def main():
data = CanTherm()
inputFile = open(sys.argv[1],'r')
oFile = open('cantherm.out','w')
readGeomFc.readInputFile(inputFile,data)
data.Entropy=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Cp=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Thermal=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Partition=len(data.MoleculeList)*len(data.Temp)*[1.0]
Entropy = data.Entropy
Cp = data.Cp
Thermal = data.Thermal
Partition = data.Partition
for i in range(len(data.MoleculeList)):
molecule = data.MoleculeList[i]
oFile.write('Molecule '+str(i+1)+':\n')
oFile.write('-----------\n\n')
molecule.printData(oFile)
oFile.write('\nThermodynamic Data\n')
Temp = data.Temp
#translation
(ent,cp,dh,q) = molecule.getTranslationThermo(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j]=Partition[i*len(Temp)+j]*q[j]
#vibrational
(ent,cp,dh,q) = molecule.getVibrationalThermo(oFile,data.Temp,data.scale)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
#Internal rotational
if molecule.numRotors != 0:
(ent,cp,dh,q) = molecule.getIntRotationalThermo_Q(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
#External rotational
(ent,cp,dh,q) = molecule.getExtRotationalThermo(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+1.985*math.log(molecule.nelec)
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j] * molecule.nelec
#print Enthalpy
H = molecule.Energy
atoms = readGeomFc.getAtoms(molecule.Mass)
atomsH = 0.0
if molecule.Etype == 'cbsqb3':
atomE = data.atomEcbsqb3
if molecule.Etype == 'g3':
atomE = data.atomEg3
for atom in atoms:
H -= atomE[atom]
atomsH += data.atomH[atom]
H = H*627.5095+atomsH
if molecule.Etype == 'cbsqb3':
b = 0
for bonds in molecule.bonds:
H += bonds*data.bondC[b]
b += 1
#MRH 30Jan2010
#This E0 will be used in the Eckart tunneling calculation
molecule.E0 = H
H += Thermal[i*len(Temp)+0]
print '%12.2f'%H + '%12.2f'%Entropy[i*len(Temp)+0],
for c in range(1,len(Temp)):
print '%12.2f'%Cp[i*len(Temp)+c],
print '\n'
#for c in range(len(Temp)):
#print '%12.2e'%Partition[i*len(Temp)+c],
#print
if len(data.MoleculeList) == 1:
return
#fit the rate coefficient
A = matrix(zeros((len(Temp),3),dtype=float))
A1 = matrix(zeros((len(Temp),2),dtype=float))
y = matrix(zeros((len(Temp),1),dtype=float))
rate = [0.0]*len(Temp)
for j in range(len(Temp)):
if (data.ReacType == 'Unimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*math.exp((Entropy[len(Temp)+j]-Entropy[j])/1.985)*math.exp(-(data.MoleculeList[1].Energy - data.MoleculeList[0].Energy)*627.5095*1.0e3/1.985/Temp[j])
kbT_h = (1.381e-23*Temp[j]/6.626e-34)
G_TS = Thermal[len(Temp)+j]*1e3+data.MoleculeList[1].Energy*627.5095*1e3-Temp[j]*Entropy[len(Temp)+j]
G_react = Thermal[j]*1e3+data.MoleculeList[0].Energy*627.5095*1e3-Temp[j]*Entropy[j]
#qTS_qA = Partition[len(Temp)+j]/Partition[j]
#exp_e_RT = math.exp(-(data.MoleculeList[1].Energy-data.MoleculeList[0].Energy)*627.5095*1e3/1.985/Temp[j])
#print kbT_h * exp_S_R * exp_H_RT
#print qTS_qA * exp_e_RT
rate[j] = kbT_h * math.exp(-(G_TS-G_react)/1.985/Temp[j])
