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collectblsandangles.py
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import math
geomfile = open("dyn.xyz").readlines()
gCatzero = geomfile[2]
gCatzero_list = gCatzero.split()
gOatzero = geomfile[3]
gOatzero_list = gOatzero.split()
#defining unit vector along CO at time=0fs
#vector components along x,y,z at t=0fs
ux = float(gCatzero_list[1]) - float(gOatzero_list[1])
uy = float(gCatzero_list[2]) - float(gOatzero_list[2])
uz = float(gCatzero_list[3]) - float(gOatzero_list[3])
#magnitude of vector at t=0fs along CO
u = ((ux**2.0) + (uy**2.0) + (uz**2.0))**(0.5)
#x,y,z of unitvector
ix = ux/u
iy = uy/u
iz = uz/u
alist = [] #list conatining lines
blist = [] #list consisting numbers of lines
linea = 0 #to count number of lines
with open("dyn.xyz",'r') as filea:
for line in filea:
alist.append(line)
blist.append(linea)
linea += 1
j = 2
k = 3
m = 1
n = 4
o = 5
thetalist = []
timelist = []
cdd_diff = []
COlist = []
CD1list = []
CD2list = []
cdddifflist = []
thetaocd1list = []
thetaocd2list = []
deltathetalist = []
thetacd1wrtinitcolist = []
thetacd2wrtinitcolist = []
# The list of the difference in between angles of initial OC-D1 and initial OC-D2
anglediff_list = []
dihedralocd_list = []
dihedralout_list = []
for l in range(1,len(blist)+1):
if j <= len(blist) and k <= len(blist):
#CO bond length, the below 3 will also be used for plane
vx = float(alist[j].split()[1]) - float(alist[k].split()[1])
vy = float(alist[j].split()[2]) - float(alist[k].split()[2])
vz = float(alist[j].split()[3]) - float(alist[k].split()[3])
v = ((vx**2.0) + (vy**2.0) + (vz**2.0))**(0.5)
#unit vectors along CO
iix = vx/v
iiy = vy/v
iiz = vz/v
COlist.append(v)
#CD1 bond length, the below 3 will also be used for plane
cd1x = (float(alist[j].split()[1]) - float(alist[n].split()[1]))
cd1y = (float(alist[j].split()[2]) - float(alist[n].split()[2]))
cd1z = (float(alist[j].split()[3]) - float(alist[n].split()[3]))
cd1 = ((cd1x**2.0) + (cd1y**2.0) + (cd1z**2.0))**(0.5)
cd1ix = cd1x/cd1
cd1iy = cd1y/cd1
cd1iz = cd1z/cd1
CD1list.append(cd1)
#OD1 for ODD plane normal
od1x = (float(alist[k].split()[1]) - float(alist[n].split()[1]))
od1y = (float(alist[k].split()[2]) - float(alist[n].split()[2]))
od1z = (float(alist[k].split()[3]) - float(alist[n].split()[3]))
od1 = ((od1x**2.0) + (od1y**2.0) + (od1z**2.0))**(0.5)
#CD2 bond length, the below 3 will also be used for plane
cd2x = (float(alist[j].split()[1]) - float(alist[o].split()[1]))
cd2y = (float(alist[j].split()[2]) - float(alist[o].split()[2]))
cd2z = (float(alist[j].split()[3]) - float(alist[o].split()[3]))
cd2 = ((cd2x**2.0) + (cd2y**2.0) + (cd2z**2.0))**(0.5)
cd2ix = cd2x/cd2
cd2iy = cd2y/cd2
cd2iz = cd2z/cd2
CD2list.append(cd2)
#OD2 for ODD plane normal
od2x = (float(alist[k].split()[1]) - float(alist[o].split()[1]))
od2y = (float(alist[k].split()[2]) - float(alist[o].split()[2]))
od2z = (float(alist[k].split()[3]) - float(alist[o].split()[3]))
od2 = ((od2x**2.0) + (od2y**2.0) + (od2z**2.0))**(0.5)
