def calculateElevels(self):
R = self.R
kb = self.kb
h = self.h
amu = self.amu
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
E=[]
#let us take k = -500, 500
m = 200
#print K
for irot in range(len(self.Harmonics)):
H = mat(zeros((2*m+1,2*m+1),dtype=complex))
kcos = self.Harmonics[irot].Kcos
ksin = self.Harmonics[irot].Ksin
for k in range(0,2*m+1):
H[k,k] = 6.023e23*h**2*(k-m)**2/8.0/math.pi**2/K[irot]/amu/1e-20/4180 + self.Harmonics[irot].A
for n in range(1,6):
if k-n >= 0:
H[k,k-n] = kcos[n-1]/2 + ksin[n-1]/2j
if k+n < 2*m+1:
H[k,k+n] = kcos[n-1]/2 - ksin[n-1]/2j
(l,v) = linalg.eigh(H)
#pdb.set_trace()
E.append(l)
return E
def printData(self, oFile):
geom = self.geom
Mass = self.Mass
oFile.write('Geometry:\n')
oFile.write('%10s' % 'Mass(amu)' + '%10s' % 'X(ang)' +
'%10s' % 'Y(ang)' + '%10s' % 'Z(ang)' + '\n')
for i in range(Mass.size):
oFile.write('%10.3f' % float(Mass[i]) +
'%10.4f' % float(geom[i, 0]) +
'%10.4f' % float(geom[i, 1]) +
'%10.4f' % float(geom[i, 2]) + '\n')
oFile.write('\nFrequencies (cm-1):\n')
Freq = self.Freq
if self.TS:
oFile.write('Imaginary Frequency: ' + str(self.imagFreq) + '\n')
for i in range(len(Freq) / 3 + 1):
for j in range(3):
if 3 * i + j < len(Freq):
oFile.write('%10.3f' % Freq[3 * i + j])
oFile.write('\n')
oFile.write('\nExternal Symmetry = ' + str(self.extSymm) + '\n')
oFile.write('Principal Moments of Inertia = ' + str(self.Iext[0]) +
' ' + str(self.Iext[1]) + ' ' + str(self.Iext[2]) + '\n')
oFile.write('Electronic Degeneracy = ' + str(self.nelec) + '\n')
if self.numRotors == 0:
return
oFile.write(
'\nFitted Harmonics V(p) = sum (A_i cos(i*p) + B_i sin(i*p)) :\n')
k = 1
K = geomUtility.calculateD32(self.geom, self.Mass, self.rotors)
for harmonic in self.Harmonics:
oFile.write('Harmonic ' + str(k) + '\n')
oFile.write('Moment of Inertia: ' + str(float(K[k - 1])) + '\n')
oFile.write('Symmetry ' + str(self.rotors[k].symm) + '\n')
oFile.write('BarrierHeight ' + str(harmonic.Barrier_Height) + '\n')
oFile.write('%12s' % 'A_i' + '%12s' % 'B_i' + '\n')
for j in range(5):
oFile.write('%12.3e' % harmonic.Kcos[j] +
'%12.3e' % harmonic.Ksin[j] + '\n')
oFile.write('\n')
k = k + 1
def calculateElevels(self):
R = self.R
kb = self.kb
h = self.h
amu = self.amu
K = geomUtility.calculateD32(self.geom, self.Mass, self.rotors)
E = []
#let us take k = -500, 500
m = 200
ke = 6.023e23 * h**2 / 8.0 / math.pi**2 / amu / 1e-20 / 4180 #frequently used quantity for the kinetic energy part of the matrix
#print K
for irot in range(len(self.Harmonics)):
H = mat(zeros((2 * m + 1, 2 * m + 1), dtype=complex))
kcos = self.Harmonics[irot].Kcos
ksin = self.Harmonics[irot].Ksin
icos = self.Harmonics[irot].Icos
isin = self.Harmonics[irot].Isin
for k in range(0, 2 * m + 1):
H[k, k] = self.Harmonics[irot].A
if self.variableInertia:
H[k, k] += ke * (k - m) * (k - m) * self.Harmonics[irot].B
else:
H[k, k] += ke * (k - m) * (k - m) / float(K[irot])
for n in range(1, 6):
if k - n >= 0:
H[k, k - n] = kcos[n - 1] / 2 + ksin[n - 1] / 2j
if self.variableInertia:
H[k, k - n] += (icos[n - 1] / 2 + isin[n - 1] /
2j) * ke * (k - m) * (k - n - m)
if k + n < 2 * m + 1:
H[k, k + n] = kcos[n - 1] / 2 - ksin[n - 1] / 2j
if self.variableInertia:
H[k, k + n] += (icos[n - 1] / 2 - isin[n - 1] /
2j) * ke * (k - m) * (k + n - m)
(l, v) = linalg.eigh(H)
#pdb.set_trace()
E.append(l)
return E
def calculateElevels(self):
R = self.R
kb = self.kb
h = self.h
amu = self.amu
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
E=[]
#let us take k = -500, 500
m = 200
ke = 6.023e23*h**2/8.0/math.pi**2/amu/1e-20/4180 #frequently used quantity for the kinetic energy part of the matrix
#print K
for irot in range(len(self.Harmonics)):
H = mat(zeros((2*m+1,2*m+1),dtype=complex))
kcos = self.Harmonics[irot].Kcos
ksin = self.Harmonics[irot].Ksin
