def dipoleCoupling(allDipoles):
numDipoles = len(allDipoles[:, 0])
#The dipoles are stored as nx3
coupling = 0
for i in range(numDipoles):
tempNeigh = np.zeros((4, 2))
op.gothrough(allDipoles[0, :], allDipoles, tempNeigh)
for j in range(3):
coupling += np.dot(allDipoles[0, :],
allDipoles[int(tempNeigh[j + 1, 0])])
return coupling / 24
def findNeighbor(coords, lattice):
original_n = coords
#Just being lazy
NN = np.zeros((24, ))
#Store the distance
tempNN = np.zeros((48, 1))
#because of the double counting
count = 0
for i in range(8):
tempN = np.zeros((4, 2))
axis = np.zeros((3, 1))
op.gothrough(original_n[i, :], original_n, tempN)
for j in range(3):
tempNN[count] = tempN[j + 1, 1]
count += 1
nnVec = original_n[int(tempN[j + 1, 0]), :] - original_n[i, :]
axis[j] = determineAxis(nnVec)
if axis[j] > 0:
anotherN = original_n[int(tempN[j + 1,
0]), :] - lattice[int(axis[j] -
1), :]
tempNN[count] = np.linalg.norm(anotherN - original_n[i, :])
count += 1
else:
anotherN = original_n[int(tempN[j + 1, 0]), :] + lattice[
-int(axis[j] + 1), :]
tempNN[count] = np.linalg.norm(anotherN - original_n[i, :])
count += 1
'''Remove Double Counting'''
count = 0
NN[0] = tempNN[0]
for i in range(48):
count2 = 0
for j in range(count):
if tempNN[i] == NN[j]:
count2 += 1
break
if count2 == 0:
NN[count] = tempNN[i]
count += 1
if count == 24:
break
else:
continue
return NN
def findMolecules(name):
#import the coordinates
lattice = np.zeros((3, 3))
original_pb = np.zeros((8, 3))
original_cl = np.zeros((24, 3))
original_c = np.zeros((8, 3))
original_n = np.zeros((8, 3))
original_h = np.zeros((48, 3))
op.in_coord(name, lattice, original_pb, original_cl, original_c,
original_n, original_h)
molecules = np.zeros((8, 3))
for i in range(8):
tempN = np.zeros((3, 2))
op.gothrough(original_c[i, :], original_n, tempN)
molecules[i] = original_n[int(tempN[0, 0]), :] - original_c[i, :]
return molecules
def findDeviation(name):
lattice = np.zeros((3, 3))
original_pb = np.zeros((8, 3))
original_cl = np.zeros((24, 3))
original_c = np.zeros((8, 3))
original_n = np.zeros((8, 3))
original_h = np.zeros((48, 3))
op.in_coord(name, lattice, original_pb, original_cl, original_c,
original_n, original_h)
#enlarge the unit cell by 8 times
pb = np.zeros((64, 3))
cl = np.zeros((192, 3))
c = np.zeros((64, 3))
n = np.zeros((64, 3))
h = np.zeros((384, 3))
op.enlarge(original_pb, pb, lattice, 8)
op.enlarge(original_cl, cl, lattice, 24)
op.enlarge(original_c, c, lattice, 8)
op.enlarge(original_n, n, lattice, 8)
op.enlarge(original_h, h, lattice, 48)
#find the center of C-N
CNCenter = np.zeros((64, 3))
for i in range(64):
temp = np.zeros((3, 2))
op.gothrough(n[i], c, temp)
CNCenter[i] = 1 / 2 * (n[i] + c[int(temp[0, 0])])
#Find the 4 molecules that surround the Cl atoms. Take N atoms as indicator. Store the index
cl_n = np.zeros((24, 4))
for i in range(24):
temp = np.zeros((4, 2))
op.gothrough(original_cl[i], CNCenter, temp)
if temp[-1, 1] > 6:
print("There is something wrong my friend.")
