def graft_HC_chain(save, readpoly, readnp, R1, R2):
fin1 = open(readpoly, 'r')
fin2 = open(readnp, 'r')
fout = open(save, 'w')
f1data = fin1.read()
data1 = f1data.splitlines()
data1 = data1[2:]
f2data = fin2.read()
data2 = f2data.splitlines()
data2 = data2[2:]
sulfur = [-1.58237, 0.899165, 0.0]
for line in data2:
s = line.split()
fout.write(
('%s %f %f %f\n') % (s[0], float(s[1]), float(s[2]), float(s[3])))
for line in data2:
s = line.split()
vec = np.sqrt((float(s[1])**2) + (float(s[2])**2) + (float(s[3])**2))
if vec == R1:
r1 = float(s[1]) / float(vec) + float(s[1])
r2 = float(s[2]) / float(vec) + float(s[2])
r3 = float(s[3]) / float(vec) + float(s[3])
#fout.write(("S %f %f %f\n")%(r1,r2,r3))
v = [r1, r2, r3]
P = rp.align_vector(readpoly, v)
for i in range(P.shape[0]):
P[i] = np.add(v, P[i])
#if(i==P.shape[1]-1):
if (i == P.shape[0] - 1):
fout.write(
('CH3 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(
('CH2 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
if vec == R2:
r1 = float(s[1]) / float(vec) + float(s[1])
r2 = float(s[2]) / float(vec) + float(s[2])
r3 = float(s[3]) / float(vec) + float(s[3])
#fout.write(("S %f %f %f\n")%(r1,r2,r3))
v = [r1, r2, r3]
P = rp.align_vector(readpoly, v)
for i in range(P.shape[0]):
P[i] = np.add(v, P[i])
#if(i==P.shape[1]-1):
if (i == P.shape[0] - 1):
fout.write(
('CH3 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(
('CH2 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
def graft_HC_chain(save,readpoly,readnp,R1,R2):
fin1 = open(readpoly,'r')
fin2 = open(readnp,'r')
fout = open(save,'w')
f1data=fin1.read()
data1=f1data.splitlines()
data1=data1[2:]
f2data=fin2.read()
data2=f2data.splitlines()
data2=data2[2:]
sulfur=[-1.58237,0.899165,0.0]
for line in data2:
s=line.split()
fout.write(('%s %f %f %f\n')%(s[0],float(s[1]),float(s[2]),float(s[3])))
for line in data2:
s=line.split()
vec=np.sqrt((float(s[1])**2)+(float(s[2])**2)+(float(s[3])**2))
if vec == R1:
r1=float(s[1])/float(vec)+float(s[1])
r2=float(s[2])/float(vec)+float(s[2])
r3=float(s[3])/float(vec)+float(s[3])
#fout.write(("S %f %f %f\n")%(r1,r2,r3))
v=[r1,r2,r3]
P=rp.align_vector(readpoly,v)
for i in range(P.shape[0]):
P[i]=np.add(v,P[i])
if(i==P.shape[1]-1):
fout.write(('CH3 %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
elif(i==0):
fout.write(('S %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
else:
fout.write(('CH2 %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
if vec == R2:
r1=float(s[1])/float(vec)+float(s[1])
r2=float(s[2])/float(vec)+float(s[2])
r3=float(s[3])/float(vec)+float(s[3])
#fout.write(("S %f %f %f\n")%(r1,r2,r3))
v=[r1,r2,r3]
P=rp.align_vector(readpoly,v)
for i in range(P.shape[0]):
P[i]=np.add(v,P[i])
if(i==P.shape[1]-1):
fout.write(('CH3 %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
elif(i==0):
fout.write(('S %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
else:
fout.write(('CH2 %f %f %f\n')%(P[i][0],P[i][1],P[i][2]))
def graft_square_faces(save, readpoly, readnp, R_face):
fin1 = open(readpoly, 'r')
fin2 = open(readnp, 'r')
fout = open(save, 'w')
f1data = fin1.read()
data1 = f1data.splitlines()
data1 = data1[2:]
f2data = fin2.read()
data2 = f2data.splitlines()