icos = self.Harmonics[irot].Icos
isin = self.Harmonics[irot].Isin
for k in range(0,2*m+1):
H[k,k] = self.Harmonics[irot].A
if self.variableInertia:
H[k,k] += ke*(k-m)*(k-m)*self.Harmonics[irot].B
else:
H[k,k] += ke*(k-m)*(k-m)/float(K[irot])
for n in range(1,6):
if k-n >= 0:
H[k,k-n] = kcos[n-1]/2 + ksin[n-1]/2j
if self.variableInertia:
H[k,k-n]+= (icos[n-1]/2 + isin[n-1]/2j)*ke*(k-m)*(k-n-m)
if k+n < 2*m+1:
H[k,k+n] = kcos[n-1]/2 - ksin[n-1]/2j
if self.variableInertia:
H[k,k+n] += (icos[n-1]/2 - isin[n-1]/2j)*ke*(k-m)*(k+n-m)
(l,v) = linalg.eigh(H)
#pdb.set_trace()
E.append(l)
return E
def printData(self,oFile):
geom = self.geom
Mass = self.Mass
oFile.write('Geometry:\n')
oFile.write('%10s'%'Mass(amu)'+'%10s'%'X(ang)'+'%10s'%'Y(ang)'+'%10s'%'Z(ang)'+'\n')
for i in range(Mass.size):
oFile.write('%10.3f'%float(Mass[i])+'%10.4f'%float(geom[i,0])+'%10.4f'%float(geom[i,1])+'%10.4f'%float(geom[i,2])+'\n')
oFile.write('\nFrequencies (cm-1):\n')
Freq = self.Freq
if self.TS:
oFile.write('Imaginary Frequency: '+str(self.imagFreq)+'\n')
for i in range(len(Freq)/3+1):
for j in range(3):
if 3*i+j <len(Freq):
oFile.write('%10.3f'%Freq[3*i+j])
oFile.write('\n')
oFile.write('\nExternal Symmetry = '+str(self.extSymm)+'\n')
oFile.write('Principal Moments of Inertia = '+str(self.Iext[0])+' '+str(self.Iext[1])+' '+str(self.Iext[2])+'\n')
oFile.write('Electronic Degeneracy = '+str(self.nelec)+'\n')
if self.numRotors == 0:
return
oFile.write('\nFitted Harmonics V(p) = sum (A_i cos(i*p) + B_i sin(i*p)) :\n' )
k = 1
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
for harmonic in self.Harmonics:
oFile.write('Harmonic '+str(k)+'\n')
oFile.write('Moment of Inertia: '+ str(float(K[k-1]))+'\n')
oFile.write('Symmetry '+str(self.rotors[k].symm)+'\n')
oFile.write('BarrierHeight '+str(harmonic.A)+'\n')
oFile.write('%12s'%'A_i'+'%12s'%'B_i'+'\n')
for j in range(5):
oFile.write('%12.3e'%harmonic.Kcos[j]+'%12.3e'%harmonic.Ksin[j]+'\n')
oFile.write('\n')
k = k+1
def getIntRotationalThermo_Q(self,oFile,Temp):
ent = [0.0]*len(Temp)
cp = [0.0]*len(Temp)
dH = [0.0]*len(Temp)
parti = [1.0]*len(Temp)
R = self.R
kb = self.kb
h = self.h
amu = self.amu
oFile.write('\n\nInternal Rotational Contributions\n')
oFile.write('%12s'%'Temperature')
#iterate over temperatures
for T in Temp:
oFile.write('%12.2f'%T)
sigma = 1.0
for rotor in self.rotors:
sigma = sigma*rotor.symm
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
for irot in range(len(self.rotors)-1):
harm = self.Harmonics[irot]
ddv = 0.0
for l in range(5):
ddv = ddv-1*harm.Kcos[l]*(l+1)**2
freq = 1.0/2.0/pi*sqrt(ddv*4180.0/K[irot]/1.0e-20/amu/6.023e23)/3.0e10
#print '%12.2f'%float(freq),
#print
#calculate the energy levels for the hindered rotors
E = self.calculateElevels()
#pdb.set_trace()
for iT in range(len(Temp)):
T = Temp[iT]
#print T,
for irot in range(len(self.rotors)-1):
sum = 0.0
vsum = 0.0
v2sum = 0.0
for e in E[irot]:
e = e - E[irot][0]
sum = sum + exp(-e*1.0e3/R/T)
vsum = vsum + e*1e3*exp(-e*1.0e3/R/T)
v2sum = v2sum + e**2*1e6*exp(-e*1.0e3/R/T)
ent[iT] = ent[iT] + R*math.log(sum)+vsum/sum/T-R*log(self.rotors[irot+1].symm)
dH[iT] = dH[iT] + vsum/sum/1.0e3
cp[iT] = cp[iT] + (v2sum*sum-vsum**2)/sum**2/R/T**2
parti[iT] = parti[iT] *sum
#print (v2sum*sum-vsum**2)/sum**2/R/T**2,
#print R*math.log(sum)+vsum/sum/T-R*log(self.rotors[irot+1].symm),
#print
oFile.write('\n%12s'%'Entropy')
for i in range(len(Temp)):
oFile.write('%12.2f'%ent[i])
oFile.write('\n%12s'%'Cp')
for i in range(len(Temp)):
oFile.write('%12.2f'%cp[i])
oFile.write('\n%12s'%'dH')
for i in range(len(Temp)):
oFile.write('%12.2f'%dH[i])
oFile.write('\n%12s'%'q_int')
for i in range(len(Temp)):
oFile.write('%12.2e'%parti[i])
oFile.write('\n')
return ent, cp , dH, parti
def getIntRotationalThermo_PG(self,oFile,Temp):
ent = []
cp = []
dH = []
