def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2 = self.hinge_atoms
center = coordinates[atom1]
axis = coordinates[atom1] - coordinates[atom2]
axis /= np.linalg.norm(axis)
angle = np.random.uniform(-self.max_amplitude, self.max_amplitude)
return Complete.about_axis(center, angle, axis)
def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2 = self.hinge_atoms
center = coordinates[atom1]
axis = coordinates[atom1] - coordinates[atom2]
axis /= numpy.linalg.norm(axis)
angle = numpy.random.uniform(-self.max_amplitude, self.max_amplitude)
return Complete.about_axis(center, angle, axis)
def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2, atom3 = self.hinge_atoms
center = coordinates[atom2]
a = coordinates[atom1] - coordinates[atom2]
b = coordinates[atom3] - coordinates[atom2]
axis = np.cross(a, b)
norm = np.linalg.norm(axis)
if norm < 1e-5:
# We suppose that atom3 is part of the affected atoms
axis = random_orthonormal(a)
else:
axis /= np.linalg.norm(axis)
angle = np.random.uniform(-self.max_amplitude, self.max_amplitude)
return Complete.about_axis(center, angle, axis)
def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2, atom3 = self.hinge_atoms
center = coordinates[atom2]
a = coordinates[atom1] - coordinates[atom2]
b = coordinates[atom3] - coordinates[atom2]
axis = numpy.cross(a, b)
norm = numpy.linalg.norm(axis)
if norm < 1e-5:
# We suppose that atom3 is part of the affected atoms
axis = random_orthonormal(a)
else:
axis /= numpy.linalg.norm(axis)
angle = numpy.random.uniform(-self.max_amplitude, self.max_amplitude)
return Complete.about_axis(center, angle, axis)
def random_dimer(molecule0, molecule1, thresholds, shoot_max):
"""Create a random dimer.
molecule0 and molecule1 are placed in one reference frame at random
relative positions. Interatomic distances are above the thresholds.
Initially a dimer is created where one interatomic distance approximates
the threshold value. Then the molecules are given an additional
separation in the range [0, shoot_max].
thresholds has the following format:
{frozenset([atom_number1, atom_number2]): distance}
"""
# apply a random rotation to molecule1
center = np.zeros(3, float)
angle = np.random.uniform(0, 2 * np.pi)
axis = random_unit()
rotation = Complete.about_axis(center, angle, axis)
cor1 = np.dot(molecule1.coordinates, rotation.r)
# select a random atom in each molecule
atom0 = np.random.randint(len(molecule0.numbers))
atom1 = np.random.randint(len(molecule1.numbers))
# define a translation of molecule1 that brings both atoms in overlap
delta = molecule0.coordinates[atom0] - cor1[atom1]
cor1 += delta
# define a random direction
direction = random_unit()
cor1 += 1 * direction
# move molecule1 along this direction until all intermolecular atomic
# distances are above the threshold values
threshold_mat = np.zeros((len(molecule0.numbers), len(molecule1.numbers)),
float)
distance_mat = np.zeros((len(molecule0.numbers), len(molecule1.numbers)),
float)
for i1, n1 in enumerate(molecule0.numbers):
for i2, n2 in enumerate(molecule1.numbers):
threshold = thresholds.get(frozenset([n1, n2]))
threshold_mat[i1, i2] = threshold**2
while True:
cor1 += 0.1 * direction
distance_mat[:] = 0
for i in 0, 1, 2:
distance_mat += np.subtract.outer(molecule0.coordinates[:, i],
cor1[:, i])**2
if (distance_mat > threshold_mat).all():
break
# translate over a random distance [0, shoot] along the same direction
# (if necessary repeat until no overlap is found)
while True:
cor1 += direction * np.random.uniform(0, shoot_max)
distance_mat[:] = 0
for i in 0, 1, 2:
distance_mat += np.subtract.outer(molecule0.coordinates[:, i],
cor1[:, i])**2
if (distance_mat > threshold_mat).all():
break
# done
dimer = Molecule(np.concatenate([molecule0.numbers, molecule1.numbers]),
np.concatenate([molecule0.coordinates, cor1]))
dimer.direction = direction
dimer.atom0 = atom0
dimer.atom1 = atom1
return dimer
def random_dimer(molecule0, molecule1, thresholds, shoot_max):
"""Create a random dimer.
molecule0 and molecule1 are placed in one reference frame at random
relative positions. Interatomic distances are above the thresholds.
Initially a dimer is created where one interatomic distance approximates
the threshold value. Then the molecules are given an additional
separation in the range [0, shoot_max].
thresholds has the following format:
{frozenset([atom_number1, atom_number2]): distance}
"""
# apply a random rotation to molecule1
center = numpy.zeros(3, float)
angle = numpy.random.uniform(0, 2*numpy.pi)
axis = random_unit()
rotation = Complete.about_axis(center, angle, axis)
cor1 = numpy.dot(molecule1.coordinates, rotation.r)
# select a random atom in each molecule
atom0 = numpy.random.randint(len(molecule0.numbers))
atom1 = numpy.random.randint(len(molecule1.numbers))
# define a translation of molecule1 that brings both atoms in overlap
delta = molecule0.coordinates[atom0] - cor1[atom1]
cor1 += delta
# define a random direction
direction = random_unit()
cor1 += 1*direction
# move molecule1 along this direction until all intermolecular atomic
# distances are above the threshold values
threshold_mat = numpy.zeros((len(molecule0.numbers), len(molecule1.numbers)), float)
distance_mat = numpy.zeros((len(molecule0.numbers), len(molecule1.numbers)), float)
for i1, n1 in enumerate(molecule0.numbers):
for i2, n2 in enumerate(molecule1.numbers):
threshold = thresholds.get(frozenset([n1, n2]))
threshold_mat[i1, i2] = threshold**2
while True:
cor1 += 0.1*direction
distance_mat[:] = 0
for i in 0, 1, 2:
distance_mat += numpy.subtract.outer(molecule0.coordinates[:, i], cor1[:, i])**2
if (distance_mat > threshold_mat).all():
break
# translate over a random distance [0, shoot] along the same direction
# (if necessary repeat until no overlap is found)
while True:
cor1 += direction*numpy.random.uniform(0, shoot_max)
distance_mat[:] = 0
for i in 0, 1, 2:
distance_mat += numpy.subtract.outer(molecule0.coordinates[:, i], cor1[:, i])**2
if (distance_mat > threshold_mat).all():
break
# done
dimer = Molecule(
numpy.concatenate([molecule0.numbers, molecule1.numbers]),
numpy.concatenate([molecule0.coordinates, cor1])
)
dimer.direction = direction
dimer.atom0 = atom0
dimer.atom1 = atom1
return dimer