data2 = data2[2:]
#####################
#AuS is length radial outward from face for Au-S distance
#####################
AuS = 1.97
vecs = np.array([[0.0, 0.0, 0.0]])
count = (6 * len(data1) + 6)
Spos = R_face + AuS
vecs = np.append(vecs, [[0.0, 0.0, Spos]], axis=0)
vecs = np.append(vecs, [[0.0, 0.0, -Spos]], axis=0)
vecs = np.append(vecs, [[0.0, Spos, 0.0]], axis=0)
vecs = np.append(vecs, [[0.0, -Spos, 0.0]], axis=0)
vecs = np.append(vecs, [[Spos, 0.0, 0.0]], axis=0)
vecs = np.append(vecs, [[-Spos, 0.0, 0.0]], axis=0)
fout.write(('%s\n\n') % (str(len(data2) + count)))
for line in data2:
s = line.split()
fout.write(
('%s %f %f %f\n') % (s[0], float(s[1]), float(s[2]), float(s[3])))
for v in range(1, vecs.shape[0]):
P = rp.align_vector(readpoly, vecs[v])
for x in range(P.shape[0]):
P[x] = np.add(vecs[v], P[x])
if (x == P.shape[0] - 1):
fout.write(('CH3 %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))
elif (x == 0):
fout.write(('S %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))
else:
fout.write(('CH2 %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))
""" import sys import os import numpy as np import rotate_polymer as rp ############################# ## Number of repeating units ############################# n = 10 ############## ### v must be [x,y,z] ################ v = [-1, -1, -1] ################# ## File to read ################# inputfile = 'HC_chain_n' + str(n) + '.xyz' ################# ## Call Function ################# rp.align_vector(inputfile, v)
import os import numpy as np import rotate_polymer as rp ############################# ## Number of repeating units ############################# n=10 ############## ### v must be [x,y,z] ################ v=[-1,-1,-1] ################# ## File to read ################# inputfile='HC_chain_n' + str(n) +'.xyz' ################# ## Call Function ################# rp.align_vector(inputfile,v)
def graft_HC_hex(save, readpoly, readnp, Rcf, Rct):
fin1 = open(readpoly, 'r')
fin2 = open(readnp, 'r')
fout = open(save, 'w')
f1data = fin1.read()
data1 = f1data.splitlines()
data1 = data1[2:]
print('length of poly is ' + str(len(data1) + 1))
f2data = fin2.read()
data2 = f2data.splitlines()
data2 = data2[2:]
centers = np.array([[0.0, 0.0, 0.0]])
centersout = np.array([[0.0, 0.0, 0.0]])
tophexes = np.array([[0.0, 0.0, 0.0]])
bothexes = np.array([[0.0, 0.0, 0.0]])
count = int(8 * len(data1) + 1)
centers = np.append(centers, [[Rcf, Rcf, Rcf]], axis=0)
centers = np.append(centers, [[Rcf, Rcf, -Rcf]], axis=0)
centers = np.append(centers, [[Rcf, -Rcf, -Rcf]], axis=0)
centers = np.append(centers, [[Rcf, -Rcf, Rcf]], axis=0)
centers = np.append(centers, [[-Rcf, Rcf, Rcf]], axis=0)
centers = np.append(centers, [[-Rcf, -Rcf, Rcf]], axis=0)
centers = np.append(centers, [[-Rcf, Rcf, -Rcf]], axis=0)
centers = np.append(centers, [[-Rcf, -Rcf, -Rcf]], axis=0)
out = 1.137380030
centersout = np.append(centersout, [[Rcf + out, Rcf + out, Rcf + out]],
axis=0)
centersout = np.append(centersout, [[Rcf + out, Rcf + out, -Rcf - out]],
axis=0)
centersout = np.append(centersout, [[Rcf + out, -Rcf - out, -Rcf - out]],
axis=0)
centersout = np.append(centersout, [[Rcf + out, -Rcf - out, Rcf + out]],
axis=0)