R = self.R
kb = self.kb
h = self.h
amu = self.amu
seed = 500
numIter = 100000
oFile.write('\n\nInternal Rotational Contributions\n')
oFile.write('%12s'%'Temperature')
#iterate over temperatures
for T in Temp:
oFile.write('%12.2f'%T)
sigma = 1.0
for rotor in self.rotors:
sigma = sigma*rotor.symm
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
print K
p = 1.0
a = 1.0
for T in Temp:
#print 'Calculating rotational entropy for T: ',T
Sq = 0.0
Scl = 0.0
S = 0.0
Hq = 0.0
Hcl = 0.0
H = 0.0
cpcl = 0.0
cpq = 0.0
Cp = 0.0
for l in range(self.numRotors):
sum = 0.0
vsumexpv = 0.0
v2sumexpv = 0.0
minpot = 5.0
for i in range(numIter):
ang = random.rand()
pot = self.Harmonics[l].getPotential(ang*360)
if (pot < minpot):
minpot = pot
for i in range(100):
ang = i*360.0/100
pot = self.Harmonics[l].getPotential(ang)-minpot
print pot
exit()
# fi = sqrt(K[l])*exp(-pot*1.0e3/R/T)
fi = exp(-pot*1.0e3/R/T)
sum = sum + fi
vsumexpv = vsumexpv + pot*1.0e3 * fi
v2sumexpv = v2sumexpv + pot**2*1.0e6 *fi
average = sum/(i+1)
parti = (2.0*math.pi*kb*T*amu*1e-20/h**2)**(0.5) *(2*math.pi) * average/self.rotors[l+1].symm
a = a*average
S = S + R*math.log(parti) + R/2 + vsumexpv/sum/T
H = H + R*T/2.0 + vsumexpv/sum #reference to the minimum of the well
Cp = Cp + R/2.0 + (v2sumexpv*sum-vsumexpv**2)/sum**2/R/T**2
sumfreq = 0.0
for k in range(len(self.hindFreq)):
harm = self.Harmonics[k]
ddv = 0.0
for l in range(5):
ddv = ddv-1*harm.Kcos[l]*(l+1)**2
freq = 1.0/2.0/pi*sqrt(ddv*4180.0/K[k]/1.0e-20/amu/6.023e23)/3.0e10
#print freq, K[l], pi, ddv, K
Sq = Sq -R*math.log( 1.0 - math.exp(-h*freq*3.0e10/kb/T)) + 6.023e23*(h*freq*3.0e10/T) / ( math.exp(h*freq*3.0e10/kb/T) - 1.0 )/4.18
Scl = Scl + R + R*math.log(kb*T/h/freq/3.0e10)
Hq = Hq + 6.023e23*(h*freq*3.0e10)/( math.exp(h*freq*3.0e10/kb/T) - 1.0 )/4.18
Hcl = Hcl + R*T
cpq = cpq + R * (h*freq*3.0e10/kb/T)**2 * math.exp(h*freq*3.0e10/kb/T)/( 1.0 - math.exp(h*freq*3.0e10/kb/T))**2
cpcl = cpcl + R
sumfreq = sumfreq +freq
H = H + Hq - Hcl
S = S + Sq - Scl
Cp = Cp + cpq - cpcl
ent.append(S)
dH.append(H/1e3)
cp.append(Cp)
oFile.write('\n%12s'%'Entropy')
for i in range(len(Temp)):
oFile.write('%12.2f'%ent[i])
oFile.write('\n%12s'%'Cp')
for i in range(len(Temp)):
oFile.write('%12.2f'%cp[i])
oFile.write('\n%12s'%'dH')
for i in range(len(Temp)):
oFile.write('%12.2f'%dH[i])
#oFile.write('\n')
return ent, cp, dH
def getIntRotationalThermo_Q(self,oFile,Temp):
ent = [0.0]*len(Temp)
cp = [0.0]*len(Temp)
dH = [0.0]*len(Temp)
parti = [1.0]*len(Temp)
R = self.R
kb = self.kb
h = self.h
amu = self.amu
# Minimum_Barrier is used to determine when a particular rotor
# should be treated as a free rotor.
# If the barrier height is less than this value, it is a free rotor.
# the default value is 0.5 kcal/mol, which is equal to ~250 Kelvin.
Minimum_Barrier = 0.5
oFile.write('\n\nInternal Rotational Contributions\n')
oFile.write('%12s'%'Temperature')
#iterate over temperatures
for T in Temp:
oFile.write('%12.2f'%T)
sigma = 1.0
for rotor in self.rotors:
sigma = sigma*rotor.symm
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)
for irot in range(len(self.rotors)-1):
harm = self.Harmonics[irot]
ddv = 0.0
for l in range(5):
ddv = ddv-1*harm.Kcos[l]*(l+1)**2
freq = 1.0/2.0/pi*sqrt(ddv*4180.0/K[irot]/1.0e-20/amu/6.023e23)/3.0e10
#print '%12.2f'%float(freq),
#cfg print self.Harmonics[irot].Barrier_Height
#print
#calculate the energy levels for the hindered rotors
E = self.calculateElevels()
#pdb.set_trace()
for iT in range(len(Temp)):
T = Temp[iT]
#print T,
for irot in range(len(self.rotors)-1):
sum = 0.0
vsum = 0.0
v2sum = 0.0
if self.Harmonics[irot].Barrier_Height > Minimum_Barrier:
for e in E[irot]:
e = e - E[irot][0]
sum = sum + exp(-e*1.0e3/R/T)
vsum = vsum + e*1e3*exp(-e*1.0e3/R/T)
v2sum = v2sum + e**2*1e6*exp(-e*1.0e3/R/T)
