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incompl_shells.py
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incompl_shells.py
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#!/opt/local/bin/python
####################################################################
# Purpose: Create xyz files of icosahedral cluster consisting of 1 #
# atom type surrounded by non complete shells of #
# another type of atoms #
####################################################################
# Elke Fasshauer #
######################################################################
import numpy as np
import math
##################Input Variables ##################################
atcore = 'Ar' # atomtype of the core atoms
atouter = 'O' # atomtype of the outer shells
rcore = 1.88 # radius of core atoms
router = 1.54 # radius of outer shell atoms
n_core = 1 #number of atoms for the longest edge
n_sec = 2 # number of complete layers of the second atom type
n_outer = 1 # don't change
#no_surfaces = 3 + 1
no_surfaces = raw_input('How many surfaces do you want to be covered? ')
no_surfaces = int(no_surfaces)
################## Definitions #####################################
phi = (1 + math.sqrt(5))/2
scale = 2.0 / math.sqrt(1+phi**2) # passt fuer einheitliche Atome
thres = 1e-10
# Definition of the surfaces
surf1 = np.array([ 1, 2,11])
surf2 = np.array([ 1, 2, 9])
surf3 = np.array([ 1, 7,11])
surf4 = np.array([ 1, 5, 7])
surf5 = np.array([ 1, 5, 9])
surf6 = np.array([ 2, 6, 9])
surf7 = np.array([ 2, 6, 8])
surf8 = np.array([ 2, 8,11])
surf9 = np.array([ 5, 9,10])
surf10 = np.array([ 6, 9,10])
surf11 = np.array([ 3, 5,10])
surf12 = np.array([ 3, 5, 7])
surf13 = np.array([ 3, 4,10])
surf14 = np.array([ 3, 4,12])
surf15 = np.array([ 3, 7,12])
surf16 = np.array([ 4, 6,10])
surf17 = np.array([ 4, 6, 8])
surf18 = np.array([ 4, 8,12])
surf19 = np.array([ 7,11,12])
surf20 = np.array([ 8,11,12])
surfaces = np.vstack((surf1,surf2,surf3,surf4,surf5,surf6,surf7,\
surf8,surf9,surf10,surf11,surf12,surf13,\
surf14,surf15,surf16,surf17,surf18,surf19,surf20))
central = np.array([0,0,0])
coords = central
####################### Functions used #############################
def vec2str(vec):
return " ".join([str(v) for v in vec])
#def unique_rows(a):
# unique_a = np.unique(a.view([('', a.dtype)]*a.shape[1]))
# return unique_a.view(a.dtype).reshape((unique_a.shape[0], a.shape[1]))
def unique_rows(a):
# order = np.lexsort(a.T)
# a = a[order]
a = np.around(a,decimals=10)
a = a[np.lexsort(a.T)]
# a = a[a[:,2].argsort()]
# a = a[a[:,1].argsort()]
# a = a[a[:,0].argsort()]
# print a
diff = np.diff(a, axis=0)
ui = np.ones(len(a), 'bool')
ui[1:] = (diff > thres).any(axis=1)
return a[ui]
####################### Programme ##################################
##################################
##### Build the core icosahedra #
##################################
if (n_core > 1):
for i in range (2,n_core+1):
kante = 2* rcore * (i-1) * scale
# Die Ecken des Ikosaeders der entsprechenden Groesse
ecke1 = np.array([ 0, -kante/2, kante/2*phi])
ecke2 = np.array([ 0, kante/2, kante/2*phi])
ecke3 = np.array([ 0, -kante/2,-kante/2*phi])
