
checked_sequence = checkSequence(sequence)
self.assertEqual(checked_sequence, sequence)
# But this is not.
sequence = 1
self.assertRaises(Error, lambda: checkSequence(sequence))
def __checkMoveVectorsFormat(self, move_vectors):
"""
Private helper function to check the format of the move vectors.
:param move_vectors: The input to check.
:returns: The validated move vectors, or None if None was given
and a reconstruction was not possible.
"""
if move_vectors is None:
# Try to reconstruct the move vectors from the before and after
# elements information.
move_vectors = self.__reconstructMoveVectors()
# Return if still None.
if move_vectors is None:
return move_vectors
# This is the error message.
msg = """The 'move_vectors' input to the KMCProcess constructor must be a
list of tuples, where the first element of each tuple refers to an atom index
and the second element is a cartesian vector of length 3, in internal
coordinates defining where the moved index goes."""
# Check that we have a sequence.
move_vectors = checkSequence(move_vectors, msg)
# Check the format of each element.
for t in move_vectors:
if not isinstance(t, tuple):
raise Error(msg)
elif not isinstance(t[0], int):
raise Error(msg)
# Check the vector.
checkSequenceOfFloats(t[1], msg)
if len(t[1]) != 3:
raise Error(msg)
# Passed all tests.
return move_vectors
def __checkRepetitions(self, repetitions):
""" """
"""
Private helper routine to check the repetitions input.
"""
# Handle the default case.
if repetitions is None:
repetitions = (1, 1, 1)
# Check that it is a sequence.
repetitions = checkSequence(
repetitions,
"The 'repetitions' input parametr is not given as a sequence of numbers."
)
# Check its length.
if len(repetitions) != 3:
raise Error(
"The 'repetitions' input parameter must have length == 3.")
# Check the values.
for val in repetitions:
if not isinstance(val, int):
raise Error(
"The 'repetitions' input paramter must be given as a list or tuple of three integers, e.g. (5,5,6)"
)
# Check for the occurance of too small values.
for val in repetitions:
if val < 1:
raise Error(
"The all elements in the 'repetitions' parameter must be larger than zero."
)
# Done.
return repetitions