# WHY IS THIS irot+1 ?!?
ent[iT] = ent[iT] + R*math.log(sum)+vsum/sum/T-R*log(self.rotors[irot+1].symm)
dH[iT] = dH[iT] + vsum/sum/1.0e3
cp[iT] = cp[iT] + (v2sum*sum-vsum**2)/sum**2/R/T**2
parti[iT] = parti[iT] *sum
else:
ent[iT] = ent[iT] + R*log( math.sqrt(8*math.pi**3 * K[irot] *kb*T*amu*1e-20) / self.rotors[irot+1].symm / h) + 0.5*R
dH[iT] = dH[iT] + 0.5*R*T/1.0e3
cp[iT] = cp[iT] + 0.5 * R
parti[iT] = parti[iT] * math.sqrt(8*math.pi**3 * K[irot] *kb*T*amu*1e-20) / self.rotors[irot+1].symm / h
#print (v2sum*sum-vsum**2)/sum**2/R/T**2,
#print R*math.log(sum)+vsum/sum/T-R*log(self.rotors[irot+1].symm),
#print
oFile.write('\n%12s'%'Entropy')
for i in range(len(Temp)):
oFile.write('%12.2f'%ent[i])
oFile.write('\n%12s'%'Cp')
for i in range(len(Temp)):
oFile.write('%12.2f'%cp[i])
oFile.write('\n%12s'%'dH')
for i in range(len(Temp)):
oFile.write('%12.2f'%dH[i])
oFile.write('\n%12s'%'q_int')
for i in range(len(Temp)):
oFile.write('%12.2e'%parti[i])
oFile.write('\n')
return ent, cp , dH, parti
#inputFiles = ['12211.log','02211.log','22211.log','11011.log','11022.log']
#inputFiles = ['111122.log','212211.log', '102022.log', '002022.log', '212122.log', '022022.log']
harmonics = file('harmonics.dat_ring','w')
energy_base = readGeomFc.readHFEnergy(inputFiles[0][:-4]+'_rot0_6.log')
numRotors = 4
harmonics.write(str(len(inputFiles))+'\n')
for files in inputFiles:
y = matrix(zeros((13,1),dtype=float))
x = matrix(zeros((13,11),dtype=float))
energy = readGeomFc.readHFEnergy(files[:-4]+'_rot0_6.log')
# harmonics.write(files+'\n')
(geom,Mass) = readGeomFc.readGeom(open(files,'r'))
inertia = open('inertia.dat','r')
(rotors) = readGeomFc.readGeneralInertia(inertia,Mass)
if (files == inputFiles[0]):
K = geomUtility.calculateD32(geom,Mass,rotors)
detD = 1.0
for i in range(numRotors):
print K[i],
detD = detD*K[i]
harmonics.write(str(float(detD))+'\n')
harmonics.write(str((energy-energy_base)*627.5095)+'\n')
if (energy < energy_base):
print files, " has lower energy"
exit()
for i in range(numRotors):
potgiven = []
for j in range(13):
angle = (-60.0 + j*120.0/12.0)*2*math.pi/360.0
fname = files[:-4]+'_rot'+str(i)+'_'+str(j)+'.log'
y[j] = (readGeomFc.readHFEnergy(fname)-energy)*627.5095
def __init__(self,file, isTS):
self.Freq = []
self.Harmonics = []
self.hindFreq = []
self.bonds = []
self.Etype = ''
self.TS = isTS
self.E0 = []
self.variableInertia = False
#read dummy line "MOL #"
line = readGeomFc.readMeaningfulLine(file)
#self.linearity = line.split()[0].upper
#read linearity
line = readGeomFc.readMeaningfulLine(file)
if line.split()[0].upper() == 'NONLINEAR' :
self.linearity = 'Nonlinear'
elif line.split()[0].upper() == 'LINEAR' :
self.linearity = 'Linear'
elif line.split()[0].upper() == 'ATOM' :
self.linearity = 'Atom'
else :
print 'Linearity keyword not recognized ' + line
exit()
#linearity = line.split()[0].upper
# read geometry
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() != 'GEOM' :
print 'Geom keyword not found in the input file' + line
exit()
if len(tokens) == 1:
#geometry is given following the GEOM keyword
line = readGeomFc.readMeaningfulLine(file)
numAtoms = int(line.split()[0])
self.geom = matrix(array(zeros((numAtoms,3),dtype=float)))
self.Mass = matrix(array(zeros((numAtoms,1),dtype=float)))
for i in range(numAtoms):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
self.geom[i,0]=double(tokens[3])
self.geom[i,1]=double(tokens[4])
self.geom[i,2]=double(tokens[5])
atomicNum = int(tokens[1])
if (atomicNum == 6): self.Mass[i]=12.0
if (atomicNum == 8): self.Mass[i]=15.99491
if (atomicNum == 1): self.Mass[i]=1.00783
if (atomicNum == 7): self.Mass[i]=14.0031
if (atomicNum == 17): self.Mass[i]=34.96885
if (atomicNum == 16): self.Mass[i]=31.97207
if (atomicNum == 9): self.Mass[i]=18.99840
#read geometry from the file
elif tokens[1].upper() == 'FILE' :
print "reading Geometry from the file: ",tokens[2]
geomFile = open(tokens[2],'r')
(self.geom,self.Mass) = readGeomFc.readGeom(geomFile);
#print self.geom
elif tokens[1].upper() == 'MM4FILE' :#mm4 option added by gmagoon
print "reading MM4 Geometry from the file: ",tokens[2]
geomFile = open(tokens[2],'r')
(self.geom,self.Mass) = readGeomFc.readMM4Geom(geomFile);
#print self.geom
else:
print 'Either give geometry or give keyword File followed by the file containing geometry data'
exit()
self.calculateMomInertia()
# read force constant or frequency data
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() == 'FORCEC' and tokens[1].upper() == 'FILE':
#MRH added following line on 2/Dec/2009
if self.linearity != 'Atom':
fcfile = open(tokens[2],'r')
self.Fc = readGeomFc.readFc(fcfile)
for i in range(0,3*self.Mass.size):
for j in range(i,3*self.Mass.size):
self.Fc[i,j] = self.Fc[j,i]
elif tokens[0].upper() == 'FORCEC' and tokens[1].upper() == 'MM4FILE':#MM4 case
if self.linearity != 'Atom':
fcfile = open(tokens[2],'r')
self.Fc = readGeomFc.readMM4Fc(fcfile)
for i in range(0,3*self.Mass.size):
for j in range(i,3*self.Mass.size):
self.Fc[i,j] = self.Fc[j,i]
elif tokens[0].upper() == "FREQ" :
line = readGeomFc.readMeaningfulLine(file)
numFreq = int(line.split()[0])
i = 0
while (i < numFreq):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
i = i+ len(tokens)
for j in tokens:
self.Freq.append(float(j))
if self.TS :
self.imagFreq = self.Freq.pop(0)
if len(self.Freq) > numFreq:
print 'More frequencies than ', numFreq, ' are specified'
else:
print 'Frequency information cannot be read, check input file again'
exit()
#read energy