ecke4 = np.array([ 0, kante/2,-kante/2*phi])
ecke5 = np.array([ kante/2,-kante/2*phi, 0])
ecke6 = np.array([ kante/2, kante/2*phi, 0])
ecke7 = np.array([ -kante/2,-kante/2*phi, 0])
ecke8 = np.array([ -kante/2, kante/2*phi, 0])
ecke9 = np.array([ kante/2*phi, 0, kante/2])
ecke10 = np.array([ kante/2*phi, 0, -kante/2])
ecke11 = np.array([-kante/2*phi, 0, kante/2])
ecke12 = np.array([-kante/2*phi, 0, -kante/2])
ecken = np.vstack((ecke1,ecke2,ecke3,ecke4,ecke5,ecke6,ecke7,\
ecke8,ecke9,ecke10,ecke11,ecke12))
latest = ecken
# print latest
for j in range (0,20):
vec1 = ecken[surfaces[j,0] -1]
vec2 = ecken[surfaces[j,1] -1]
vec3 = ecken[surfaces[j,2] -1]
#print j+1
#print surfaces[j,0], surfaces[j,1], surfaces[j,2]
# print ' '.join(map(str, vec1))
# print ' '.join(map(str, vec2))
# print ' '.join(map(str, vec3))
normkante = (vec2-vec1) / np.linalg.norm(vec2-vec1)
normlauf = (vec3-vec2) / np.linalg.norm(vec3-vec2)
if (i > 2):
for k in range (1,i):
kantatom = vec1 + (k * normkante * 2 * rcore * scale)
latest = np.vstack((latest,kantatom))
# print vec1
# print kantatom
for l in range (1,k+1):
flatom = kantatom + l * normlauf * 2 * rcore * scale
latest = np.vstack((latest,flatom))
#print kantatom
# Entferne Duplikate innerhalb der Liste
unique = unique_rows(latest)
# vereine die Koordianten der letzten Schicht mit allen anderen
coords = np.vstack((coords,unique))
#############################################
##### Layers of second atom type ############
#############################################
for i in range (1,n_sec+1):
kante = kante = (rcore * (2*n_core-1) + (2*i-1) *router) * scale
# Die Ecken des Ikosaeders der entsprechenden Groesse
ecke1 = np.array([ 0, -kante/2, kante/2*phi])
ecke2 = np.array([ 0, kante/2, kante/2*phi])
ecke3 = np.array([ 0, -kante/2,-kante/2*phi])
ecke4 = np.array([ 0, kante/2,-kante/2*phi])
ecke5 = np.array([ kante/2,-kante/2*phi, 0])
ecke6 = np.array([ kante/2, kante/2*phi, 0])
ecke7 = np.array([ -kante/2,-kante/2*phi, 0])
ecke8 = np.array([ -kante/2, kante/2*phi, 0])
ecke9 = np.array([ kante/2*phi, 0, kante/2])
ecke10 = np.array([ kante/2*phi, 0, -kante/2])
ecke11 = np.array([-kante/2*phi, 0, kante/2])
ecke12 = np.array([-kante/2*phi, 0, -kante/2])
ecken = np.vstack((ecke1,ecke2,ecke3,ecke4,ecke5,ecke6,ecke7,\
ecke8,ecke9,ecke10,ecke11,ecke12))
latest = ecken
#print latest
for j in range (0,20):
vec1 = ecken[surfaces[j,0] -1]
vec2 = ecken[surfaces[j,1] -1]
vec3 = ecken[surfaces[j,2] -1]
#print j+1
#print surfaces[j,0], surfaces[j,1], surfaces[j,2]
# print ' '.join(map(str, vec1))
# print ' '.join(map(str, vec2))
# print ' '.join(map(str, vec3))
normkante = (vec2-vec1) / np.linalg.norm(vec2-vec1)
normlauf = (vec3-vec2) / np.linalg.norm(vec3-vec2)
atdist = kante / (n_core+i-1)
for k in range (1,n_core + i):
kantatom = vec1 + (k * normkante * atdist)
latest = np.vstack((latest,kantatom))
# print vec1
# print kantatom
for l in range (1,k+1):
flatom = kantatom + l * normlauf * atdist
latest = np.vstack((latest,flatom))
#print kantatom
# Entferne Duplikate innerhalb der Liste
unique = unique_rows(latest)
if i == 1:
coords2nd = unique
else:
