def generate_cell_angle_gamma_frame(atoms,
molecule1_atoms_index,
space_group,
sigma=0.1):
st = ase_atoms_to_structure(atoms)
old_positions = st.getXYZ()
old_xyz = old_positions[0]
molecule1_vectors = np.array(
[old_positions[i] for i in molecule1_atoms_index])
a, b, c, alpha, beta, gamma = atoms.get_cell_lengths_and_angles()
new_cell_params = [a, b, c, alpha, beta, gamma + random_draw(sigma)]
atoms.set_cell(new_cell_params, scale_atoms=True)
new_cell_params = atoms.get_cell()
new_xyz = atoms.get_positions()[0]
new_a_vector, new_b_vector, new_c_vector = new_cell_params[
0], new_cell_params[1], new_cell_params[2]
new_molecule1_vectors = get_xyz_after_move(old_xyz, new_xyz,
molecule1_vectors)
sites = []
for pos in new_molecule1_vectors:
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
site = np.dot(
rot, pos
) + trans_a * new_a_vector + trans_b * new_b_vector + trans_c * new_c_vector
sites.append(site)
new_positions = np.array(sites)
atoms.set_positions(new_positions)
def generate_translate_frame(atoms,
molecule1_atoms_index,
space_group,
sigma=0.1):
st = ase_atoms_to_structure(atoms)
my_atoms = atoms.copy()
my_atoms.set_positions(st.getXYZ())
current_XYZ = st.getXYZ()
molecule1_XYZ = [current_XYZ[i] for i in molecule1_atoms_index]
translation = [random_draw(sigma), random_draw(sigma), random_draw(sigma)]
molecule1_XYZ_after_translation = []
for row in molecule1_XYZ:
new_row = row + translation
molecule1_XYZ_after_translation.append(new_row)
sites = []
cell_params = my_atoms.get_cell()
for pos in molecule1_XYZ_after_translation:
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
site = np.dot(rot, pos) + trans_a * cell_params[
0] + trans_b * cell_params[1] + trans_c * cell_params[2]
sites.append(site)
new_positions = np.array(sites)
ret_atoms = Atoms(get_name(atoms.get_atomic_numbers()),
positions=new_positions,
cell=my_atoms.get_cell(),
pbc=[1, 1, 1])
return ret_atoms
def generate_cell_length_c_frame(atoms,
molecule1_atoms_index,
space_group,
sigma=0.1):
name = get_name(atoms.get_atomic_numbers())
st = ase_atoms_to_structure(atoms)
my_atoms = atoms.copy()
my_atoms.set_positions(st.getXYZ())
molecules = molecule_lists(my_atoms)
old_positions = my_atoms.get_positions()
molecule1_vectors = np.array([old_positions[i] for i in molecules[0]])
# set the perturbation
new_atoms = my_atoms.copy()
a, b, c, alpha, beta, gamma = my_atoms.get_cell_lengths_and_angles()
if a != b and b != c and c != a:
new_a, new_b, new_c = a, b, c + random_draw(sigma)
elif a != b and b == c:
new_a, new_c = a, c + random_draw(sigma)
new_b = new_c
elif a != b and a == c:
new_c, new_b = c + random_draw(sigma), b
new_a = new_c
elif a == b and a != c:
new_b, new_c = b, c + random_draw(sigma)
new_a = new_b
else:
new_c = c + random_draw(sigma)
new_a = new_c
new_b = new_c
# scaled_atoms = True
new_atoms.set_cell([new_a, new_b, new_c, alpha, beta, gamma],
scale_atoms=True)
new_cell_params = new_atoms.get_cell()
new_a_vector, new_b_vector, new_c_vector = new_cell_params[
0], new_cell_params[1], new_cell_params[2]
new_molecule1_vectors = get_xyz_after_move(my_atoms.get_positions()[0],
new_atoms.get_positions()[0],
molecule1_vectors)
sites = []
for pos in new_molecule1_vectors:
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
site = np.dot(
rot, pos
) + trans_a * new_a_vector + trans_b * new_b_vector + trans_c * new_c_vector
sites.append(site)
new_positions = np.array(sites)
ret_atoms = Atoms(name,
positions=new_positions,
cell=new_atoms.get_cell(),
pbc=[1, 1, 1])
return ret_atoms
def generate_rotation_frame(atoms,
molecule1_atoms_index,
space_group,
mu=0.1,
sigma=0.1):
st = ase_atoms_to_structure(atoms)