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner' :
kappa = 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[1].imagFreq/Temp[j])**2
print kappa
rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[1].imagFreq/Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart' :
delV1 = data.MoleculeList[1].E0-data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[1].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart' :
delV1 = data.MoleculeList[1].E0-data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[1].imagFreq)
if data.numProds == 1 :
delV2 = data.MoleculeList[1].E0-data.MoleculeList[2].E0
else :
delV2 = data.MoleculeList[1].E0-data.MoleculeList[2].E0-data.MoleculeList[3].E0
alpha2 = 2*math.pi*delV2/6.022e23/6.626e-34/3.00e10*4184/(-1*data.MoleculeList[1].imagFreq)
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
elif (data.ReacType == 'Bimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*(82.05746*Temp[j]/1.0)*math.exp((Entropy[2*len(Temp)+j]-Entropy[len(Temp)+j]-Entropy[j])/1.985)*math.exp(-(data.MoleculeList[2].Energy - data.MoleculeList[0].Energy - data.MoleculeList[1].Energy)*627.5095*1.0e3/1.985/Temp[j])
kbT_h = (1.381e-23*Temp[j]/6.626e-34)
exp_S_R = math.exp((Entropy[2*len(Temp)+j]-Entropy[len(Temp)+j]-Entropy[j])/1.985)
exp_H_RT = math.exp(-(Thermal[2*len(Temp)+j]-Thermal[len(Temp)+j]-Thermal[j])*1e3/1.985/Temp[j])
rate[j] = kbT_h * exp_S_R * exp_H_RT
#wigner correction
#rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[2].imagFreq/Temp[j])**2
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner' :
rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[2].imagFreq/Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart' :
delV1 = data.MoleculeList[2].E0-data.MoleculeList[0].E0-data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[2].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart' :
delV1 = data.MoleculeList[2].E0-data.MoleculeList[0].E0-data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[2].imagFreq)
if data.numProds == 1 :
delV2 = data.MoleculeList[2].E0-data.MoleculeList[3].E0
else :
delV2 = data.MoleculeList[2].E0-data.MoleculeList[3].E0-data.MoleculeList[4].E0
alpha2 = 2*math.pi*delV2/6.022e23/6.626e-34/3.00e10*4184/(-1*data.MoleculeList[2].imagFreq)
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
A[j,:] = mat([1.0, math.log(Temp[j]), -1.0/1.985/Temp[j]])
y[j] = log(rate[j])
A1[j,:] = mat([1.0, -1.0/1.985/Temp[j]])
b = linalg.inv(transpose(A)*A)*(transpose(A)*y)
b1 = linalg.inv(transpose(A1)*A1)*(transpose(A1)*y)
oFile.write('\n\nRate Data: Modified Arrhenius format\n')
oFile.write('r = A*(T/1000)^n*exp(-Ea/R/T)'+'%12.2e'%(exp(b[0])*1000.0**float(b[1]))+'%6.2f'%b[1]+'%12.2f'%(b[2]/1.0e3)+'\n')
oFile.write('r = A*T^n*exp(-Ea/R/T)'+'%12.2e'%(exp(b[0]))+'%6.2f'%b[1]+'%12.2f'%(b[2]/1.0e3)+'\n')
oFile.write('%12s'%'Temperature'+'%12s'%'Rate'+'%12s\n'%'Fit Rate')
for j in range(len(Temp)):
fitrate = exp(b[0])*Temp[j]**float(b[1])*exp(-b[2]/1.985/Temp[j])
oFile.write('%12.2f'%Temp[j]+'%12.2e'%rate[j]+'%12.2e\n'%fitrate)
oFile.write('\n\n')