# vereine die Koordianten der letzten Schicht mit allen anderen
coords2nd = np.vstack((coords2nd,unique))
# print coords2nd
##############################################
## Outer Atom Layers (incomplete shells) #####
##############################################
for i in range (1,n_outer+1):
kante = (rcore * (2*n_core-1) + router * (2*n_sec) + (2*i-1) *router) * scale
# Die Ecken des Ikosaeders der entsprechenden Groesse
ecke1 = np.array([ 0, -kante/2, kante/2*phi])
ecke2 = np.array([ 0, kante/2, kante/2*phi])
ecke3 = np.array([ 0, -kante/2,-kante/2*phi])
ecke4 = np.array([ 0, kante/2,-kante/2*phi])
ecke5 = np.array([ kante/2,-kante/2*phi, 0])
ecke6 = np.array([ kante/2, kante/2*phi, 0])
ecke7 = np.array([ -kante/2,-kante/2*phi, 0])
ecke8 = np.array([ -kante/2, kante/2*phi, 0])
ecke9 = np.array([ kante/2*phi, 0, kante/2])
ecke10 = np.array([ kante/2*phi, 0, -kante/2])
ecke11 = np.array([-kante/2*phi, 0, kante/2])
ecke12 = np.array([-kante/2*phi, 0, -kante/2])
ecken = np.vstack((ecke1,ecke2,ecke3,ecke4,ecke5,ecke6,ecke7,\
ecke8,ecke9,ecke10,ecke11,ecke12))
ecken_true = [0,0,0,0,0,0,0,0,0,0,0,0]
latest = np.vstack((ecke1,ecke2))
# latest = ecken
# print latest
for j in range (0,no_surfaces):
vec1 = ecken[surfaces[j,0] -1]
vec2 = ecken[surfaces[j,1] -1]
vec3 = ecken[surfaces[j,2] -1]
#print j+1
# print surfaces[j,0], surfaces[j,1], surfaces[j,2]
ecken_true[surfaces[j,0]-1] = 1
ecken_true[surfaces[j,1]-1] = 1
ecken_true[surfaces[j,2]-1] = 1
# print ' '.join(map(str, vec1))
# print ' '.join(map(str, vec2))
# print ' '.join(map(str, vec3))
normkante = (vec2-vec1) / np.linalg.norm(vec2-vec1)
normlauf = (vec3-vec2) / np.linalg.norm(vec3-vec2)
atdist = kante / (n_core+n_sec+i-1)
for k in range (1,n_core + n_sec + i):
kantatom = vec1 + (k * normkante * atdist)
latest = np.vstack((latest,kantatom))
# print vec1
# print kantatom
for l in range (1,k+1):
flatom = kantatom + l * normlauf * atdist
latest = np.vstack((latest,flatom))
#print kantatom
print 'Removing additional corners'
print ecken_true
for m in range (11,0,-1):
if ecken_true[m] == 0:
ecken = np.delete(ecken,m,0)
latest = np.vstack((latest,ecken))
# print latest
# Entferne Duplikate innerhalb der Liste
unique = unique_rows(latest)
# vereine die Koordianten der letzten Schicht mit allen anderen
coords2nd = np.vstack((coords2nd,unique))
#########################################
# Write Output
#########################################
if (n_core == 1):
xyz_1st = []
xyz_1st.append(vec2str(coords))
else:
xyz_1st = [vec2str(coord) for coord in coords]
xyz_2nd = [vec2str(coord) for coord in coords2nd]
lines_1st = []
for coord in xyz_1st:
line = '%s %s' %(atcore,coord)
lines_1st.append(line)
print_1st = '\n'.join(lines_1st)
lines_2nd = []
for coord in xyz_2nd:
line = '%s %s' %(atouter,coord)
lines_2nd.append(line)
print_2nd = '\n'.join(lines_2nd)
no_core_atoms = len(lines_1st)
no_outer_atoms = len(lines_2nd)
no_atoms = no_core_atoms + no_outer_atoms
outlist = [print_1st,print_2nd]
#print outlist
outlines = '\n'.join(outlist)
#print outlines
outfile = open("%s%s_ico_%d.xyz" %(atouter,atcore,no_atoms), mode="w")
outfile.writelines(outlines)