sys.exit()
cl_n[i, :] = temp[:, 0]
#Assume the ideal ideal hydrogen bond number is 1 for each Cl atom
NumHBond = np.zeros((24, 1))
r0 = 2.2
B = 0.3
for i in range(24):
for j in range(4):
tempH = np.zeros((3, 2))
indexN = int(cl_n[i, j])
op.gothrough(n[indexN], h, tempH)
for k in range(3):
dij = np.linalg.norm(original_cl[i, :] - h[int(tempH[k, 0])])
NumHBond[i, 0] += countFD(r0, B, dij)
deviation = np.zeros((8, 1))
deviation = np.square(NumHBond - 1)
totDevi = np.sum(deviation)
return totDevi
def euler(index_pb, original_pb, cl):
pb = original_pb[int(index_pb), :]
temp_cl = np.zeros((6, 2))
the_cl = np.zeros((6, 3))
op.gothrough(pb, cl, temp_cl)
for i in range(6):
the_cl[i, :] = cl[int(temp_cl[i][0]), :]
#Determine the new x,y,z principal axis
axis_index = np.full((3, 2), -1)
#x-x, y-y, z-z
max_xyz = np.zeros((3, 1))
for i in range(6):
for j in range(i, 6, 1):
for k in range(3):
distance = abs(the_cl[i][k] - the_cl[j][k])
if distance > max_xyz[k]:
max_xyz[k] = distance
axis_index[k][0] = i
axis_index[k][1] = j
principal = np.zeros((3, 3))
#x,y,z new principal axis
for i in range(3):
principal[i, :] = the_cl[int(axis_index[i][0])] - the_cl[int(
axis_index[i][1])]
if principal[i][i] < 0:
principal[i, :] = -1 * principal[i, :]
principal[i, :] = principal[i, :] / np.linalg.norm(principal[i, :])
##===z followed by y followed by x===####
alpha = ma.asin(-principal[2][1] / ma.sqrt(1 - principal[2][0]**2))
beta = ma.asin(principal[2][0])
gamma = ma.asin(-principal[1][0] / ma.sqrt(1 - principal[2][0]**2))
return alpha * 180 / ma.pi, beta * 180 / ma.pi, gamma * 180 / ma.pi
def findNHBond(name):
#import the coordinates
lattice = np.zeros((3,3));
original_pb = np.zeros((8,3));
original_cl = np.zeros((24,3));
original_c = np.zeros((8,3));
original_n = np.zeros((8,3));
original_h = np.zeros((48,3));
op.in_coord(name, lattice, original_pb, original_cl, original_c, original_n, original_h);
#enlarge the unit cell by 8 times
pb = np.zeros((64,3));
cl = np.zeros((192,3));
c = np.zeros((64,3));
n = np.zeros((64,3));
h = np.zeros((384,3));
op.enlarge(original_pb,pb,lattice,8);
op.enlarge(original_cl,cl,lattice,24);
op.enlarge(original_c,c,lattice,8);
op.enlarge(original_n,n,lattice,8);
op.enlarge(original_h,h,lattice,48);
the_n = np.zeros((8,3));
index_n = np.zeros((8,1));
the_c = np.zeros((8,3));
index_c = np.zeros((8,1));
the_cl = np.zeros((8,12,3));
the_pb = np.zeros((8,8,3));
distance_o_cl = np.zeros((8,12));
distance_h_cl = np.zeros((8,3));
#first get one small cell
count = 0;
for i in range(64):
temp_n = n[i];
temp_center = np.zeros((3,1));
temp_cn = np.zeros((64,2));
op.gothrough(temp_n,c,temp_cn);
temp_c = c[int(temp_cn[0][0])];
op.midpoint(temp_c,temp_n,temp_center);#determine the center coordinate
#determine the neighbor Cl atoms
temp_o_cl = np.zeros((12,2));
op.gothrough(temp_center, cl, temp_o_cl);
#determine the neighbor Pb atoms
temp_o_pb = np.zeros((8,2));
op.gothrough(temp_center,pb,temp_o_pb);
if temp_o_cl[11][1] > 5.5:
continue;
else:
#determine the H(N) atoms in this unit cell
temp_h_n = np.zeros((3,2));
op.gothrough(temp_n, h, temp_h_n);
temp_nh_cl = np.zeros((3,2));
for j in range(3):
op.gothrough(h[int(temp_h_n[j][0])],cl,temp_nh_cl[j,:]);
#decide whether we choose this unit cell or not, trying to avoid overlap
count2 = 0;
for j in range(count+1):
indicator1 = np.linalg.norm(temp_o_cl[:,1] - distance_o_cl[j,:]);
indicator2 = np.linalg.norm(temp_nh_cl[:,1] - distance_h_cl[j,:]);
# print(indicator1)
# print(indicator2)
if indicator1 > 0.0000001 and indicator2 > 0.0000001:
count2 = count2 + 1;
continue;
else:
break;
if count2 == count+1:
distance_o_cl[count,:] = temp_o_cl[:,1];
distance_h_cl[count,:] = temp_nh_cl[:,1];
the_n[count] = temp_n;
the_c[count] = temp_c;
index_n[count] = i;
index_c[count] = temp_cn[0][0];
for k in range(12):
the_cl[count][k] = cl[int(temp_o_cl[k][0])];
for k in range(8):
the_pb[count][k] = pb[int(temp_o_pb[k][0])];
count = count + 1;
#rearrange the chlorine atoms
for i in range(8):
op.rearrange(the_cl[i]);
#After spliting into small cell, let's calculate the hydrogen bonds length.