my_atoms = atoms.copy()
my_atoms.set_positions(st.getXYZ())
current_XYZ = st.getXYZ()
molecule1_XYZ = [current_XYZ[i] for i in molecule1_atoms_index]
delta_theta_x = random_draw(mu, sigma)
delta_theta_y = random_draw(mu, sigma)
delta_theta_z = random_draw(mu, sigma)
pi = math.pi
theta_x = delta_theta_x / 180 * pi
theta_y = delta_theta_y / 180 * pi
theta_z = delta_theta_z / 180 * pi
cos_theta_x, sin_theta_x = math.cos(theta_x), math.sin(theta_x)
cos_theta_y, sin_theta_y = math.cos(theta_y), math.sin(theta_y)
cos_theta_z, sin_theta_z = math.cos(theta_z), math.sin(theta_z)
rotation_x = [[1, 0, 0], [0, cos_theta_x, -sin_theta_x],
[0, sin_theta_x, cos_theta_x]]
rotation_y = [[cos_theta_y, 0, sin_theta_y], [0, 1, 0],
[-sin_theta_y, 0, cos_theta_y]]
rotation_z = [[cos_theta_z, -sin_theta_z, 0],
[sin_theta_z, cos_theta_z, 0], [0, 0, 1]]
molecule1_XYZ_after_rotate = np.matmul(np.array(molecule1_XYZ),
np.array(rotation_x))
cell_params = my_atoms.get_cell()
all_new_molecules = []
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
translation = trans_a * cell_params[0] + trans_b * cell_params[
1] + trans_c * cell_params[2]
translation_span = [translation for i in molecule1_atoms_index]
new_molecule = np.matmul(molecule1_XYZ_after_rotate,
rot) + translation_span
all_new_molecules.append(new_molecule)
new_XYZ_to_set = []
molecule1, molecule2, molecule3, moleclue4 = all_new_molecules[:]
for row1, row2, row3, row4 in zip(molecule1, molecule2, molecule3,
moleclue4):
new_XYZ_to_set.append(row1)
new_XYZ_to_set.append(row2)
new_XYZ_to_set.append(row3)
new_XYZ_to_set.append(row4)
writer = Atoms(get_name(atoms.get_atomic_numbers()),
positions=np.array(new_XYZ_to_set),
cell=atoms.get_cell(),
pbc=[1, 1, 1])
return writer
def move_molecule1(atoms, space_group):
print("atoms.get_distance(1,5): ",
atoms.get_distance(1, 5, mic=False, vector=True))
print("atoms.get_distance(1,21): ",
atoms.get_distance(1, 21, mic=False, vector=True))
a, b, c, alpha, beta, gamma = atoms.get_cell_lengths_and_angles()
X = atoms.get_positions()
old_scaled_position = atoms.get_scaled_positions()
print("a, b, c, alpha, beta, gamma: ", a, b, c, alpha, beta, gamma)
#print("X: ", X)
#print("old_scaled_position: ", old_scaled_position)
molecule1 = molecule_lists(atoms)[0]
st = ase_atoms_to_structure(atoms)
x_com1 = center_of_mass(st, molecule1)
X_molecule1 = np.array([X[x - 1] for x in molecule1])
#print("X_molecule1: ", X_molecule1)
F = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
delta_a, delta_b, delta_c = random_draw(0.1, 0.1), random_draw(
0.1, 0.1), random_draw(0.1, 0.1)
new_F = F + np.array([[delta_a, 0, 0], [0, delta_b, 0], [0, 0, delta_c]])
x_com1_new = np.dot(x_com1, new_F)
diff_com = x_com1_new - x_com1
#print("diff_com: ", diff_com)
new_X = []
for i, row in enumerate(X):
if i + 1 in molecule1:
new_X.append(row + diff_com)
else:
new_X.append(row)
L = atoms.get_cell()
new_L = np.dot(L, new_F)
new_atoms = atoms.copy()
new_atoms.set_positions(new_X)
new_atoms.set_cell(new_L, scale_atoms=False)
scaled_positions = new_atoms.get_scaled_positions()
molecule1_scaled_positions = [scaled_positions[i - 1] for i in molecule1]
final_scaled_positions = get_equivalent_sites(molecule1_scaled_positions,
space_group)
#print("final_scaled_positions: ", final_scaled_positions)
new_atoms.set_scaled_positions(final_scaled_positions)
print("new_atoms.get_distance(1,5): ",
new_atoms.get_distance(1, 5, mic=False, vector=True))
print("new_atoms.get_distance(1,21): ",
new_atoms.get_distance(1, 21, mic=False, vector=True))
return new_atoms
def get_com(atoms, molecule_lists):
"""
return a (n_molecules, 3) for center of mass