centersout = np.append(centersout, [[-Rcf - out, Rcf + out, Rcf + out]],
axis=0)
centersout = np.append(centersout, [[-Rcf - out, -Rcf - out, Rcf + out]],
axis=0)
centersout = np.append(centersout, [[-Rcf - out, Rcf + out, -Rcf - out]],
axis=0)
centersout = np.append(centersout, [[-Rcf - out, -Rcf - out, -Rcf - out]],
axis=0)
for line in data2:
s = line.split()
csv = [s[1], s[2], s[3]]
cf = LA.norm(csv)
vec = np.sqrt((float(s[1])**2) + (float(s[2])**2) + (float(s[3])**2))
if vec == Rct and float(s[3]) >= 0.0 and float(s[2]) >= 0 and float(
s[1]) >= 0:
count += int((2 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
diff = np.subtract(centers[rv], v)
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
if LA.norm(diff) <= 2.0:
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
addout = np.multiply(1.97, cfv)
tophexes = np.append(tophexes,
np.add(addout,
np.subtract(v, 1.393 * diff)),
axis=0)
tophexes = np.append(tophexes,
np.add(addout, np.add(v, 4 * diff)),
axis=0)
if vec == Rct and float(s[3]) >= 0.0 and float(s[2]) <= 0 and float(
s[1]) <= 0:
count += int((2 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
diff = np.subtract(centers[rv], v)
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
if LA.norm(diff) <= 2.0:
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
addout = np.multiply(1.97, cfv)
tophexes = np.append(tophexes,
np.add(addout,
np.subtract(v, 1.393 * diff)),
axis=0)
tophexes = np.append(tophexes,
np.add(addout, np.add(v, 4 * diff)),
axis=0)
if vec == Rct and float(s[3]) <= 0.0 and float(s[2]) >= 0 and float(
s[1]) <= 0:
count += int((2 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
diff = np.subtract(centers[rv], v)
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
if LA.norm(diff) <= 2.0:
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
addout = np.multiply(1.97, cfv)
tophexes = np.append(tophexes,
np.add(addout,
np.subtract(v, 1.393 * diff)),
axis=0)
tophexes = np.append(tophexes,
np.add(addout, np.add(v, 4 * diff)),
axis=0)
if vec == Rct and float(s[3]) <= 0.0 and float(s[2]) <= 0 and float(
s[1]) >= 0:
count += int((2 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
diff = np.subtract(centers[rv], v)
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
if LA.norm(diff) <= 2.0:
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
addout = np.multiply(1.97, cfv)
tophexes = np.append(tophexes,
np.add(addout,
np.subtract(v, 1.393 * diff)),
axis=0)
tophexes = np.append(tophexes,
np.add(addout, np.add(v, 4 * diff)),
axis=0)
V = [[0, 0, 0]]
if vec == Rct and float(s[3]) >= 0.0 and float(s[2]) >= 0 and float(
s[1]) <= 0:
count += int((1 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
k = np.subtract(V, centers[rv])
knor = LA.norm(k)
kt = [
float(k[0][0]) / float(knor),
float(k[0][1]) / float(knor),
float(k[0][2]) / float(knor)
]
K = [[0, -kt[2], kt[1]], [kt[2], 0, -kt[0]],
[-kt[1], kt[0], 0]]
###
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
###
v1 = np.subtract(centers[rv], v)
vn = [v1[0][0], v1[0][1], v1[0][2]]
vnor = LA.norm(vn)
vt = [
float(vn[0]) / float(vnor),
float(vn[1]) / float(vnor),
float(vn[2]) / float(vnor)
]
###
theta = np.pi / 7
theta2 = 2 * np.pi - theta
R = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta), K),
np.multiply((1 - np.cos(theta)), np.dot(K, K))))
R2 = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta2), K),
np.multiply((1 - np.cos(theta2)), np.dot(K, K))))
if LA.norm(v1) <= 2.0:
addout = np.multiply(1.97, cfv)
nnfac = 4.49429
u1 = np.add(np.multiply(Rct, cfv), np.multiply(nnfac, vt))
u = [u1[0], u1[1], u1[2]]
vr = np.dot(R, u)
vr2 = np.dot(R2, u)
bothexes = np.append(bothexes,
np.add([addout], [vr]),
axis=0)
bothexes = np.append(bothexes,
np.add([addout], [vr2]),
axis=0)
V = [[0, 0, 0]]
if vec == Rct and float(s[3]) >= 0.0 and float(s[2]) <= 0 and float(
s[1]) >= 0:
count += int((1 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
k = np.subtract(V, centers[rv])
knor = LA.norm(k)
kt = [
float(k[0][0]) / float(knor),
float(k[0][1]) / float(knor),
float(k[0][2]) / float(knor)
]
K = [[0, -kt[2], kt[1]], [kt[2], 0, -kt[0]],
[-kt[1], kt[0], 0]]
###
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
###
v1 = np.subtract(centers[rv], v)
vn = [v1[0][0], v1[0][1], v1[0][2]]
vnor = LA.norm(vn)
vt = [
float(vn[0]) / float(vnor),
float(vn[1]) / float(vnor),
float(vn[2]) / float(vnor)
]
###
theta = np.pi / 7
theta2 = 2 * np.pi - theta
R = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta), K),
np.multiply((1 - np.cos(theta)), np.dot(K, K))))
R2 = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta2), K),
np.multiply((1 - np.cos(theta2)), np.dot(K, K))))
if LA.norm(v1) <= 2.0:
addout = np.multiply(1.97, cfv)
nnfac = 4.49429
u1 = np.add(np.multiply(Rct, cfv), np.multiply(nnfac, vt))
u = [u1[0], u1[1], u1[2]]
vr = np.dot(R, u)
vr2 = np.dot(R2, u)
bothexes = np.append(bothexes,
np.add([addout], [vr]),
axis=0)
bothexes = np.append(bothexes,
np.add([addout], [vr2]),
axis=0)
V = [[0, 0, 0]]
if vec == Rct and float(s[3]) <= 0.0 and float(s[2]) <= 0 and float(
s[1]) <= 0:
count += int((1 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
k = np.subtract(V, centers[rv])
knor = LA.norm(k)
kt = [
float(k[0][0]) / float(knor),
float(k[0][1]) / float(knor),
float(k[0][2]) / float(knor)
]
K = [[0, -kt[2], kt[1]], [kt[2], 0, -kt[0]],
[-kt[1], kt[0], 0]]
###
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
###
v1 = np.subtract(centers[rv], v)
vn = [v1[0][0], v1[0][1], v1[0][2]]
vnor = LA.norm(vn)
vt = [
float(vn[0]) / float(vnor),
float(vn[1]) / float(vnor),
float(vn[2]) / float(vnor)
]
###
theta = np.pi / 7
theta2 = 2 * np.pi - theta
R = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta), K),
np.multiply((1 - np.cos(theta)), np.dot(K, K))))
R2 = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta2), K),
np.multiply((1 - np.cos(theta2)), np.dot(K, K))))
if LA.norm(v1) <= 2.0:
addout = np.multiply(1.97, cfv)
nnfac = 4.49429
u1 = np.add(np.multiply(Rct, cfv), np.multiply(nnfac, vt))
u = [u1[0], u1[1], u1[2]]
vr = np.dot(R, u)
vr2 = np.dot(R2, u)
bothexes = np.append(bothexes,
np.add([addout], [vr]),
axis=0)
bothexes = np.append(bothexes,
np.add([addout], [vr2]),
axis=0)
V = [[0, 0, 0]]
if vec == Rct and float(s[3]) <= 0.0 and float(s[2]) >= 0 and float(
s[1]) >= 0:
count += int((1 / 3.) * len(data1) + 1)
r1 = float(s[1])
r2 = float(s[2])
r3 = float(s[3])
v = [[r1, r2, r3]]