#Every Hydrogen atom keep its first two shortest distances between Cl
the_nh = np.zeros((8,3,3));
the_ch = np.zeros((8,3,3));
for i in range(8):
temp_h_n = np.zeros((3,2));
temp_h_c = np.zeros((3,2));
op.gothrough(the_n[i],h,temp_h_n);
op.gothrough(the_c[i],h,temp_h_c);
for j in range(3):
the_nh[i][j] = h[int(temp_h_n[j][0])];
the_ch[i][j] = h[int(temp_h_c[j][0])];
#3rd method
r0 = 2.2;
B = 0.3;
numHBond = np.zeros((8,1));
for i in range(8):
for j in range(3):
for k in range(12):
dij = np.linalg.norm(the_nh[i][j] - the_cl[i][k]);
numHBond[i,0] += countFD(r0,B,dij);
#print(numHBond)
aveBond = np.sum(numHBond)/24;
return aveBond;
def findNHBond(name):
#import the coordinates
lattice = np.zeros((3, 3))
original_pb = np.zeros((8, 3))
original_cl = np.zeros((24, 3))
original_c = np.zeros((8, 3))
original_n = np.zeros((8, 3))
original_h = np.zeros((48, 3))
op.in_coord(name, lattice, original_pb, original_cl, original_c,
original_n, original_h)
#enlarge the unit cell by 8 times
pb = np.zeros((64, 3))
cl = np.zeros((192, 3))
c = np.zeros((64, 3))
n = np.zeros((64, 3))
h = np.zeros((384, 3))
op.enlarge(original_pb, pb, lattice, 8)
op.enlarge(original_cl, cl, lattice, 24)
op.enlarge(original_c, c, lattice, 8)
op.enlarge(original_n, n, lattice, 8)
op.enlarge(original_h, h, lattice, 48)
the_n = np.zeros((8, 3))
index_n = np.zeros((8, 1))
the_c = np.zeros((8, 3))
index_c = np.zeros((8, 1))
the_cl = np.zeros((8, 12, 3))
the_pb = np.zeros((8, 8, 3))
distance_o_cl = np.zeros((8, 12))
distance_h_cl = np.zeros((8, 3))
#first get one small cell
count = 0
for i in range(64):
temp_n = n[i]
temp_center = np.zeros((3, 1))
temp_cn = np.zeros((64, 2))
op.gothrough(temp_n, c, temp_cn)
temp_c = c[int(temp_cn[0][0])]
op.midpoint(temp_c, temp_n, temp_center)
#determine the center coordinate
#determine the neighbor Cl atoms
temp_o_cl = np.zeros((12, 2))
op.gothrough(temp_center, cl, temp_o_cl)
#determine the neighbor Pb atoms
temp_o_pb = np.zeros((8, 2))
op.gothrough(temp_center, pb, temp_o_pb)
if temp_o_cl[11][1] > 5.5:
continue
else:
#determine the H(N) atoms in this unit cell
temp_h_n = np.zeros((3, 2))
op.gothrough(temp_n, h, temp_h_n)
temp_nh_cl = np.zeros((3, 2))
for j in range(3):
op.gothrough(h[int(temp_h_n[j][0])], cl, temp_nh_cl[j, :])
#decide whether we choose this unit cell or not, trying to avoid overlap
count2 = 0
for j in range(count + 1):
indicator1 = np.linalg.norm(temp_o_cl[:, 1] -
distance_o_cl[j, :])
indicator2 = np.linalg.norm(temp_nh_cl[:, 1] -
distance_h_cl[j, :])
# print(indicator1)
# print(indicator2)
if indicator1 > 0.0000001 and indicator2 > 0.0000001:
count2 = count2 + 1
continue
else:
break
if count2 == count + 1:
distance_o_cl[count, :] = temp_o_cl[:, 1]
distance_h_cl[count, :] = temp_nh_cl[:, 1]
the_n[count] = temp_n
the_c[count] = temp_c
index_n[count] = i
index_c[count] = temp_cn[0][0]
for k in range(12):
the_cl[count][k] = cl[int(temp_o_cl[k][0])]
for k in range(8):
the_pb[count][k] = pb[int(temp_o_pb[k][0])]
count = count + 1
#rearrange the chlorine atoms
for i in range(8):
op.rearrange(the_cl[i])
#After spliting into small cell, let's calculate the hydrogen bonds length.