oFile.write('Rate Data: Arrhenius format\n')
oFile.write('r = A*exp(-Ea/R/T)'+'%12.2e'%(exp(b1[0]))+'%12.2f'%(b1[1]/1.0e3)+'\n')
oFile.write('%12s'%'Temperature'+'%12s'%'Rate'+'%12s\n'%'Fit Rate')
for j in range(len(Temp)) :
fitrate2 = exp(b1[0])*exp(-b1[1]/1.985/Temp[j])
oFile.write('%12.2f'%Temp[j]+'%12.2e'%rate[j]+'%12.2e\n'%fitrate2)
oFile.write('\n\n')
oFile.close()
memory = ' 1000MB '
multi = ' 2'
#file = open(sys.argv[1],'r')
inertia = open('inertia.dat', 'r')
result = open('dihed_energy.out', 'w')
outputName = '0.log'
energy = readGeomFc.readHFEnergy(outputName)
outFile = open('0.log', 'r')
(geom, Mass) = readGeomFc.readGeom(outFile)
(rotors) = readGeomFc.readGeneralInertia(inertia, Mass)
numRotors = len(rotors) - 1
atoms = readGeomFc.getAtoms(Mass)
diheds = numRotors * [0]
for i in range(numRotors):
result.write('%10.3f' % diheds[i])
result.write('%14.7f' % energy + '\n')
for i in range(12**(numRotors)):
# diheds = random.rand(len(rotors)-1)*360
irem = i
for j in range(len(rotors) - 1):
diheds[j] = (irem - irem / 12 * 12) * 30.0
irem = irem / 12
result.write('%10.3f' % diheds[j])
result.write('\n')
#file = open(sys.argv[1],'r')
inertia = open('inertia.dat','r')
result = open('dihed_energy.out','w')
outputName = '0.log'
energy = readGeomFc.readHFEnergy(outputName)
outFile = open('0.log','r')
(geom,Mass) = readGeomFc.readGeom(outFile)
(rotors) = readGeomFc.readGeneralInertia(inertia,Mass)
numRotors = len(rotors)-1
atoms = readGeomFc.getAtoms(Mass)
diheds=numRotors*[0]
for i in range(numRotors):
result.write('%10.3f'%diheds[i])
result.write('%14.7f'%energy+'\n')
for i in range(12**(numRotors)):
# diheds = random.rand(len(rotors)-1)*360
irem = i
for j in range(len(rotors)-1):
diheds[j] = (irem-irem/12*12)*30.0
irem = irem/12
result.write('%10.3f'%diheds[j])
result.write('\n')
def main():
data = CanTherm()
inputFile = open(sys.argv[1],'r')
#determine the output file name by removing the contents of the input filename following the first period and appending the .canout suffix
periodPosition = sys.argv[1].rfind(".")
outfilename = sys.argv[1][0:periodPosition]+".canout"
oFile = open(outfilename,'w')
readGeomFc.readInputFile(inputFile,data)
data.Entropy=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Cp=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Thermal=len(data.MoleculeList)*len(data.Temp)*[0.0]
data.Partition=len(data.MoleculeList)*len(data.Temp)*[1.0]
Entropy = data.Entropy
Cp = data.Cp
Thermal = data.Thermal
Partition = data.Partition
Entropy298=0.0
Thermal298=0.0
for i in range(len(data.MoleculeList)):
molecule = data.MoleculeList[i]
oFile.write('Molecule '+str(i+1)+':\n')
oFile.write('-----------\n\n')
molecule.printData(oFile)
oFile.write('\nThermodynamic Data\n')
Temp = data.Temp
temp298 = [298.15] #use 298.15 K as well; this will be used below for printing Hf298, S298
#translation
(ent,cp,dh,q) = molecule.getTranslationThermo(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j]=Partition[i*len(Temp)+j]*q[j]
(ent298,cp298,dh298,q298) = molecule.getTranslationThermo(oFile,temp298)