#CD1 - CD2
cd1d2 = abs(cd2 - cd1)
cdddifflist.append(cd1d2)
#ANgle O-C-D1
thetaocd1 = (math.acos(((iix*cd1ix)+(iiy*cd1iy)+(iiz*cd1iz))/(1.0*1.0)))*(180.0/3.141593)
thetaocd1list.append(thetaocd1)
#ANgle O-C-D1 wrt initial CO vector
thetacd1wrtinitco = (math.acos(((ix*cd1ix)+(iy*cd1iy)+(iz*cd1iz))/(1.0*1.0)))*(180.0/3.141593)
thetacd1wrtinitcolist.append(thetacd1wrtinitco)
#Angle O-C-D2
thetaocd2 = (math.acos(((iix*cd2ix)+(iiy*cd2iy)+(iiz*cd2iz))/(1.0*1.0)))*(180.0/3.141593)
thetaocd2list.append(thetaocd2)
#ANgle O-C-D2 wrt initial CO vector
thetacd2wrtinitco = (math.acos(((ix*cd2ix)+(iy*cd2iy)+(iz*cd2iz))/(1.0*1.0)))*(180.0/3.141593)
thetacd2wrtinitcolist.append(thetacd2wrtinitco)
# OCD1 - OCD2
deltatheta = abs(thetaocd2 - thetaocd1)
deltathetalist.append(deltatheta)
#Angle differnce wrt initial CO vector
angle_diff = abs(thetacd2wrtinitco - thetacd1wrtinitco)
anglediff_list.append(angle_diff)
#normal vector of OCD1
plncod1x = (vy*cd1z)-(vz*cd1y)
plncod1y = (vz*cd1x)-(vx*cd1z)
plncod1z = (vx*cd1y)-(vy*cd1x)
plncod1 = ((plncod1x**2.0)+(plncod1y**2.0)+(plncod1z**2.0))**0.5
#normal vector of OCD2
plncod2x = (vy*cd2z)-(vz*cd2y)
plncod2y = (vz*cd2x)-(vx*cd2z)
plncod2z = (vx*cd2y)-(vy*cd2x)
plncod2 = ((plncod2x**2.0)+(plncod2y**2.0)+(plncod2z**2.0))**0.5
#normal vector of CDD
plncddx = (cd1y*cd2z)-(cd1z*cd2y)
plncddy = (cd1z*cd2x)-(cd1x*cd2z)
plncddz = (cd1x*cd2y)-(cd1y*cd2x)
plncdd = ((plncddx**2.0)+(plncddy**2.0)+(plncddz**2.0))**0.5
#normal vector of ODD
plnoddx = (od1y*od2z)-(od1z*od2y)
plnoddy = (od1z*od2x)-(od1x*od2z)
plnoddz = (od1x*od2y)-(od1y*od2x)
plnodd = ((plnoddx**2.0)+(plnoddy**2.0)+(plnoddz**2.0))**0.5
# angle between normals of planes
dihedralocd = (math.acos(((plncod1x*plncod2x)+(plncod1y*plncod2y)+(plncod1z*plncod2z))/(plncod1*plncod2)))*(180.0/3.141593)
dihedralocd_list.append(180.0-dihedralocd)
dihedralcdd_odd = (math.acos(((plncddx*plnoddx)+(plncddy*plnoddy)+(plncddz*plnoddz))/(plncdd*plnodd)))*(180.0/3.141593)
dihedralout_list.append(dihedralcdd_odd)
#Timelist
time = alist[m].split()[2]
timelist.append(time)
#Angle of CO wrt CO vector at t=0fs
if ux == vx and uy == vy and uz == vz :
theta = 0.0
thetalist.append(theta)
else:
theta = (math.acos(((ix*iix)+(iy*iiy)+(iz*iiz))/(1.0*1.0)))*(180.0/3.141593)
thetalist.append(theta)
m = m + 6
k = k + 6
j = j + 6
n = n + 6
o = o + 6
l += 1
#print(thetacd1wrtinitcolist)
#for p in range(0,len(timelist)):
# if float(timelist[p]) < 30.0 :
# cd1x = (float(alist[2].split()[1]) - float(alist[n].split()[1]))
# cd1y = (float(alist[2].split()[2]) - float(alist[n].split()[2]))
# cd1z = (float(alist[2].split()[3]) - float(alist[n].split()[3]))
# cd1 = ((cd1x**2.0) + (cd1y**2.0) + (cd1z**2.0))**0.5
# # unit vectors along CD1
# cd1ix = cd1x/cd1
# cd1iy = cd1y/cd1
# cd1iz = cd1z/cd1
# angle of CD1 with initial axis along C=O
# thetacd1 = (math.acos(((ux*cd1ix)+(uy*cd1iy)+(uz*cd1iz))/(u*cd1)))*(180.0/3.141593)
# thetacd1list.append(thetacd1)
# cd2x = (float(alist[2].split()[1]) - float(alist[o].split()[1]))
# cd2y = (float(alist[2].split()[2]) - float(alist[o].split()[2]))
# cd2z = (float(alist[2].split()[3]) - float(alist[o].split()[3]))
# cd2 = ((cd2x**2.0) + (cd2y**2.0) + (cd2z**2.0))**0.5
# unit vectors along CD2
# cd2ix = cd2x/cd2
# cd2iy = cd2y/cd2
# cd2iz = cd2z/cd2
# angle of CD2 with initial axis along C=O
# thetacd2 = (math.acos(((ux*cd2ix)+(uy*cd2iy)+(uz*cd2iz))/(u*cd2)))*(180.0/3.141593)
# thetacd2list.append(thetacd2)
# angle_diff = abs(thetacd1 - thetacd2)
# cdd = abs(cd1 - cd2)
# time = alist[m].split()[2]
# timelist.append(time)
# p += 1
# n = n + 6
# o = o + 6
# r = r + 6
# cdd_diff.append(cdd)
# anglediff_list.append(angle_diff)
# time = alist[m].split()[2]
# timelist.append(time)
with open("intcoors.txt",'w') as fileb:
for n in range(0,len(timelist)):
fileb.write("{0} {1:5f} {2:5f} {3:5f} {4:5f} {5:5f} {6:5f}\n".format(timelist[n],COlist[n],CD1list[n],CD2list[n],thetaocd1list[n],thetaocd2list[n],dihedralocd_list[n]))
n += 1
add = 0.0
add1 = 0.0
add2 = 0.0
add3 = 0.0
add4 = 0.0
#print(anglediff_list)
with open("anglecorrelation.txt",'w') as filee:
for q in range(0,len(timelist)):
if float(timelist[q]) < 11.0:
add = add + cdddifflist[q]
add1 = add1 + anglediff_list[q]
add2 = add2 + deltathetalist[q]
add3 = add3 + dihedralocd_list[q]
add4 = add4 + dihedralout_list[q]
mean_cdd = add/(q+1)
mean_angdiffwrtinitco = add1/(q+1)
mean_angdiff = add2/(q+1)
mean_dihedralocd = add3/(q+1)
mean_dihedralout = add4/(q+1)
filee.write("{0} {1:5f} {2:5f} {3:5f} {4:5f} {5:5f} {6:5f} \n".format(timelist[q],thetalist[q],mean_cdd,mean_angdiff,mean_angdiffwrtinitco,mean_dihedralocd,mean_dihedralout))
q += 1
#listc = []
#liste = []
#linenumb = 0
#Perpendicular velocities of C and O at 0.5 fs
#with open("veloc05.txt",'r') as filef:
# for line in filef:
# listc.append(line)
# liste.append(linenumb)
# linenumb += 1
#CO vecor 0.5 fs
#vvx = float(alist[8].split()[1]) - float(alist[9].split()[1])
#vvy = float(alist[8].split()[2]) - float(alist[9].split()[2])
#vvz = float(alist[8].split()[3]) - float(alist[9].split()[3])
#vv = ((vvx**2.0) + (vvy**2.0) + (vvz**2.0))**(0.5)
#unit vectors along CO at 0.5 fs
#vix = vvx/vv
#viy = vvy/vv
#viz = vvz/vv
#velocity vector of C at 0.5 fs
#vcx = float(listc[1].split()[0])
#vcy = float(listc[1].split()[1])
#vcz = float(listc[1].split()[2])
#vc = ((vcx**2.0) + (vcy**2.0) + (vcz**2.0))**(0.5)
#unit vectors of veloc of C at 0.5 fs
#vcix = vcx/vc
#vciy = vcy/vc
#vciz = vcz/vc
#velocity vector of O at 0.5 fs
#vox = float(listc[2].split()[0])
#voy = float(listc[2].split()[1])
#voz = float(listc[2].split()[2])
#vo = ((vox**2.0) + (voy**2.0) + (voz**2.0))**(0.5)
#unit vectors of veloc of O at 0.5 fs
#voix = vox/vo
#voiy = voy/vo
#voiz = voz/vo
#angleperpC = (math.asin(((vcix*vix)+(vciy*viy)+(vciz*viz))/(1.0*1.0)))*(180.0/3.141593)
#angleperpO = (math.asin(((voix*vix)+(voiy*viy)+(voiz*viz))/(1.0*1.0)))*(180.0/3.141593)
#vcperp = vc*math.sin(angleperpC)
#voperp = vo*math.sin(angleperpO)
#with open("perpveloc.txt",'w') as fileg:
# fileg.write("0.5 {0:5f}\n".format(voperp-vcperp))