the_nh = np.zeros((8, 3, 3))
the_ch = np.zeros((8, 3, 3))
for i in range(8):
temp_h_n = np.zeros((3, 2))
temp_h_c = np.zeros((3, 2))
op.gothrough(the_n[i], h, temp_h_n)
op.gothrough(the_c[i], h, temp_h_c)
for j in range(3):
the_nh[i][j] = h[int(temp_h_n[j][0])]
the_ch[i][j] = h[int(temp_h_c[j][0])]
#Now starting to calculate the LJ terms
#For all Cl atoms in one small cell
HCl_6LJ = np.zeros((8, 1))
HCl_12LJ = np.zeros((8, 1))
CHCl_6LJ = np.zeros((8, 1))
CHCl_12LJ = np.zeros((8, 1))
NCl_6LJ = np.zeros((8, 1))
NCl_12LJ = np.zeros((8, 1))
CCl_6LJ = np.zeros((8, 1))
CCl_12LJ = np.zeros((8, 1))
for i in range(8):
for j in range(12):
dij_NCl = np.linalg.norm(the_n[i] - the_cl[i, j])
dij_CCl = np.linalg.norm(the_c[i] - the_cl[i, j])
NCl_6LJ[i, 0] += count6LJ(dij_NCl)
NCl_12LJ[i, 0] += count12LJ(dij_NCl)
CCl_6LJ[i, 0] += count6LJ(dij_CCl)
CCl_12LJ[i, 0] += count12LJ(dij_CCl)
for j in range(3):
for k in range(12):
dij = np.linalg.norm(the_nh[i][j] - the_cl[i][k])
dij_CH = np.linalg.norm(the_ch[i][j] - the_cl[i][k])
HCl_6LJ[i, 0] += count6LJ(dij)
HCl_12LJ[i, 0] += count12LJ(dij)
CHCl_6LJ[i, 0] += count6LJ(dij_CH)
CHCl_12LJ[i, 0] += count12LJ(dij_CH)
#For the nearest 3 Cl atoms for H
# for i in range(8):
# for j in range(12):
# dij_NCl = np.linalg.norm(the_n[i] - the_cl[i,j]);
# NCl_6LJ[i,0] += count6LJ(dij_NCl);
# NCl_12LJ[i,0] += count12LJ(dij_NCl);
#
# for j in range(3):
# tempCl = np.zeros((3,2));
# op.gothrough(the_nh[i,j],the_cl[i],tempCl);
# for k in range(3):
# dij = tempCl[k,1];
# HCl_6LJ[i,0] += count6LJ(dij);
# HCl_12LJ[i,0] += count12LJ(dij);
return np.sum(HCl_6LJ), np.sum(HCl_12LJ), np.sum(CHCl_6LJ),\
np.sum(CHCl_12LJ),np.sum(NCl_6LJ), np.sum(NCl_12LJ),np.sum(CCl_6LJ), np.sum(CCl_12LJ)
def findChargeCenter(name):
'''Atoms and Charge should be one-to-one correspondance'''
#import the coordinates
lattice = np.zeros((3, 3))
original_pb = np.zeros((8, 3))
original_cl = np.zeros((24, 3))
original_c = np.zeros((8, 3))
original_n = np.zeros((8, 3))
original_h = np.zeros((48, 3))
op.in_coord(name, lattice, original_pb, original_cl, original_c,
original_n, original_h)
#enlarge the unit cell by 8 times
pb = np.zeros((64, 3))
cl = np.zeros((192, 3))
c = np.zeros((64, 3))
n = np.zeros((64, 3))
h = np.zeros((384, 3))
op.enlarge(original_pb, pb, lattice, 8)
op.enlarge(original_cl, cl, lattice, 24)
op.enlarge(original_c, c, lattice, 8)
op.enlarge(original_n, n, lattice, 8)
op.enlarge(original_h, h, lattice, 48)
the_n = np.zeros((8, 3))
index_n = np.zeros((8, 1))
the_c = np.zeros((8, 3))
index_c = np.zeros((8, 1))
the_cl = np.zeros((8, 12, 3))
the_pb = np.zeros((8, 8, 3))
distance_o_cl = np.zeros((8, 12))