Entropy298=Entropy298+ent298[0]
Thermal298=Thermal298+dh298[0]
#vibrational
(ent,cp,dh,q) = molecule.getVibrationalThermo(oFile,data.Temp,data.scale)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
(ent298,cp298,dh298,q298) = molecule.getVibrationalThermo(oFile,temp298,data.scale)
Entropy298=Entropy298+ent298[0]
Thermal298=Thermal298+dh298[0]
#Internal rotational
if molecule.numRotors != 0:
(ent,cp,dh,q) = molecule.getIntRotationalThermo_Q(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
(ent298,cp298,dh298,q298) = molecule.getIntRotationalThermo_Q(oFile,temp298)
Entropy298=Entropy298+ent298[0]
Thermal298=Thermal298+dh298[0]
#External rotational
(ent,cp,dh,q) = molecule.getExtRotationalThermo(oFile,data.Temp)
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+ent[j]
Cp[i*len(Temp)+j]=Cp[i*len(Temp)+j]+cp[j]
Thermal[i*len(Temp)+j]=Thermal[i*len(Temp)+j]+dh[j]
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j]*q[j]
(ent298,cp298,dh298,q298) = molecule.getExtRotationalThermo(oFile,temp298)
Entropy298=Entropy298+ent298[0]
Thermal298=Thermal298+dh298[0]
for j in range(len(Temp)):
Entropy[i*len(Temp)+j]=Entropy[i*len(Temp)+j]+1.9872*math.log(molecule.nelec)
Partition[i*len(Temp)+j] = Partition[i*len(Temp)+j] * molecule.nelec
Entropy298=Entropy298+1.9872*math.log(molecule.nelec)
#print Enthalpy
H = molecule.Energy
if not molecule.Etype == 'mm4':#for the MM4 case, the value passed in should be in kcal/mol and should not require unit adjustments or atomization energy information
atoms = readGeomFc.getAtoms(molecule.Mass)
atomsH = 0.0
#atomsH0 = 0.0
if molecule.Etype == 'cbsqb3':
atomE = data.atomEcbsqb3
if molecule.Etype == 'cbsqb3uf':
atomE = data.atomEcbsqb3uf
if molecule.Etype == 'g3':
atomE = data.atomEg3
if molecule.Etype == 'klip_1':
atomE = data.atomEKlip_1
if molecule.Etype == 'klip_2':
atomE = data.atomEKlip_2
if molecule.Etype == 'klip_2_cc':
atomE = data.atomEKlip_2_cc
for atom in atoms:
H -= atomE[atom]
atomsH += data.atomH[atom]
# atomsH0 += data.atomH0[atom]
H = H*627.5095+atomsH
# H0 = H*627.5095+atomsH0
if (molecule.Etype == 'cbsqb3' or molecule.Etype == 'cbsqb3uf') :
b = 0
for bonds in molecule.bonds:
H += bonds*data.bondC[b]
b += 1
#MRH 30Jan2010
#This E0 will be used in the Eckart tunneling calculation
molecule.E0 = H
H298 = H + Thermal298
H += Thermal[i*len(Temp)+0]
print '%12.2f'%H298 + '%12.2f'%Entropy298,
# print '%12.2f'%float(H*4.187) + '%12.2f'%float(Entropy[i*len(Temp)+0]*4.187)
for c in range(0,len(Temp)):
print '%12.2f'%Cp[i*len(Temp)+c],
print '\n'
oFile.write("Hf298 S298 Cps:\n")
oFile.write(str(H298)+" "+ str(Entropy298))
# print '%12.2f'%float(H*4.187) + '%12.2f'%float(Entropy[i*len(Temp)+0]*4.187)
for c in range(0,len(Temp)):
oFile.write(" "+str(Cp[i*len(Temp)+c]))
# print '\n'
#for c in range(len(Temp)):
#print '%12.2e'%Partition[i*len(Temp)+c],
#print
if data.fitcp:
FitCp.FitHeatCapacity(Temp,Cp, molecule.linearity, molecule.Freq, molecule.numRotors, molecule.R, oFile)
if len(data.MoleculeList) == 1:
return
#fit the rate coefficient