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if (tokens[0].upper() != 'ENERGY'):
print 'Energy information not given'
exit()
if tokens[1].upper() == 'FILE' :
print 'Reading energy from file: ', tokens[2]
energyFile = open(tokens[2],'r')
if (tokens[3].upper() == 'CBS-QB3'):
self.Etype = 'cbsqb3'
elif (tokens[3].upper() == 'CBS-QB3_ULTRAFINE'):
self.Etype = 'cbsqb3uf'
print 'Warning: "Regular" (non-ultrafine) CBS-QB3 values will be used for P, N as a first approximation'
elif (tokens[3].upper() == 'G3'):
self.Etype = 'g3'
elif (tokens[3].upper() == 'KLIP_1'):
self.Etype = 'klip_1'
elif (tokens[3].upper() == 'KLIP_2'):
self.Etype = 'klip_2'
elif (tokens[3].upper() == 'KLIP_2_CC'):
self.Etype = 'klip_2_cc'
self.Energy = readGeomFc.readEnergy(energyFile, self.Etype)
print self.Energy, self.Etype
elif (len(tokens) == 3):
self.Energy = float(tokens[1])
if (tokens[2].upper() == 'CBS-QB3'):
self.Etype = 'cbsqb3'
elif (tokens[2].upper() == 'CBS-QB3_ULTRAFINE'):
self.Etype = 'cbsqb3uf'
print 'Warning: "Regular" (non-ultrafine) CBS-QB3 values will be used for P, N as a first approximation'
elif (tokens[2].upper() == 'G3'):
self.Etype = 'g3'
elif (tokens[2].upper() == 'Klip_1'):
self.Etype = 'klip_1'
elif (tokens[2].upper() == 'Klip_2'):
self.Etype = 'klip_2'
elif (tokens[2].upper() == 'KLIP_2_CC'):
self.Etype = 'klip_2_cc'
elif (tokens[2].upper() == 'MM4'):
self.Etype = 'mm4'
print self.Etype.upper(),' Energy: ',self.Energy
else :
print 'Cannot read the Energy'
exit()
#read external symmetry
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'EXTSYM'):
print 'Extsym keyword required'
exit()
self.extSymm = float(line.split()[1])
#read electronic degeneracy
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'NELEC'):
print 'Nelec keyword required'
exit()
self.nelec = int(line.split()[1])
#read rotor information
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'ROTORS'):
print 'Rotors keyword required'
exit()
self.numRotors = int(line.split()[1])
if self.numRotors == 0:
#Line added by MRH o 2/Dec/2009
#If no rotors exist and molecule is not a single atom, still need to:
# (1) Check if frequencies are already computed
# (2) Read in the BAC information
if self.linearity != 'Atom':
self.rotors = []
if (len(self.Freq) == 0):
#calculate frequencies from force constant
self.getFreqFromFc()
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
for bond in tokens:
self.bonds.append(float(bond))
return
# If the molecule is a single atom, no rotors exist, no frequencies need
# calculating, and no BAC information needs to be read
else:
return
rotorFile = line.split()[2]
inertiaFile = open(rotorFile,'r')
#print self.Mass
(self.rotors)= readGeomFc.readGeneralInertia(inertiaFile,self.Mass)
if len(self.rotors)-1 != self.numRotors :
print "The number of rotors specified in file, ",rotorFile,' is different than, ',self.numRotors
if (len(self.Freq) == 0):
#calculate frequencies from force constant
#Added by MRH on 2/Dec/2009
if self.linearity != 'Atom':
self.getFreqFromFc()
else :
if self.linearity != 'Atom':
self.getFreqFromFreq()
#read potential information for rotors
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() != 'POTENTIAL':
print 'No information for potential given'
exit()
if tokens[1].upper() == 'SEPARABLE':
if tokens[2].upper() == 'FILES':
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if len(tokens) != self.numRotors :
print 'give a separate potential file for each rotor'
for files in tokens:
Kcos=[]
Ksin =[]
harmonic = Harmonics(5,Kcos,Ksin)
harmonic.fitPotential(files)
self.Harmonics.append(harmonic)
elif tokens[2].upper().startswith('MM4FILES'):
if tokens[2].upper() == 'MM4FILES_INERTIA':#whether to consider variable inertia or not
self.variableInertia=True
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if len(tokens) != self.numRotors :
print 'give a separate potential file for each rotor'
line = readGeomFc.readMeaningfulLine(file)#the next line contains V0 (kcal/mol) followed by the rotor dihedrals (degrees) for the minimum energy conformation
rotinfo = line.split()
V0 = float(rotinfo[0])
K = geomUtility.calculateD32(self.geom,self.Mass,self.rotors)#get the rotor moments of inertia for the minimum energy conformation, which will be used during the Fourier fit
i = 0
for files in tokens:
i=i+1
dihedralMinimum = float(rotinfo[i])
Kcos=[]
Ksin =[]
harmonic = Harmonics(5,Kcos,Ksin)
harmonic.fitMM4Potential(files, V0, dihedralMinimum,self.variableInertia, self.rotors[i], float(K[i-1]))
self.Harmonics.append(harmonic)
elif tokens[2].upper() == 'HARMONIC':
for i in range(self.numRotors):
line = readGeomFc.readMeaningfulLine(file)
numFit = int(line.split()[0])
Ksin = []
Kcos = []
for i in range(numFit):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
Kcos.append(tokens[0])
Ksin.append(tokens[0])
harmonic = Harmonics(numFit,Kcos,Ksin)
self.Harmonics.append(harmonic)
elif tokens[1].upper() == 'NONSEPARABLE':
line = readGeomFc.readMeaningfulLine(file)
self.potentialFile = line.split()[0]
# read the energy base
#line = readGeomFc.readMeaningfulLine(file)
#tokens = line.split()
#if (tokens[0].upper() != 'ENERGYBASE'):
# print 'Keyword EnergyBase required'
# exit()
#self.ebase=float(tokens[1])
# read the bonds
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
for bond in tokens:
self.bonds.append(float(bond))
#read the random seed number
'''line = readGeomFc.readMeaningfulLine(file)
def getIntRotationalThermo_Q(self, oFile, Temp):
ent = [0.0] * len(Temp)
cp = [0.0] * len(Temp)
dH = [0.0] * len(Temp)
parti = [1.0] * len(Temp)