distance_h_cl = np.zeros((8, 3))
# mapToOrigin = np.zeros((8,2));# Tell which original molecule they actually correspond to
# mapToOrigin[:,0] = np.arange(0,8,1);
mapToOrigin = np.zeros((8, 1))
#first get one small cell
count = 0
for i in range(64):
temp_n = n[i]
temp_center = np.zeros((3, 1))
temp_cn = np.zeros((64, 2))
op.gothrough(temp_n, c, temp_cn)
temp_c = c[int(temp_cn[0][0])]
op.midpoint(temp_c, temp_n, temp_center)
#determine the center coordinate
#determine the neighbor Cl atoms
temp_o_cl = np.zeros((12, 2))
op.gothrough(temp_center, cl, temp_o_cl)
#determine the neighbor Pb atoms
temp_o_pb = np.zeros((8, 2))
op.gothrough(temp_center, pb, temp_o_pb)
if temp_o_cl[11][1] > 5.5:
continue
else:
#determine the H(N) atoms in this unit cell
temp_h_n = np.zeros((3, 2))
op.gothrough(temp_n, h, temp_h_n)
temp_nh_cl = np.zeros((3, 2))
for j in range(3):
op.gothrough(h[int(temp_h_n[j][0])], cl, temp_nh_cl[j, :])
#decide whether we choose this unit cell or not, trying to avoid overlap
count2 = 0
for j in range(count + 1):
indicator1 = np.linalg.norm(temp_o_cl[:, 1] -
distance_o_cl[j, :])
indicator2 = np.linalg.norm(temp_nh_cl[:, 1] -
distance_h_cl[j, :])
if indicator1 > 0.0000001 and indicator2 > 0.0000001:
count2 = count2 + 1
continue
else:
break
if count2 == count + 1:
distance_o_cl[count, :] = temp_o_cl[:, 1]
distance_h_cl[count, :] = temp_nh_cl[:, 1]
the_n[count] = temp_n
the_c[count] = temp_c
index_n[count] = i
mapToOrigin[count] = i % 8
index_c[count] = temp_cn[0][0]
for k in range(12):
the_cl[count][k] = cl[int(temp_o_cl[k][0])]
for k in range(8):
the_pb[count][k] = pb[int(temp_o_pb[k][0])]
count = count + 1
#rearrange the chlorine atoms
for i in range(8):
op.rearrange(the_cl[i])
#Find the hydrogen atoms in each of the cell
the_nh = np.zeros((8, 3, 3))
the_ch = np.zeros((8, 3, 3))
for i in range(8):
temp_h_n = np.zeros((3, 2))
temp_h_c = np.zeros((3, 2))
op.gothrough(the_n[i], h, temp_h_n)
op.gothrough(the_c[i], h, temp_h_c)
for j in range(3):
the_nh[i][j] = h[int(temp_h_n[j][0])]
the_ch[i][j] = h[int(temp_h_c[j][0])]
'''Charges. Could be replaced with Bader Charge'''
qCl = -1
qPb = 2
qC = -2
qN = -3
qH = 1
orgoCenter = np.zeros((8, 3))
inorgoCenter = np.zeros((8, 3))
for i in range(8):
tempCenter = np.zeros((1, 3))
for j in range(8):
tempCenter += abs(qPb) * the_pb[i][j][:]
for j in range(12):
tempCenter += abs(qCl) * the_cl[i][j][:]
inorgoCenter[i, :] = tempCenter / (8 * abs(qPb) + 12 * abs(qCl))
pullBackFactor = np.round(
np.matmul(np.linalg.inv(lattice),
n[int(index_n[i])] - n[int(mapToOrigin[i])]))
inorgoCenter[i, :] = inorgoCenter[i, :] - np.matmul(