A = matrix(zeros((len(Temp),3),dtype=float))
A1 = matrix(zeros((len(Temp),2),dtype=float))
y = matrix(zeros((len(Temp),1),dtype=float))
rate = [0.0]*len(Temp)
for j in range(len(Temp)):
if (data.ReacType == 'Unimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*math.exp((Entropy[len(Temp)+j]-Entropy[j])/1.9872)*math.exp(-(data.MoleculeList[1].Energy - data.MoleculeList[0].Energy)*627.5095*1.0e3/1.9872/Temp[j])
kbT_h = (1.381e-23*Temp[j]/6.626e-34)
G_TS = Thermal[len(Temp)+j]*1e3+data.MoleculeList[1].Energy*627.5095*1e3-Temp[j]*Entropy[len(Temp)+j]
G_react = Thermal[j]*1e3+data.MoleculeList[0].Energy*627.5095*1e3-Temp[j]*Entropy[j]
#qTS_qA = Partition[len(Temp)+j]/Partition[j]
#exp_e_RT = math.exp(-(data.MoleculeList[1].Energy-data.MoleculeList[0].Energy)*627.5095*1e3/1.9872/Temp[j])
#print kbT_h * exp_S_R * exp_H_RT
#print qTS_qA * exp_e_RT
rate[j] = kbT_h * math.exp(-(G_TS-G_react)/1.9872/Temp[j])
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner' :
kappa = 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[1].imagFreq/Temp[j])**2
print kappa
rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[1].imagFreq/Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart' :
delV1 = data.MoleculeList[1].E0-data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[1].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart' :
delV1 = data.MoleculeList[1].E0-data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[1].imagFreq)
if data.numProds == 1 :
delV2 = data.MoleculeList[1].E0-data.MoleculeList[2].E0
else :
delV2 = data.MoleculeList[1].E0-data.MoleculeList[2].E0-data.MoleculeList[3].E0
delV2 = delV2 / 6.022e23 * 4184
alpha2 = 2*math.pi*delV2/6.626e-34/3.00e10/(-1*data.MoleculeList[1].imagFreq)
if (alpha1<alpha2):
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
else:
# reverse the direction: pass delV2 and alpha1 in place of alpha2
rate[j] *= Eckart.computeTunnelingCorrection(delV2,Temp[j],alpha2,alpha1)
elif (data.ReacType == 'Bimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*(82.05746*Temp[j]/1.0)*math.exp((Entropy[2*len(Temp)+j]-Entropy[len(Temp)+j]-Entropy[j])/1.9872)*math.exp(-(data.MoleculeList[2].Energy - data.MoleculeList[0].Energy - data.MoleculeList[1].Energy)*627.5095*1.0e3/1.9872/Temp[j])
kbT_hC = (1.381e-23*Temp[j]/6.626e-34)*(82.05746*Temp[j]/1.0)
G_TS = Thermal[2*len(Temp)+j]*1e3+data.MoleculeList[2].Energy*627.5095*1e3-Temp[j]*Entropy[2*len(Temp)+j]
G_react1 = Thermal[len(Temp)+j]*1e3+data.MoleculeList[1].Energy*627.5095*1e3-Temp[j]*Entropy[len(Temp)+j]
G_react2 = Thermal[j]*1e3+data.MoleculeList[0].Energy*627.5095*1e3-Temp[j]*Entropy[j]
rate[j] = kbT_hC * math.exp(-(G_TS-G_react1-G_react2)/1.9872/Temp[j])
#wigner correction
#rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[2].imagFreq/Temp[j])**2
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner' :
rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[2].imagFreq/Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart' :
