def optimise(cluster_name):
cluster = ASE_read(cluster_name + '.traj')
cluster_optimised = RunMinimisation(cluster).get_cluster()
cluster_optimised.set_calculator(None)
cluster_name_opt = cluster_name + '_Opt'
ASE_write(cluster_name_opt + '.traj', cluster_optimised)
return cluster_name_opt, cluster_optimised
def rotate_top(angle,atom_to_remove,name,only_rotate_second_later=False,Optimise=False):
angle = radians(float(angle))
angle = float(angle)
if not Optimise:
cluster = copy.deepcopy(cluster_main)
else:
cluster = copy.deepcopy(cluster_main_optimised)
rotate_around_x = cluster[3].x; rotate_around_y = cluster[3].y;
first_layer_to_rotate = [9,6,18,15,12]
second_layer_to_rotate = [24,22,20,38,36,34,32,30,28,26]
rotate_atoms = second_layer_to_rotate
if not only_rotate_second_later:
rotate_atoms += first_layer_to_rotate
for atom in atom_to_remove:
del cluster[atom]
for index2 in range(len(rotate_atoms)):
if atom < rotate_atoms[index2]:
rotate_atoms[index2] -= 1
if Optimise:
cluster = RunMinimisation(cluster).get_cluster()
cluster.set_calculator(None)
for index in rotate_atoms:
old_x = cluster[index].x - rotate_around_x; old_y = cluster[index].y - rotate_around_y
new_x = old_x*cos(angle) - old_y*sin(angle) + (rotate_around_x)
new_y = old_x*sin(angle) + old_y*cos(angle) + (rotate_around_y)
cluster[index].x = new_x; cluster[index].y = new_y
#view(cluster)
#import pdb; pdb.set_trace()
if Optimise:
name += '_Opt'
ASE_write(name+'.traj',cluster,'traj')
print '---------------------------'
def optimise(cluster_name):
cluster = ASE_read(cluster_name + '.traj')
cluster_optimised = RunMinimisation(cluster).get_cluster()
cluster_name_opt = cluster_name + '_Opt'
ASE_write(cluster_name_opt + '.traj', cluster_optimised)
return cluster_name_opt
symbol = 'Au'
r0 = 2.8840
latticeconstant = r0 * (2.0)**0.5
cluster_main = Decahedron(symbol, 3, 3, 0, latticeconstant=latticeconstant)
cluster_main_optimised = RunMinimisation(cluster_main).get_cluster()
cluster_main_optimised.set_calculator(None)
'''
def rotate_top(angle,atom_to_remove,name):
angle = radians(float(angle))
angle = float(angle)
cluster = copy.deepcopy(cluster_main)
rotate_around_x = cluster[3].x; rotate_around_y = cluster[3].y;
first_layer_to_rotate = [19,23,7,11,15]
second_layer_to_rotate = [27,8,54,24,51,48,20,45,42,16,39,36,12,33,30]
for index in (first_layer_to_rotate+second_layer_to_rotate):
old_x = cluster[index].x - rotate_around_x; old_y = cluster[index].y - rotate_around_y
new_x = old_x*cos(angle) - old_y*sin(angle) + (rotate_around_x)
new_y = old_x*sin(angle) + old_y*cos(angle) + (rotate_around_y)
cluster[index].x = new_x; cluster[index].y = new_y
for index in atom_to_remove:
def optimise(cluster, cluster_name):
cluster_optimised = RunMinimisation(cluster).get_cluster()
cluster_name_opt = cluster_name + '_Opt'
ASE_write(cluster_name_opt + '.traj', cluster_optimised)
return cluster_name_opt
