def transform_coordinates(self, coordinates, argument=None):
"""
Translate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the translation.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the translation.
#. argument (object): Any python object. Not used in this generator.
"""
# get atoms group center
center = np.sum(coordinates, 0)/coordinates.shape[0]
# translate to origin
rotatedCoordinates = coordinates-center
# get normalized direction vectors
leftVector = FLOAT_TYPE( rotatedCoordinates[1,:]-rotatedCoordinates[0,:] )
leftVector /= FLOAT_TYPE( np.linalg.norm(leftVector) )
rightVector = FLOAT_TYPE( rotatedCoordinates[2,:]-rotatedCoordinates[0,:] )
rightVector /= FLOAT_TYPE( np.linalg.norm(rightVector) )
# get rotation axis
rotationAxis = np.cross(leftVector, rightVector)
if rotationAxis[0]==rotationAxis[1]==rotationAxis[2]==0.:
rotationAxis = np.array(1-2*np.random.random(3), dtype=FLOAT_TYPE)
rotationAxis /= FLOAT_TYPE( np.linalg.norm(rotationAxis) )
# create shrink flag
if self.__shrink is None:
shrink = (1-2*generate_random_float())>0
else:
shrink = self.__shrink
# get rotation angles
if self.__symmetric:
angleLeft = angleRight = FLOAT_TYPE(generate_random_float()*self.__amplitude)
else:
angleLeft = FLOAT_TYPE(generate_random_float()*self.__amplitude)
angleRight = FLOAT_TYPE(generate_random_float()*self.__amplitude)
# create directions
if shrink:
angleLeft *= FLOAT_TYPE(-1)
angleRight *= FLOAT_TYPE( 1)
else:
angleLeft *= FLOAT_TYPE( 1)
angleRight *= FLOAT_TYPE(-1)
# rotate
if self.__agitate[0]:
rotationMatrix = get_rotation_matrix(rotationAxis, angleLeft)
rotatedCoordinates[1,:] = np.dot( rotationMatrix, rotatedCoordinates[1,:])
if self.__agitate[1]:
rotationMatrix = get_rotation_matrix(rotationAxis, angleRight)
rotatedCoordinates[2,:] = np.dot( rotationMatrix, rotatedCoordinates[2,:])
# translate back from center and return
return np.array(rotatedCoordinates+center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply
the rotation.
#. argument (object): The rotation angle.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying
the rotation.
"""
if coordinates.shape[0] <= 1:
# atoms where removed, fall back to random translation
return coordinates + generate_random_vector(
minAmp=self.__amplitude[0], maxAmp=self.__amplitude[1])
else:
# get atoms group center and rotation axis
center, _, _, _, X, Y, Z = get_principal_axis(coordinates)
rotationAxis = [X, Y, Z][self.__axis]
# get rotation matrix
rotationMatrix = get_rotation_matrix(rotationAxis, argument)
# translate to origin
rotatedCoordinates = coordinates - center
# rotate
for idx in range(rotatedCoordinates.shape[0]):
rotatedCoordinates[idx, :] = np.dot(rotationMatrix,
rotatedCoordinates[idx, :])
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates + center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply
the rotation.
#. argument (object): Not used here.
:Returns:
#. coordinates (np.ndarray): The new coordinates after
applying the rotation.
"""
# get rotation angle
rotationAngle = (1 - 2 * generate_random_float()) * self.amplitude
# get rotation matrix
rotationMatrix = get_rotation_matrix(self.__axis, rotationAngle)
# get atoms group center and rotation axis
center, _, _, _, _, _, _ = get_principal_axis(coordinates)
# translate to origin
rotatedCoordinates = coordinates - center
# rotate
for idx in range(rotatedCoordinates.shape[0]):
rotatedCoordinates[idx, :] = np.dot(rotationMatrix,
rotatedCoordinates[idx, :])
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates + center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the rotation.
#. argument (object): Any python object. Not used in this generator.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the rotation.
"""
# get rotation angle
rotationAngle = (1-2*generate_random_float())*self.amplitude
# get atoms group center and rotation axis
center,_,_,_,X,Y,Z =get_principal_axis(coordinates)
rotationAxis = [X,Y,Z][self.__axis]
# get rotation matrix
rotationMatrix = get_rotation_matrix(rotationAxis, rotationAngle)
# translate to origin
rotatedCoordinates = coordinates-center
# rotate
for idx in range(rotatedCoordinates.shape[0]):
rotatedCoordinates[idx,:] = np.dot( rotationMatrix, rotatedCoordinates[idx,:])
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates+center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the rotation
#. argument (object): Any python object. Not used in this generator.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the rotation.