delV1 = data.MoleculeList[2].E0-data.MoleculeList[0].E0-data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[2].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart' :
delV1 = data.MoleculeList[2].E0-data.MoleculeList[0].E0-data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2*math.pi*delV1/6.626e-34/3.00e10/(-1*data.MoleculeList[2].imagFreq)
if data.numProds == 1 :
delV2 = data.MoleculeList[2].E0-data.MoleculeList[3].E0
else :
delV2 = data.MoleculeList[2].E0-data.MoleculeList[3].E0-data.MoleculeList[4].E0
delV2 = delV2 / 6.022e23 * 4184
alpha2 = 2*math.pi*delV2/6.626e-34/3.00e10/(-1*data.MoleculeList[2].imagFreq)
if (alpha1<alpha2):
rate[j] *= Eckart.computeTunnelingCorrection(delV1,Temp[j],alpha1,alpha2)
else:
# reverse the direction: pass delV2 and alpha1 in place of alpha2
rate[j] *= Eckart.computeTunnelingCorrection(delV2,Temp[j],alpha2,alpha1)
A[j,:] = mat([1.0, math.log(Temp[j]), -1.0/1.9872/Temp[j]])
y[j] = log(rate[j])
A1[j,:] = mat([1.0, -1.0/1.9872/Temp[j]])
b = linalg.inv(transpose(A)*A)*(transpose(A)*y)
b1 = linalg.inv(transpose(A1)*A1)*(transpose(A1)*y)
oFile.write('\n\nRate Data: Modified Arrhenius format\n')
oFile.write('r = A*(T/1000)^n*exp(-Ea/R/T)'+'%12.2e'%(exp(b[0])*1000.0**float(b[1]))+'%6.2f'%b[1]+'%12.2f'%(b[2]/1.0e3)+'\n')
oFile.write('r = A*T^n*exp(-Ea/R/T)'+'%12.2e'%(exp(b[0]))+'%6.2f'%b[1]+'%12.2f'%(b[2]/1.0e3)+'\n')
oFile.write('%12s'%'Temperature'+'%12s'%'Rate'+'%12s\n'%'Fit Rate')
for j in range(len(Temp)):
fitrate = exp(b[0])*Temp[j]**float(b[1])*exp(-b[2]/1.9872/Temp[j])
oFile.write('%12.2f'%Temp[j]+'%12.2e'%rate[j]+'%12.2e\n'%fitrate)
oFile.write('\n\n')
oFile.write('Rate Data: Arrhenius format\n')
oFile.write('r = A*exp(-Ea/R/T)'+'%12.2e'%(exp(b1[0]))+'%12.2f'%(b1[1]/1.0e3)+'\n')
oFile.write('%12s'%'Temperature'+'%12s'%'Rate'+'%12s\n'%'Fit Rate')
for j in range(len(Temp)) :
fitrate2 = exp(b1[0])*exp(-b1[1]/1.9872/Temp[j])
oFile.write('%12.2f'%Temp[j]+'%12.2e'%rate[j]+'%12.2e\n'%fitrate2)
oFile.write('\n\n')
oFile.close()
def main():
data = CanTherm()
inputFile = open(sys.argv[1], 'r')
#determine the output file name by removing the contents of the input filename following the first period and appending the .canout suffix
periodPosition = sys.argv[1].rfind(".")
outfilename = sys.argv[1][0:periodPosition] + ".canout"
oFile = open(outfilename, 'w')
readGeomFc.readInputFile(inputFile, data)
data.Entropy = len(data.MoleculeList) * len(data.Temp) * [0.0]
data.Cp = len(data.MoleculeList) * len(data.Temp) * [0.0]
data.Thermal = len(data.MoleculeList) * len(data.Temp) * [0.0]
data.Partition = len(data.MoleculeList) * len(data.Temp) * [1.0]
Entropy = data.Entropy
Cp = data.Cp
Thermal = data.Thermal
Partition = data.Partition
Entropy298 = 0.0
Thermal298 = 0.0
for i in range(len(data.MoleculeList)):
molecule = data.MoleculeList[i]
oFile.write('Molecule ' + str(i + 1) + ':\n')
oFile.write('-----------\n\n')
molecule.printData(oFile)
oFile.write('\nThermodynamic Data\n')
Temp = data.Temp
temp298 = [
298.15
] #use 298.15 K as well; this will be used below for printing Hf298, S298
#translation
(ent, cp, dh, q) = molecule.getTranslationThermo(oFile, data.Temp)