for rv in range(1, centers.shape[0]):
k = np.subtract(V, centers[rv])
knor = LA.norm(k)
kt = [
float(k[0][0]) / float(knor),
float(k[0][1]) / float(knor),
float(k[0][2]) / float(knor)
]
K = [[0, -kt[2], kt[1]], [kt[2], 0, -kt[0]],
[-kt[1], kt[0], 0]]
###
csv = [centers[rv][0], centers[rv][1], centers[rv][2]]
cf = LA.norm(csv)
cfv = [
float(csv[0]) / float(cf),
float(csv[1]) / float(cf),
float(csv[2]) / float(cf)
]
###
v1 = np.subtract(centers[rv], v)
vn = [v1[0][0], v1[0][1], v1[0][2]]
vnor = LA.norm(vn)
vt = [
float(vn[0]) / float(vnor),
float(vn[1]) / float(vnor),
float(vn[2]) / float(vnor)
]
###
theta = np.pi / 7
theta2 = 2 * np.pi - theta
R = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta), K),
np.multiply((1 - np.cos(theta)), np.dot(K, K))))
R2 = np.add(
np.identity(3),
np.add(np.multiply(np.sin(theta2), K),
np.multiply((1 - np.cos(theta2)), np.dot(K, K))))
if LA.norm(v1) <= 2.0:
addout = np.multiply(1.97, cfv)
nnfac = 4.49429
u1 = np.add(np.multiply(Rct, cfv), np.multiply(nnfac, vt))
u = [u1[0], u1[1], u1[2]]
vr = np.dot(R, u)
vr2 = np.dot(R2, u)
bothexes = np.append(bothexes,
np.add([addout], [vr]),
axis=0)
bothexes = np.append(bothexes,
np.add([addout], [vr2]),
axis=0)
fout.write(('%s\n\n') % (str(len(data2) + count)))
for line in data2:
s = line.split()
fout.write(
('%s %f %f %f\n') % (s[0], float(s[1]), float(s[2]), float(s[3])))
for v in range(1, centersout.shape[0]):
P = rp.align_vector(readpoly, centersout[v])
for i in range(P.shape[0]):
P[i] = np.add(centersout[v], P[i])
if (i == P.shape[0] - 1):
fout.write(('CH3 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(('CH2 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
for v in range(1, tophexes.shape[0]):
P = rp.align_vector(readpoly, tophexes[v])
for i in range(P.shape[0]):
P[i] = np.add(tophexes[v], P[i])
if (i == P.shape[0] - 1):
fout.write(('CH3 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(('CH2 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
for v in range(1, bothexes.shape[0]):
P = rp.align_vector(readpoly, bothexes[v])
for i in range(P.shape[0]):
P[i] = np.add(bothexes[v], P[i])
if (i == P.shape[0] - 1):
fout.write(('CH3 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(('CH2 %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
def graft_PEO_hex(save, readpoly, readnp, R1, R2):
fin1 = open(readpoly, 'r')
fin2 = open(readnp, 'r')
fout = open(save, 'w')
f1data = fin1.read()
data1 = f1data.splitlines()
data1 = data1[2:]
print('length of poly is ' + str(len(data1)))
f2data = fin2.read()
data2 = f2data.splitlines()
data2 = data2[2:]
centers = np.array([[0.0, 0.0, 0.0]])
hexes = np.array([[0.0, 0.0, 0.0]])
count = 0
for line in data2:
s = line.split()
vec = np.sqrt((float(s[1])**2) + (float(s[2])**2) + (float(s[3])**2))
if vec == R1:
count += int(len(data1) + 1)
r1 = float(s[1]) / float(vec) + float(s[1])
r2 = float(s[2]) / float(vec) + float(s[2])
r3 = float(s[3]) / float(vec) + float(s[3])
v = [[r1, r2, r3]]
centers = np.append(centers, v, axis=0)
if vec == R2:
count += int(len(data1) + 1)
r1 = float(s[1]) / float(vec) + float(s[1])
r2 = float(s[2]) / float(vec) + float(s[2])
r3 = float(s[3]) / float(vec) + float(s[3])
v = [[r1, r2, r3]]