R = self.R
kb = self.kb
h = self.h
amu = self.amu
# Minimum_Barrier is used to determine when a particular rotor
# should be treated as a free rotor.
# If the barrier height is less than this value, it is a free rotor.
# the default value is 0.5 kcal/mol, which is equal to ~250 Kelvin.
Minimum_Barrier = 0.5
oFile.write('\n\nInternal Rotational Contributions\n')
oFile.write('%12s' % 'Temperature')
#iterate over temperatures
for T in Temp:
oFile.write('%12.2f' % T)
sigma = 1.0
for rotor in self.rotors:
sigma = sigma * rotor.symm
K = geomUtility.calculateD32(self.geom, self.Mass, self.rotors)
for irot in range(len(self.rotors) - 1):
harm = self.Harmonics[irot]
ddv = 0.0
for l in range(5):
ddv = ddv - 1 * harm.Kcos[l] * (l + 1)**2
freq = 1.0 / 2.0 / pi * sqrt(
ddv * 4180.0 / K[irot] / 1.0e-20 / amu / 6.023e23) / 3.0e10
#print '%12.2f'%float(freq),
#cfg print self.Harmonics[irot].Barrier_Height
#print
#calculate the energy levels for the hindered rotors
E = self.calculateElevels()
#pdb.set_trace()
for iT in range(len(Temp)):
T = Temp[iT]
#print T,
for irot in range(len(self.rotors) - 1):
sum = 0.0
vsum = 0.0
v2sum = 0.0
if self.Harmonics[irot].Barrier_Height > Minimum_Barrier:
for e in E[irot]:
e = e - E[irot][0]
sum = sum + exp(-e * 1.0e3 / R / T)
vsum = vsum + e * 1e3 * exp(-e * 1.0e3 / R / T)
v2sum = v2sum + e**2 * 1e6 * exp(-e * 1.0e3 / R / T)
# WHY IS THIS irot+1 ?!?
ent[iT] = ent[iT] + R * math.log(
sum) + vsum / sum / T - R * log(
self.rotors[irot + 1].symm)
dH[iT] = dH[iT] + vsum / sum / 1.0e3
cp[iT] = cp[iT] + (v2sum * sum -
vsum**2) / sum**2 / R / T**2
parti[iT] = parti[iT] * sum / self.rotors[irot + 1].symm
else:
ent[iT] = ent[iT] + R * log(
math.sqrt(
8 * math.pi**3 * K[irot] * kb * T * amu * 1e-20) /
self.rotors[irot + 1].symm / h) + 0.5 * R
dH[iT] = dH[iT] + 0.5 * R * T / 1.0e3
cp[iT] = cp[iT] + 0.5 * R
parti[iT] = parti[iT] * math.sqrt(
8 * math.pi**3 * K[irot] * kb * T * amu *
1e-20) / self.rotors[irot + 1].symm / h
#print (v2sum*sum-vsum**2)/sum**2/R/T**2,
#print R*math.log(sum)+vsum/sum/T-R*log(self.rotors[irot+1].symm),
#print
oFile.write('\n%12s' % 'Entropy')
for i in range(len(Temp)):
oFile.write('%12.2f' % ent[i])
oFile.write('\n%12s' % 'Cp')
for i in range(len(Temp)):
oFile.write('%12.2f' % cp[i])
oFile.write('\n%12s' % 'dH')
for i in range(len(Temp)):
oFile.write('%12.2f' % dH[i])
oFile.write('\n%12s' % 'q_int')
for i in range(len(Temp)):
oFile.write('%12.2e' % parti[i])
oFile.write('\n')
return ent, cp, dH, parti
def getIntRotationalThermo_PG(self, oFile, Temp):
ent = []
cp = []
dH = []
R = self.R
kb = self.kb
h = self.h
amu = self.amu
seed = 500
numIter = 100000
oFile.write('\n\nInternal Rotational Contributions\n')
oFile.write('%12s' % 'Temperature')
#iterate over temperatures
for T in Temp:
oFile.write('%12.2f' % T)
sigma = 1.0
for rotor in self.rotors:
sigma = sigma * rotor.symm
K = geomUtility.calculateD32(self.geom, self.Mass, self.rotors)
print K
p = 1.0
a = 1.0
for T in Temp:
#print 'Calculating rotational entropy for T: ',T
Sq = 0.0
Scl = 0.0
S = 0.0
Hq = 0.0
Hcl = 0.0
H = 0.0
cpcl = 0.0
cpq = 0.0
Cp = 0.0
for l in range(self.numRotors):
sum = 0.0
vsumexpv = 0.0
v2sumexpv = 0.0
minpot = 5.0
for i in range(numIter):
ang = random.rand()
pot = self.Harmonics[l].getPotential(ang * 360)
if (pot < minpot):
minpot = pot
for i in range(100):
ang = i * 360.0 / 100
pot = self.Harmonics[l].getPotential(ang) - minpot
print pot
exit()
# fi = sqrt(K[l])*exp(-pot*1.0e3/R/T)
fi = exp(-pot * 1.0e3 / R / T)
sum = sum + fi
vsumexpv = vsumexpv + pot * 1.0e3 * fi
v2sumexpv = v2sumexpv + pot**2 * 1.0e6 * fi
average = sum / (i + 1)
parti = (2.0 * math.pi * kb * T * amu * 1e-20 / h**2)**(
0.5) * (2 * math.pi) * average / self.rotors[l +
1].symm
a = a * average
S = S + R * math.log(parti) + R / 2 + vsumexpv / sum / T
H = H + R * T / 2.0 + vsumexpv / sum #reference to the minimum of the well
Cp = Cp + R / 2.0 + (v2sumexpv * sum -
vsumexpv**2) / sum**2 / R / T**2
sumfreq = 0.0
for k in range(len(self.hindFreq)):
harm = self.Harmonics[k]
ddv = 0.0
for l in range(5):
ddv = ddv - 1 * harm.Kcos[l] * (l + 1)**2
freq = 1.0 / 2.0 / pi * sqrt(
ddv * 4180.0 / K[k] / 1.0e-20 / amu / 6.023e23) / 3.0e10
#print freq, K[l], pi, ddv, K
Sq = Sq - R * math.log(
1.0 - math.exp(-h * freq * 3.0e10 / kb / T)) + 6.023e23 * (
h * freq * 3.0e10 / T) / (
math.exp(h * freq * 3.0e10 / kb / T) - 1.0) / 4.18
Scl = Scl + R + R * math.log(kb * T / h / freq / 3.0e10)
Hq = Hq + 6.023e23 * (h * freq * 3.0e10) / (
math.exp(h * freq * 3.0e10 / kb / T) - 1.0) / 4.18
Hcl = Hcl + R * T
cpq = cpq + R * (h * freq * 3.0e10 / kb / T)**2 * math.exp(
h * freq * 3.0e10 / kb /
T) / (1.0 - math.exp(h * freq * 3.0e10 / kb / T))**2
cpcl = cpcl + R
sumfreq = sumfreq + freq
H = H + Hq - Hcl
S = S + Sq - Scl
Cp = Cp + cpq - cpcl
ent.append(S)
dH.append(H / 1e3)
cp.append(Cp)
oFile.write('\n%12s' % 'Entropy')
for i in range(len(Temp)):
oFile.write('%12.2f' % ent[i])
oFile.write('\n%12s' % 'Cp')
for i in range(len(Temp)):
oFile.write('%12.2f' % cp[i])
oFile.write('\n%12s' % 'dH')
for i in range(len(Temp)):