for j in range(len(Temp)):
Entropy[i * len(Temp) + j] = Entropy[i * len(Temp) + j] + ent[j]
Cp[i * len(Temp) + j] = Cp[i * len(Temp) + j] + cp[j]
Thermal[i * len(Temp) + j] = Thermal[i * len(Temp) + j] + dh[j]
Partition[i * len(Temp) + j] = Partition[i * len(Temp) + j] * q[j]
(ent298, cp298, dh298,
q298) = molecule.getTranslationThermo(oFile, temp298)
Entropy298 = Entropy298 + ent298[0]
Thermal298 = Thermal298 + dh298[0]
#vibrational
(ent, cp, dh,
q) = molecule.getVibrationalThermo(oFile, data.Temp, data.scale)
for j in range(len(Temp)):
Entropy[i * len(Temp) + j] = Entropy[i * len(Temp) + j] + ent[j]
Cp[i * len(Temp) + j] = Cp[i * len(Temp) + j] + cp[j]
Thermal[i * len(Temp) + j] = Thermal[i * len(Temp) + j] + dh[j]
Partition[i * len(Temp) + j] = Partition[i * len(Temp) + j] * q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
(ent298, cp298, dh298,
q298) = molecule.getVibrationalThermo(oFile, temp298, data.scale)
Entropy298 = Entropy298 + ent298[0]
Thermal298 = Thermal298 + dh298[0]
#Internal rotational
if molecule.numRotors != 0:
(ent, cp, dh,
q) = molecule.getIntRotationalThermo_Q(oFile, data.Temp)
for j in range(len(Temp)):
Entropy[i * len(Temp) +
j] = Entropy[i * len(Temp) + j] + ent[j]
Cp[i * len(Temp) + j] = Cp[i * len(Temp) + j] + cp[j]
Thermal[i * len(Temp) + j] = Thermal[i * len(Temp) + j] + dh[j]
Partition[i * len(Temp) +
j] = Partition[i * len(Temp) + j] * q[j]
#print '%12.2f'%float(ent[j]),
#print '\n'
(ent298, cp298, dh298,
q298) = molecule.getIntRotationalThermo_Q(oFile, temp298)
Entropy298 = Entropy298 + ent298[0]
Thermal298 = Thermal298 + dh298[0]
#External rotational
(ent, cp, dh, q) = molecule.getExtRotationalThermo(oFile, data.Temp)
for j in range(len(Temp)):
Entropy[i * len(Temp) + j] = Entropy[i * len(Temp) + j] + ent[j]
Cp[i * len(Temp) + j] = Cp[i * len(Temp) + j] + cp[j]
Thermal[i * len(Temp) + j] = Thermal[i * len(Temp) + j] + dh[j]
Partition[i * len(Temp) + j] = Partition[i * len(Temp) + j] * q[j]
(ent298, cp298, dh298,
q298) = molecule.getExtRotationalThermo(oFile, temp298)
Entropy298 = Entropy298 + ent298[0]
Thermal298 = Thermal298 + dh298[0]
for j in range(len(Temp)):
Entropy[i * len(Temp) +
j] = Entropy[i * len(Temp) +
j] + 1.9872 * math.log(molecule.nelec)
Partition[i * len(Temp) +
j] = Partition[i * len(Temp) + j] * molecule.nelec
Entropy298 = Entropy298 + 1.9872 * math.log(molecule.nelec)
#print Enthalpy
H = molecule.Energy
if not molecule.Etype == 'mm4': #for the MM4 case, the value passed in should be in kcal/mol and should not require unit adjustments or atomization energy information
atoms = readGeomFc.getAtoms(molecule.Mass)
atomsH = 0.0
#atomsH0 = 0.0
if molecule.Etype == 'cbsqb3':
atomE = data.atomEcbsqb3
if molecule.Etype == 'cbsqb3uf':
atomE = data.atomEcbsqb3uf
if molecule.Etype == 'g3':
atomE = data.atomEg3
if molecule.Etype == 'klip_1':
atomE = data.atomEKlip_1
if molecule.Etype == 'klip_2':
atomE = data.atomEKlip_2
if molecule.Etype == 'klip_2_cc':
atomE = data.atomEKlip_2_cc
for atom in atoms:
H -= atomE[atom]