lattice, pullBackFactor)
for i in range(8):
tempCenter = np.zeros((1, 3))
for j in range(3):
tempCenter += abs(qH) * the_nh[i][j][:]
for j in range(3):
tempCenter += abs(qH) * the_ch[i][j][:]
tempCenter += abs(qC) * the_c[i, :] + abs(qN) * the_n[i, :]
orgoCenter[i, :] = tempCenter / (6 * abs(qH) + abs(qC) + abs(qN))
pullBackFactor = np.round(
np.matmul(np.linalg.inv(lattice),
n[int(index_n[i])] - n[int(mapToOrigin[i])]))
orgoCenter[i, :] = orgoCenter[i, :] - np.matmul(
lattice, pullBackFactor)
mapToOrigin = np.argsort(mapToOrigin, axis=0)
orgo = orgoCenter[np.int64(mapToOrigin[:, 0]).reshape([8, 1]), [0, 1, 2]]
inorgo = inorgoCenter[np.int64(mapToOrigin[:, 0]).reshape([8, 1]),
[0, 1, 2]]
return orgo, inorgo
NIcouple = np.zeros((200, 1))
NHighSymCouple = np.zeros((200, 1))
'''One body term'''
d2 = np.zeros((200, 8))
d4 = np.zeros((200, 8))
for i in range(200):
name = 'rand_' + str(i + 51) + '.xsf'
NN[i, :], original_N = findNN(name)
molecules[i] = findMolecules(name)
#Find the nearest high symmetry position
for j in range(8):
tempHighSym = np.zeros((3, 2))
op.gothrough(original_N[j, :], highSym, tempHighSym)
dipoleNHighSym[i, j, :] = original_N[j, :] - highSym[int(
tempHighSym[0, 0])]
d2[i] = np.square(np.linalg.norm(dipoleNHighSym[i], axis=1))
# d2[i] = np.square(np.linalg.norm(molecules[i],axis=1));
d4[i] = np.sum(np.power(dipoleNHighSym[i], 4), axis=1)
# for j in range(8):
# d2[i,j] = molecules[i,j,0]**2 + molecules[i,j,1]**2 + molecules[i,j,2]**2;
# d4[i,j] = molecules[i,j,0]**4 + molecules[i,j,1]**4 + molecules[i,j,2]**4;
print(np.sum(d2[i]))
# print(molecules)
# aveNN[i] = np.mean(NN[i,:]);
for j in range(4):
for k in range(3):
diff_pb[j][k] = round(diff_pb[j][k] / lattice[k][k])
all_pb[i][j] = all_pb[i][j] - np.matmul(diff_pb[j], lattice)
for j in range(12):
for k in range(3):
diff_i[j][k] = round(diff_i[j][k] / lattice[k][k])
all_i[i][j] = all_i[i][j] - np.matmul(diff_i[j], lattice)
'''Get the rotation of each molecule. phi, cos(theta)'''
molecules = np.zeros((numStruct, 4, 2))
for i in range(numStruct):
for j in range(4):
tempN = np.zeros((3, 2))
op.gothrough(all_c[i][j], all_n[i], tempN)
tempMolecule = all_n[i][int(tempN[0][0])] - all_c[i][j]
tempMolecule = tempMolecule / np.linalg.norm(tempMolecule)
molecules[i][j][1] = tempMolecule[2]
x = tempMolecule[0]
y = tempMolecule[1]
if tempMolecule[1] > 0:
molecules[i][j][0] = ma.acos(x / (x**2 + y**2)**0.5) / ma.pi * 180
else:
molecules[i][j][0] = 360 - ma.acos(
x / (x**2 + y**2)**0.5) / ma.pi * 180
fig1 = plt.figure(figsize=(20, 16))
mole1 = fig1.add_subplot(2, 2, 1)
mole1.plot(molecules[:, 0, 0])
plt.title('Molecule 1', fontsize=20)