hexes = np.append(hexes, v, axis=0)
fout.write(('%s\n\n') % (str(len(data2) + count)))
for line in data2:
s = line.split()
fout.write(
('%s %f %f %f\n') % (s[0], float(s[1]), float(s[2]), float(s[3])))
for v in range(1, centers.shape[0]):
P = rp.align_vector(readpoly, centers[v])
for i in range(P.shape[0]):
P[i] = np.add(centers[v], P[i])
if (i == P.shape[0] - 1):
fout.write(('OH %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(('O %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
newhexes = np.array([[0.0, 0.0, 0.0]])
for v in range(1, hexes.shape[0]):
for i in range(1, centers.shape[0]):
findhexes = np.subtract(centers[i], hexes[v])
norm = np.sqrt(findhexes[0]**2 + findhexes[1]**2 + findhexes[2]**2)
if norm <= 3.18 / (3.96 / np.sqrt(2)):
newhexes = np.append(
newhexes,
[np.add(centers[i], np.multiply(1.28931, findhexes))],
axis=0)
for v in range(1, newhexes.shape[0]):
P = rp.align_vector(readpoly, newhexes[v])
for i in range(P.shape[0]):
P[i] = np.add(newhexes[v], P[i])
#if(i==P.shape[1]-1):
if (i == P.shape[0] - 1):
fout.write(('OH %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
elif (i == 0):
fout.write(('S %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
else:
fout.write(('O %f %f %f\n') % (P[i][0], P[i][1], P[i][2]))
def graft_square_faces(save, readpoly, readnp, R, sulfur_distance):
fin1 = open(readpoly, 'r')
fin2 = open(readnp, 'r')
fout = open(save, 'w')
f1data = fin1.read()
data1 = f1data.splitlines()
data1 = data1[2:]
f2data = fin2.read()
data2 = f2data.splitlines()
data2 = data2[2:]
#####################
#AuSmultiplies a unit vestor to control the AuS initial distance
## AuS^2+.25^2= actual AuS distance ^2
###############3
AuS = 1
s_s = sulfur_distance / np.sqrt(2)
##once the positions of the middle gold atom in the square face is found, four
##chians will be started at the s_s offset away
vecs = np.array([[0.0, 0.0, 0.0]])
counter = 0
for line in data2:
s = line.split()
vec = np.sqrt((float(s[1])**2) + (float(s[2])**2) + (float(s[3])**2))
if vec == R:
counter += int(4 * (len(data1) + 1))
for i in range(0, 4):
if (float(s[1]) != 0):
r2 = s_s * (int(i < 2) * (1 - (2 * i))) + float(s[2])
r3 = s_s * int(i > 1) * (5 - (2 * i)) + float(s[3])
r1 = AuS * float(s[1]) / float(vec) + float(s[1])
elif (float(s[2]) != 0):
r1 = s_s * (int(i < 2) * (1 - (2 * i))) + float(s[1])
r3 = s_s * int(i > 1) * (5 - (2 * i)) + float(s[3])
r2 = AuS * float(s[2]) / float(vec) + float(s[2])
else:
r1 = s_s * (int(i < 2) * (1 - (2 * i))) + float(s[1])
r2 = s_s * int(i > 1) * (5 - (2 * i)) + float(s[2])
r3 = AuS * float(s[3]) / float(vec) + float(s[3])
vecs = np.append(vecs, [[r1, r2, r3]], axis=0)
fout.write(('%s\n\n') % (str(len(data2) + counter)))
for line in data2:
s = line.split()
fout.write(
('%s %f %f %f\n') % (s[0], float(s[1]), float(s[2]), float(s[3])))
for v in range(1, vecs.shape[0]):
P = rp.align_vector(readpoly, vecs[v])
for x in range(P.shape[0]):
P[x] = np.add(vecs[v], P[x])
if (x == P.shape[0] - 1):
fout.write(('OH %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))
elif (x == 0):
fout.write(('S %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))
else:
fout.write(('O %f %f %f\n') % (P[x][0], P[x][1], P[x][2]))