oFile.write('%12.2f' % dH[i])
#oFile.write('\n')
return ent, cp, dH
def __init__(self, file, isTS):
self.Freq = []
self.Harmonics = []
self.hindFreq = []
self.bonds = []
self.Etype = ''
self.TS = isTS
self.E0 = []
self.variableInertia = False
#read dummy line "MOL #"
line = readGeomFc.readMeaningfulLine(file)
#self.linearity = line.split()[0].upper
#read linearity
line = readGeomFc.readMeaningfulLine(file)
if line.split()[0].upper() == 'NONLINEAR':
self.linearity = 'Nonlinear'
elif line.split()[0].upper() == 'LINEAR':
self.linearity = 'Linear'
elif line.split()[0].upper() == 'ATOM':
self.linearity = 'Atom'
else:
print 'Linearity keyword not recognized ' + line
exit()
#linearity = line.split()[0].upper
# read geometry
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() != 'GEOM':
print 'Geom keyword not found in the input file' + line
exit()
if len(tokens) == 1:
#geometry is given following the GEOM keyword
line = readGeomFc.readMeaningfulLine(file)
numAtoms = int(line.split()[0])
self.geom = matrix(array(zeros((numAtoms, 3), dtype=float)))
self.Mass = matrix(array(zeros((numAtoms, 1), dtype=float)))
for i in range(numAtoms):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
self.geom[i, 0] = double(tokens[3])
self.geom[i, 1] = double(tokens[4])
self.geom[i, 2] = double(tokens[5])
atomicNum = int(tokens[1])
if (atomicNum == 6): self.Mass[i] = 12.0
if (atomicNum == 8): self.Mass[i] = 15.99491
if (atomicNum == 1): self.Mass[i] = 1.00783
if (atomicNum == 7): self.Mass[i] = 14.0031
if (atomicNum == 17): self.Mass[i] = 34.96885
if (atomicNum == 16): self.Mass[i] = 31.97207
if (atomicNum == 9): self.Mass[i] = 18.99840
#read geometry from the file
elif tokens[1].upper() == 'FILE':
print "reading Geometry from the file: ", tokens[2]
geomFile = open(tokens[2], 'r')
(self.geom, self.Mass) = readGeomFc.readGeom(geomFile)
#print self.geom
elif tokens[1].upper() == 'MM4FILE': #mm4 option added by gmagoon
print "reading MM4 Geometry from the file: ", tokens[2]
geomFile = open(tokens[2], 'r')
(self.geom, self.Mass) = readGeomFc.readMM4Geom(geomFile)
#print self.geom
else:
print 'Either give geometry or give keyword File followed by the file containing geometry data'
exit()
self.calculateMomInertia()
# read force constant or frequency data
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() == 'FORCEC' and tokens[1].upper() == 'FILE':
#MRH added following line on 2/Dec/2009
if self.linearity != 'Atom':
fcfile = open(tokens[2], 'r')
self.Fc = readGeomFc.readFc(fcfile)
for i in range(0, 3 * self.Mass.size):
for j in range(i, 3 * self.Mass.size):
self.Fc[i, j] = self.Fc[j, i]
elif tokens[0].upper() == 'FORCEC' and tokens[1].upper(
) == 'MM4FILE': #MM4 case
if self.linearity != 'Atom':
fcfile = open(tokens[2], 'r')
self.Fc = readGeomFc.readMM4Fc(fcfile)
for i in range(0, 3 * self.Mass.size):
for j in range(i, 3 * self.Mass.size):
self.Fc[i, j] = self.Fc[j, i]
elif tokens[0].upper() == "FREQ":
line = readGeomFc.readMeaningfulLine(file)
numFreq = int(line.split()[0])
i = 0
while (i < numFreq):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
i = i + len(tokens)
for j in tokens:
self.Freq.append(float(j))
if self.TS:
self.imagFreq = self.Freq.pop(0)
if len(self.Freq) > numFreq:
print 'More frequencies than ', numFreq, ' are specified'
else:
print 'Frequency information cannot be read, check input file again'
exit()
#read energy
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if (tokens[0].upper() != 'ENERGY'):
print 'Energy information not given'
exit()
if tokens[1].upper() == 'FILE':
print 'Reading energy from file: ', tokens[2]
energyFile = open(tokens[2], 'r')
if (tokens[3].upper() == 'CBS-QB3'):
self.Etype = 'cbsqb3'
elif (tokens[3].upper() == 'CBS-QB3_ULTRAFINE'):
self.Etype = 'cbsqb3uf'
print 'Warning: "Regular" (non-ultrafine) CBS-QB3 values will be used for P, N as a first approximation'
elif (tokens[3].upper() == 'G3'):
self.Etype = 'g3'
elif (tokens[3].upper() == 'KLIP_1'):
self.Etype = 'klip_1'
elif (tokens[3].upper() == 'KLIP_2'):
self.Etype = 'klip_2'
elif (tokens[3].upper() == 'KLIP_2_CC'):
self.Etype = 'klip_2_cc'
self.Energy = readGeomFc.readEnergy(energyFile, self.Etype)
print self.Energy, self.Etype
elif (len(tokens) == 3):
self.Energy = float(tokens[1])
if (tokens[2].upper() == 'CBS-QB3'):
self.Etype = 'cbsqb3'
elif (tokens[2].upper() == 'CBS-QB3_ULTRAFINE'):
self.Etype = 'cbsqb3uf'
print 'Warning: "Regular" (non-ultrafine) CBS-QB3 values will be used for P, N as a first approximation'
elif (tokens[2].upper() == 'G3'):
self.Etype = 'g3'
elif (tokens[2].upper() == 'Klip_1'):
self.Etype = 'klip_1'
elif (tokens[2].upper() == 'Klip_2'):
self.Etype = 'klip_2'
elif (tokens[2].upper() == 'KLIP_2_CC'):
self.Etype = 'klip_2_cc'
elif (tokens[2].upper() == 'MM4'):
self.Etype = 'mm4'
print self.Etype.upper(), ' Energy: ', self.Energy
else:
print 'Cannot read the Energy'
exit()
#read external symmetry
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'EXTSYM'):
print 'Extsym keyword required'
exit()
self.extSymm = float(line.split()[1])
#read electronic degeneracy
