def shift_x(normalised_length,
length_1,
length_2,
angle,
layer='1st_layer',
Use_optimised_structure=False):
name = 'Au38_Octa_' + str(length_1) + '_' + str(length_2) + '_' + str(
angle)
angle = float(radians(float(angle)))
if Use_optimised_structure:
cluster = copy.deepcopy(cluster_main_Opt)
cluster.set_calculator(None)
name += '_Opt'
else:
cluster = copy.deepcopy(cluster_main)
x_neighbour_length = cluster[16].x - cluster[32].x
z_neighbour_length = cluster[37].z - cluster[23].z
#neighbour_length = (x_neighbour_length**2.0 + z_neighbour_length**2.0)**0.5
neighbour_length = normalised_length
layer_1 = [24, 19, 21, 35]
layer_2 = [23, 22, 3, 18, 17, 34, 36, 37, 20]
for index in layer_1:
cluster[index].x += length_1 * cos(angle) * neighbour_length
cluster[index].z += length_1 * sin(angle) * neighbour_length
#if layer == '2nd_layer':
for index in layer_2:
cluster[index].x += length_2 * cos(angle) * neighbour_length
cluster[index].z += length_2 * sin(angle) * neighbour_length
ASE_write(name + '.traj', cluster, 'traj')
return name
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')
def makeMotif(motif_inputs, latticeconstant, remove_atoms=[]):
if isinstance(motif_inputs, int) or len(motif_inputs) == 1:
if isinstance(motif_inputs, int):
motif_inputs = [motif_inputs]
cluster = Icosahedron(symbol,
motif_inputs[0],
latticeconstant=latticeconstant)
name = 'Ico'
elif len(motif_inputs) == 2:
cluster = Octahedron(symbol,
motif_inputs[0],
motif_inputs[1],
latticeconstant=latticeconstant)
name = 'Octa'
elif len(motif_inputs) == 3:
cluster = Decahedron(symbol,
motif_inputs[0],
motif_inputs[1],
motif_inputs[2],
latticeconstant=latticeconstant)
name = 'Deca'
else:
print "Error"
import pdb
pdb.set_trace()
exit()
remove_atoms.sort(reverse=True)
if any(remove_atoms.count(x) > 1 for x in remove_atoms):
print 'You have got two of the same atom entered in to this list, check this.'
print 'remove_atoms = ' + str(remove_atoms)
import pdb
pdb.set_trace()
exit()
for remove_atom_index in remove_atoms:
del cluster[remove_atom_index]
name += '_' + symbol + str(len(cluster))
motif_details = ''
for motif_input in motif_inputs:
motif_details += str(motif_input) + '_'
motif_details = motif_details[:-1]
name += '_' + motif_details
if not remove_atoms == []:
name += '_atoms_removed_' + str(len(remove_atoms)) + '_cluster_'
counter = 1
while True:
if not name + str(counter) + '.traj' in os.listdir('.'):
name += str(counter)
break
counter += 1
ASE_write(name + '.traj', cluster, 'traj')
return name
output_cluster[index].position = new_atom_position
return output_cluster
rCut_low = 2.8840
rCut_high = round(rCut_low * (2.0)**0.5, 4)
rCut_resolution = 0.0005
mode = 'total'
symbol = 'Au'
latticeconstant = rCut_high
cluster_main = Octahedron(symbol, 4, 1, latticeconstant=latticeconstant)
cluster_main = move_cluster_to_COM(cluster_main)
original_cluster_name = 'Au39_original'
ASE_write(original_cluster_name + '.traj', cluster_main)
original_cluster_name_opt = optimise(original_cluster_name)
def run_CNA_program(Cluster_1_name, Cluster_2_name):
Cluster_1 = ASE_read(Cluster_1_name + '.traj')
print 'Made ' + str(Cluster_1_name)
Cluster_2 = ASE_read(Cluster_2_name + '.traj')
print 'Made ' + str(Cluster_2_name)
Structural_Recognition_Program(Cluster_1,
Cluster_2,
rCut_low,
rCut_high,
rCut_resolution,
mode,
name_1=Cluster_1_name,
index].x + Shearing_Matrix[2][1] * output_cluster[
index].y + Shearing_Matrix[2][2] * output_cluster[index].z
return output_cluster
rCut_low = 2.8840
rCut_high = round(rCut_low * (2.0)**0.5, 4)
rCut_resolution = 0.0005
mode = 'total'
symbol = 'Au'
latticeconstant = rCut_high
cluster_main = Decahedron(symbol, 3, 2, 0, latticeconstant=latticeconstant)
cluster_main = move_cluster_to_COM(cluster_main)
original_cluster_name = 'Au39_original'
ASE_write(original_cluster_name + '.traj', cluster_main)
original_cluster_name_Opt, cluster_main_Opt = optimise(original_cluster_name)
def run_CNA_program(Cluster_1_name, Cluster_2_name):
Cluster_1 = ASE_read(Cluster_1_name + '.traj')
print 'Made ' + str(Cluster_1_name)
Cluster_2 = ASE_read(Cluster_2_name + '.traj')
print 'Made ' + str(Cluster_2_name)
CNA_run = Structural_Recognition_Program(Cluster_1,
Cluster_2,
rCut_low,
rCut_high,
rCut_resolution,
mode,
name_1=Cluster_1_name,
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