"""
ret_arr = []
st = ase_atoms_to_structure(atoms)
for molecule_list in molecule_lists:
com = center_of_mass(st, molecule_list)
ret_arr.append(com)
return np.array(ret_arr)
def generate_cell_angle_frame(atoms,
molecule1_atoms_index,
space_group,
mu=0.1,
sigma=0.1):
# get names and molecule idx
name = get_name(atoms.get_atomic_numbers())
st = ase_atoms_to_structure(atoms)
my_atoms = atoms.copy()
my_atoms.set_positions(st.getXYZ())
molecules = molecule_lists(my_atoms)
old_positions = my_atoms.get_positions()
molecule1_vectors = np.array([old_positions[i] for i in molecules[0]])
# set the perturbation
new_atoms = my_atoms.copy()
a, b, c, alpha, beta, gamma = my_atoms.get_cell_lengths_and_angles()
new_cell_params = [a, b, c]
for angle in [alpha, beta, gamma]:
if angle != 90:
new_cell_params.append(angle + random_draw(mu, sigma))
else:
new_cell_params.append(angle)
new_atoms.set_cell(new_cell_params, scale_atoms=True)
new_cell_params = new_atoms.get_cell()
new_a_vector, new_b_vector, new_c_vector = new_cell_params[
0], new_cell_params[1], new_cell_params[2]
new_molecule1_vectors = get_xyz_after_move(my_atoms.get_positions()[0],
new_atoms.get_positions()[0],
molecule1_vectors)
sites = []
for pos in new_molecule1_vectors:
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
site = np.dot(
rot, pos
) + trans_a * new_a_vector + trans_b * new_b_vector + trans_c * new_c_vector
sites.append(site)
new_positions = np.array(sites)
ret_atoms = Atoms(name,
positions=new_positions,
cell=new_atoms.get_cell(),
pbc=[1, 1, 1])
return ret_atoms
def change_cell_length(atoms, space_group):
name = get_name(atoms.get_atomic_numbers())
#molecule1, molecule2, molecule3, molecule4 = molecule_lists(atoms)[0], molecule_lists(atoms)[1], molecule_lists(atoms)[2], molecule_lists(atoms)[3] # [1,5,9,13,17,21,etc]
st = ase_atoms_to_structure(atoms)
#print("myxyz: ", st.getXYZ())
my_atoms = atoms.copy()
my_atoms.set_positions(st.getXYZ())
molecules = []
for molecule in st.molecule:
mole_list = []
for atom in molecule.atom:
mole_list.append(atom.index - 1)
molecules.append(mole_list)
old_positions = my_atoms.get_positions()
#get xyz coordinate for original molecules
molecule1_vectors = np.array([old_positions[i] for i in molecules[0]])
cell_params = my_atoms.get_cell()
new_atoms = my_atoms.copy()
new_atoms.set_cell(cell_params +
np.array([[3.0, 0, 0], [0, 3.0, 0], [0.0, 0, 3.0]]),
scale_atoms=True)
new_cell_params = new_atoms.get_cell()
new_a_vector, new_b_vector, new_c_vector = new_cell_params[
0], new_cell_params[1], new_cell_params[2]
new_molecule1_vectors = get_xyz_after_move(my_atoms.get_positions()[0],
new_atoms.get_positions()[0],
molecule1_vectors)
sites = []
for pos in new_molecule1_vectors:
for rot, trans in space_group.get_symop():
trans_a, trans_b, trans_c = trans[:]
site = np.dot(
rot, pos
) + trans_a * new_a_vector + trans_b * new_b_vector + trans_c * new_c_vector
sites.append(site)
new_positions = np.array(sites)
writer = Atoms(name,
positions=new_positions,
cell=new_atoms.get_cell(),
pbc=[1, 1, 1])
return writer
def calculate(self, atoms=None, properties=['energy'],
system_changes=ase.calculators.calculator.all_changes,
compute_hessian=False):
"""
calculate properties
"""
super(Calculator, self).calculate(atoms, properties, system_changes)
st = ase_atoms_to_structure(atoms)
mm.mmlewis_apply(st)
mm.mmffld_enterMol(self.mmffld_handle, st.handle)
mm.mmffld_deleteMol(self.mmffld_handle, st.handle)
(ret_force_array, ret_energy_array) = mm.mmffld_getEnergyForce( self.mmffld_handle)
self.results['energy'] = ret_energy_array
if 'force' in properties:
self.results['force'] = ret_force_array