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'NELEC'):
print 'Nelec keyword required'
exit()
self.nelec = int(line.split()[1])
#read rotor information
line = readGeomFc.readMeaningfulLine(file)
if (line.split()[0].upper() != 'ROTORS'):
print 'Rotors keyword required'
exit()
self.numRotors = int(line.split()[1])
if self.numRotors == 0:
#Line added by MRH o 2/Dec/2009
#If no rotors exist and molecule is not a single atom, still need to:
# (1) Check if frequencies are already computed
# (2) Read in the BAC information
if self.linearity != 'Atom':
self.rotors = []
if (len(self.Freq) == 0):
#calculate frequencies from force constant
self.getFreqFromFc()
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
for bond in tokens:
self.bonds.append(float(bond))
return
# If the molecule is a single atom, no rotors exist, no frequencies need
# calculating, and no BAC information needs to be read
else:
return
rotorFile = line.split()[2]
inertiaFile = open(rotorFile, 'r')
#print self.Mass
(self.rotors) = readGeomFc.readGeneralInertia(inertiaFile, self.Mass)
if len(self.rotors) - 1 != self.numRotors:
print "The number of rotors specified in file, ", rotorFile, ' is different than, ', self.numRotors
if (len(self.Freq) == 0):
#calculate frequencies from force constant
#Added by MRH on 2/Dec/2009
if self.linearity != 'Atom':
self.getFreqFromFc()
else:
if self.linearity != 'Atom':
self.getFreqFromFreq()
#read potential information for rotors
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if tokens[0].upper() != 'POTENTIAL':
print 'No information for potential given'
exit()
if tokens[1].upper() == 'SEPARABLE':
if tokens[2].upper() == 'FILES':
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if len(tokens) != self.numRotors:
print 'give a separate potential file for each rotor'
for files in tokens:
Kcos = []
Ksin = []
harmonic = Harmonics(5, Kcos, Ksin)
harmonic.fitPotential(files)
self.Harmonics.append(harmonic)
elif tokens[2].upper().startswith('MM4FILES'):
if tokens[2].upper(
) == 'MM4FILES_INERTIA': #whether to consider variable inertia or not
self.variableInertia = True
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
if len(tokens) != self.numRotors:
print 'give a separate potential file for each rotor'
line = readGeomFc.readMeaningfulLine(
file
) #the next line contains V0 (kcal/mol) followed by the rotor dihedrals (degrees) for the minimum energy conformation
rotinfo = line.split()
V0 = float(rotinfo[0])
K = geomUtility.calculateD32(
self.geom, self.Mass, self.rotors
) #get the rotor moments of inertia for the minimum energy conformation, which will be used during the Fourier fit
i = 0
for files in tokens:
i = i + 1
dihedralMinimum = float(rotinfo[i])
Kcos = []
Ksin = []
harmonic = Harmonics(5, Kcos, Ksin)
harmonic.fitMM4Potential(files, V0, dihedralMinimum,
self.variableInertia,
self.rotors[i], float(K[i - 1]))
self.Harmonics.append(harmonic)
elif tokens[2].upper() == 'HARMONIC':
for i in range(self.numRotors):
line = readGeomFc.readMeaningfulLine(file)
numFit = int(line.split()[0])
Ksin = []
Kcos = []
for i in range(numFit):
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
Kcos.append(tokens[0])
Ksin.append(tokens[0])
harmonic = Harmonics(numFit, Kcos, Ksin)
self.Harmonics.append(harmonic)
elif tokens[1].upper() == 'NONSEPARABLE':
line = readGeomFc.readMeaningfulLine(file)
self.potentialFile = line.split()[0]
# read the energy base
#line = readGeomFc.readMeaningfulLine(file)
#tokens = line.split()
#if (tokens[0].upper() != 'ENERGYBASE'):
# print 'Keyword EnergyBase required'
# exit()
#self.ebase=float(tokens[1])
# read the bonds
line = readGeomFc.readMeaningfulLine(file)
tokens = line.split()
for bond in tokens:
self.bonds.append(float(bond))
#read the random seed number
'''line = readGeomFc.readMeaningfulLine(file)
#inputFiles = ['12211.log','02211.log','22211.log','11011.log','11022.log']
#inputFiles = ['111122.log','212211.log', '102022.log', '002022.log', '212122.log', '022022.log']
harmonics = file('harmonics.dat_ring', 'w')
energy_base = readGeomFc.readHFEnergy(inputFiles[0][:-4] + '_rot0_6.log')
numRotors = 4
harmonics.write(str(len(inputFiles)) + '\n')
for files in inputFiles:
y = matrix(zeros((13, 1), dtype=float))
x = matrix(zeros((13, 11), dtype=float))
energy = readGeomFc.readHFEnergy(files[:-4] + '_rot0_6.log')
# harmonics.write(files+'\n')
(geom, Mass) = readGeomFc.readGeom(open(files, 'r'))
inertia = open('inertia.dat', 'r')
(rotors) = readGeomFc.readGeneralInertia(inertia, Mass)
if (files == inputFiles[0]):
K = geomUtility.calculateD32(geom, Mass, rotors)
detD = 1.0
for i in range(numRotors):
print(K[i])
detD = detD * K[i]
harmonics.write(str(float(detD)) + '\n')
harmonics.write(str((energy - energy_base) * ha_to_kcal) + '\n')
if (energy < energy_base):
print(files, " has lower energy")
exit()
for i in range(numRotors):
potgiven = []
for j in range(13):
angle = (-60.0 + j * 120.0 / 12.0) * 2 * math.pi / 360.0
fname = files[:-4] + '_rot' + str(i) + '_' + str(j) + '.log'
y[j] = (readGeomFc.readHFEnergy(fname) - energy) * ha_to_kcal