#######################################################################
# Ico Structures Vs lots of other Ico structures
#######################################################################
#######################################################################
#######################################################################
Main_CNA_signatures_to_monitor = [[5, 5, 5], [4, 2, 1], [4, 2, 2]]
CNA_signatures_for_defect_icos = [[5, 4, 4], [4, 3, 3]]
CNA_signatures_for_111_surfaces = [[3, 2, 2], [3, 1, 1], [3, 0, 0]]
CNA_signatures_for_100_surfaces = [[2, 1, 1]]
CNA_signatures_for_110_surfaces = [[2, 0, 0]]
CNA_signatures_to_monitor = Main_CNA_signatures_to_monitor + CNA_signatures_for_defect_icos + CNA_signatures_for_111_surfaces + CNA_signatures_for_100_surfaces + CNA_signatures_for_110_surfaces
# 55 ico vs ico cluster - Rosette structure
motif_inputs = 3
cluster_main_ico, original_cluster_name_ico = makeMotif(
motif_inputs, latticeconstant)
ASE_write(original_cluster_name_ico + '.traj', cluster_main_ico)
Cluster_CNA_profile(original_cluster_name_ico, CNA_signatures_to_monitor)
vertex_atom = 18
atoms_around_vertex = [42, 36, 35, 46, 17]
rosette_cluster = makeRossetteReconstruction(cluster_main_ico, vertex_atom,
atoms_around_vertex)
rosette_cluster_name_ico = original_cluster_name_ico + '_rosette'
ASE_write(rosette_cluster_name_ico + '.traj', rosette_cluster)
run_CNA_program(original_cluster_name_ico, rosette_cluster_name_ico)
Cluster_CNA_profile(rosette_cluster_name_ico, CNA_signatures_to_monitor)
### Optimized
original_cluster_name_ico_opt = optimise(cluster_main_ico,
original_cluster_name_ico)
Cluster_CNA_profile(original_cluster_name_ico_opt, CNA_signatures_to_monitor)
rosette_cluster_name_ico_opt = optimise(rosette_cluster,
rosette_cluster_name_ico)
cluster_optimised = RunMinimisation(cluster).get_cluster() cluster_name_opt = cluster_name + '_Opt' ASE_write(cluster_name_opt+'.traj',cluster_optimised) return cluster_name_opt ####################################################################### ####################################################################### ####################################################################### # Ico Structures Vs lots of other structures ####################################################################### ####################################################################### ####################################################################### # 55 ico vs ico cluster - Rosette structure motif_inputs = 3 cluster_main_ico, original_cluster_name_ico = makeMotif(motif_inputs,latticeconstant) ASE_write(original_cluster_name_ico+'.traj',cluster_main_ico) vertex_atom = 18 atoms_around_vertex = [42,36,35,46,17] rosette_cluster = makeRossetteReconstruction(cluster_main_ico,vertex_atom,atoms_around_vertex) rosette_cluster_name_ico = original_cluster_name_ico + '_rosette' ASE_write(rosette_cluster_name_ico+'.traj',rosette_cluster) run_CNA_program(original_cluster_name_ico,rosette_cluster_name_ico) ### Optimized original_cluster_name_ico_opt = optimise(cluster_main_ico, original_cluster_name_ico) rosette_cluster_name_ico_opt = optimise(rosette_cluster, rosette_cluster_name_ico) run_CNA_program(original_cluster_name_ico_opt,rosette_cluster_name_ico_opt) ####################################################################### # 55 deca vs ico cluster - Rosette structure cluster_main_deca, original_cluster_name_deca = makeMotif([3,3,0],latticeconstant) ASE_write(original_cluster_name_deca+'.traj',cluster_main_deca) run_CNA_program(original_cluster_name_deca, rosette_cluster_name_ico)
delete()
print '---------------------------'
def move_cluster_to_COM(cluster):
COM = cluster.get_center_of_mass()
for atom in cluster:
atom.position -= COM
return cluster
symbol = 'Au'
cluster_main = Octahedron(symbol, 4, 1)
cluster_main = move_cluster_to_COM(cluster_main)
original_cluster_name = 'Au38_original'
ASE_write(original_cluster_name + '.traj', cluster_main)
rCut_low = 2.8840
rCut_high = round(rCut_low * (2.0)**0.5, 4)
rCut_resolution = 0.0005
mode = 'total'
def run_CNA_program(Cluster_1_name, Cluster_2_name):
Cluster_1 = ASE_read(Cluster_1_name + '.traj')
print 'Made ' + str(Cluster_1_name)
Cluster_2 = ASE_read(Cluster_2_name + '.traj')
print 'Made ' + str(Cluster_2_name)
Structural_Recognition_Program(Cluster_1,
Cluster_2,
rCut_low,