def transform_coordinates(self, coordinates, argument):
"""
Rotate 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 (float): The move distance.
"""
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 translation amplitude
amplitude = FLOAT_TYPE(argument)
# get vector of translation
_, _, _, _, X, Y, Z = get_principal_axis(coordinates)
vector = [X, Y, Z][self.__axis]
# amplify vector
vector *= FLOAT_TYPE(amplitude)
# translate and return
return coordinates + vector
def __get_group_axis__(self, coordinates):
if self.__mustComputeGroupAxis:
_, _, _, _, X, Y, Z = get_principal_axis(coordinates)
axis = [X, Y, Z][self.__groupAxis["symmetry"]]
else:
axis = self.__groupAxis["fixed"]
return axis
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] <= 1:
# atoms where removed, fall back to random translation
return coordinates + generate_random_vector(
minAmp=self.__amplitude[0], maxAmp=self.__amplitude[1])
else:
# get translation amplitude
maxAmp = self.amplitude[1] - self.amplitude[0]
if self.direction is None:
amplitude = (1 - 2 * generate_random_float()) * maxAmp
elif self.direction:
amplitude = generate_random_float() * maxAmp
else:
amplitude = -generate_random_float() * maxAmp
# get axis of translation
_, _, _, _, X, Y, Z = get_principal_axis(coordinates)
translationAxis = [X, Y, Z][self.__axis]
# compute baseVector
baseVector = FLOAT_TYPE(
np.sign(amplitude) * translationAxis * self.amplitude[0])
# compute translation vector
vector = baseVector + translationAxis * FLOAT_TYPE(amplitude)
# translate and return
return coordinates + vector
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):
"""
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 axis
_,_,_,_,X,Y,Z =get_principal_axis(coordinates)
axis = [X,Y,Z][self.axis]
# generate translation axis
translationAxis = generate_vectors_in_solid_angle(direction=axis,
maxAngle=self.__angle,
numberOfVectors=1)[0]
# get translation amplitude
maxAmp = self.amplitude[1]-self.amplitude[0]
if self.direction is None:
amplitude = (1-2*generate_random_float())*maxAmp
elif self.direction:
amplitude = generate_random_float()*maxAmp
else:
amplitude = -generate_random_float()*maxAmp
# compute baseVector
baseVector = FLOAT_TYPE(np.sign(amplitude)*translationAxis*self.amplitude[0])
# compute translation vector
vector = baseVector + translationAxis*FLOAT_TYPE(amplitude)
# translate and return
return coordinates+vector
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 __get_group_axis__(self, coordinates):
if self.__mustComputeGroupAxis:
_,_,_,_,X,Y,Z = get_principal_axis(coordinates)
axis = [X,Y,Z][self.__groupAxis["symmetry"]]
else:
axis = self.__groupAxis["fixed"]
return axis
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 along_axis_2():
# run engine translation along axis 2
xyzPath="along2.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
_,_,_,_,X,Y,Z =get_principal_axis(ENGINE.realCoordinates)
print("Translation along symmetry axis 2: ", Z)
[g.set_move_generator(TranslationAlongSymmetryAxisGenerator(amplitude=0.5, axis=2)) for g in ENGINE.groups]
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)
def about_axis_2():
# run engine rotation about axis 2
xyzPath="about2.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
_,_,_,_,X,Y,Z =get_principal_axis(ENGINE.realCoordinates)
print("Rotation about symmetry axis 2: ", Z)
[g.set_move_generator(RotationAboutSymmetryAxisGenerator(amplitude=10, axis=2)) for g in ENGINE.groups]
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)
def __get_orientation_axis__(self):
if self.__mustComputeOrientationAxis:
coordinates = self.group._get_engine().realCoordinates[self.__orientationAxis["symmetry"][0]]
_,_,_,_,X,Y,Z = get_principal_axis(coordinates)
axis = [X,Y,Z][self.__orientationAxis["symmetry"][1]]
else:
axis = self.__orientationAxis["fixed"]
return axis
def __get_orientation_axis__(self):
if self.__mustComputeOrientationAxis:
coordinates = self.group._get_engine().realCoordinates[
self.__orientationAxis["symmetry"][0]]
_, _, _, _, X, Y, Z = get_principal_axis(coordinates)
axis = [X, Y, Z][self.__orientationAxis["symmetry"][1]]
else:
axis = self.__orientationAxis["fixed"]
return axis
def about_111_axis():
# run engine rotation about defined axis
xyzPath="about111.xyz"
axis=(1,1,1)
if os.path.isfile(xyzPath): os.remove(xyzPath)
_,_,_,_,X,Y,Z =get_principal_axis(ENGINE.realCoordinates)
print("Rotation about user defined axis: ",axis)
[g.set_move_generator(RotationAboutAxisGenerator(amplitude=10, axis=axis)) for g in ENGINE.groups]
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)
def transform_coordinates(self, coordinates, argument):
"""
Rotate 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 (float): The move distance.
"""
# get translation amplitude
amplitude = FLOAT_TYPE(argument)
# get vector of translation
_,_,_,_,X,Y,Z =get_principal_axis(coordinates)
vector = [X,Y,Z][self.__axis]
# amplify vector
vector *= FLOAT_TYPE(amplitude)
# translate and return
return coordinates+vector