"""
# get rotation axis
n = 0
while n<PRECISION:
rotationAxis = 1-2*np.random.random(3)
n = np.linalg.norm(rotationAxis)
rotationAxis /= n
# get rotation angle
rotationAngle = (1-2*generate_random_float())*self.amplitude
# get rotation matrix
rotationMatrix = get_rotation_matrix(rotationAxis, rotationAngle)
# get atoms group center
center = np.sum(coordinates, 0)/coordinates.shape[0]
# translate to origin
rotatedCoordinates = coordinates-center
# rotate
for idx in range(rotatedCoordinates.shape[0]):
rotatedCoordinates[idx,:] = np.dot( rotationMatrix, rotatedCoordinates[idx,:])
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates+center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply
the rotation.
#. argument (object): Any python object. Not used in this
generator.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying
the rotation.
"""
if coordinates.shape[0] <= 1:
# atoms where removed, fall back to random translation
return coordinates + generate_random_vector(
minAmp=self.__amplitude[0], maxAmp=self.__amplitude[1])
else:
# get rotation axis
n = 0
while n < PRECISION:
rotationAxis = 1 - 2 * np.random.random(3)
n = np.linalg.norm(rotationAxis)
rotationAxis /= n
# get rotation angle
rotationAngle = (1 - 2 * generate_random_float()) * self.amplitude
# get rotation matrix
rotationMatrix = get_rotation_matrix(rotationAxis, rotationAngle)
# get atoms group center
center = np.sum(coordinates, 0) / coordinates.shape[0]
# translate to origin
rotatedCoordinates = coordinates - center
# rotate
for idx in range(rotatedCoordinates.shape[0]):
rotatedCoordinates[idx, :] = np.dot(rotationMatrix,
rotatedCoordinates[idx, :])
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates + center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
Translate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the translation.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the translation.
#. argument (object): Any python object. Not used in this generator.
"""
if coordinates.shape[0] != 3:
# atoms where removed, fall back to random translation
return coordinates + generate_random_vector(
minAmp=self.__amplitude[0], maxAmp=self.__amplitude[1])
else:
# get atoms group center
center = np.sum(coordinates, 0) / coordinates.shape[0]
# translate to origin
rotatedCoordinates = coordinates - center
# get normalized direction vectors
leftVector = FLOAT_TYPE(rotatedCoordinates[1, :] -
rotatedCoordinates[0, :])
leftVector /= FLOAT_TYPE(np.linalg.norm(leftVector))
rightVector = FLOAT_TYPE(rotatedCoordinates[2, :] -
rotatedCoordinates[0, :])
rightVector /= FLOAT_TYPE(np.linalg.norm(rightVector))
# get rotation axis
rotationAxis = np.cross(leftVector, rightVector)
if rotationAxis[0] == rotationAxis[1] == rotationAxis[2] == 0.:
rotationAxis = np.array(1 - 2 * np.random.random(3),
dtype=FLOAT_TYPE)
rotationAxis /= FLOAT_TYPE(np.linalg.norm(rotationAxis))
# create shrink flag
if self.__shrink is None:
shrink = (1 - 2 * generate_random_float()) > 0
else:
shrink = self.__shrink
# get rotation angles
if self.__symmetric:
angleLeft = angleRight = FLOAT_TYPE(generate_random_float() *
self.__amplitude)
else:
angleLeft = FLOAT_TYPE(generate_random_float() *
self.__amplitude)
angleRight = FLOAT_TYPE(generate_random_float() *
self.__amplitude)
# create directions
if shrink:
angleLeft *= FLOAT_TYPE(-1)
angleRight *= FLOAT_TYPE(1)
else:
angleLeft *= FLOAT_TYPE(1)
angleRight *= FLOAT_TYPE(-1)
# rotate
if self.__agitate[0]:
rotationMatrix = get_rotation_matrix(rotationAxis, angleLeft)
rotatedCoordinates[1, :] = np.dot(rotationMatrix,
rotatedCoordinates[1, :])
if self.__agitate[1]:
rotationMatrix = get_rotation_matrix(rotationAxis, angleRight)
rotatedCoordinates[2, :] = np.dot(rotationMatrix,
rotatedCoordinates[2, :])
# translate back from center and return
return np.array(rotatedCoordinates + center, dtype=FLOAT_TYPE)