atomsH += data.atomH[atom]
# atomsH0 += data.atomH0[atom]
H = H * 627.5095 + atomsH
# H0 = H*627.5095+atomsH0
if (molecule.Etype == 'cbsqb3' or molecule.Etype == 'cbsqb3uf'):
b = 0
for bonds in molecule.bonds:
H += bonds * data.bondC[b]
b += 1
#MRH 30Jan2010
#This E0 will be used in the Eckart tunneling calculation
molecule.E0 = H
H298 = H + Thermal298
H += Thermal[i * len(Temp) + 0]
print '%12.2f' % H298 + '%12.2f' % Entropy298,
# print '%12.2f'%float(H*4.187) + '%12.2f'%float(Entropy[i*len(Temp)+0]*4.187)
for c in range(0, len(Temp)):
print '%12.2f' % Cp[i * len(Temp) + c],
print '\n'
oFile.write("Hf298 S298 Cps:\n")
oFile.write(str(H298) + " " + str(Entropy298))
# print '%12.2f'%float(H*4.187) + '%12.2f'%float(Entropy[i*len(Temp)+0]*4.187)
for c in range(0, len(Temp)):
oFile.write(" " + str(Cp[i * len(Temp) + c]))
# print '\n'
#for c in range(len(Temp)):
#print '%12.2e'%Partition[i*len(Temp)+c],
#print
if data.fitcp:
FitCp.FitHeatCapacity(Temp, Cp, molecule.linearity, molecule.Freq,
molecule.numRotors, molecule.R, oFile)
if len(data.MoleculeList) == 1:
return
#fit the rate coefficient
A = matrix(zeros((len(Temp), 3), dtype=float))
A1 = matrix(zeros((len(Temp), 2), dtype=float))
y = matrix(zeros((len(Temp), 1), dtype=float))
rate = [0.0] * len(Temp)
for j in range(len(Temp)):
if (data.ReacType == 'Unimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*math.exp((Entropy[len(Temp)+j]-Entropy[j])/1.9872)*math.exp(-(data.MoleculeList[1].Energy - data.MoleculeList[0].Energy)*627.5095*1.0e3/1.9872/Temp[j])
kbT_h = (1.381e-23 * Temp[j] / 6.626e-34)
G_TS = Thermal[len(Temp) + j] * 1e3 + data.MoleculeList[
1].Energy * 627.5095 * 1e3 - Temp[j] * Entropy[len(Temp) + j]
G_react = Thermal[j] * 1e3 + data.MoleculeList[
0].Energy * 627.5095 * 1e3 - Temp[j] * Entropy[j]
#qTS_qA = Partition[len(Temp)+j]/Partition[j]
#exp_e_RT = math.exp(-(data.MoleculeList[1].Energy-data.MoleculeList[0].Energy)*627.5095*1e3/1.9872/Temp[j])
#print kbT_h * exp_S_R * exp_H_RT
#print qTS_qA * exp_e_RT
rate[j] = kbT_h * math.exp(-(G_TS - G_react) / 1.9872 / Temp[j])
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner':
kappa = 1.0 + 1.0 / 24.0 * (
1.44 * data.MoleculeList[1].imagFreq / Temp[j])**2
print kappa
rate[j] *= 1.0 + 1.0 / 24.0 * (
1.44 * data.MoleculeList[1].imagFreq / Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart':
delV1 = data.MoleculeList[1].E0 - data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2 * math.pi * delV1 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[1].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(
delV1, Temp[j], alpha1, alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart':
delV1 = data.MoleculeList[1].E0 - data.MoleculeList[0].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2 * math.pi * delV1 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[1].imagFreq)
if data.numProds == 1:
delV2 = data.MoleculeList[1].E0 - data.MoleculeList[2].E0
else:
delV2 = data.MoleculeList[1].E0 - data.MoleculeList[
2].E0 - data.MoleculeList[3].E0
delV2 = delV2 / 6.022e23 * 4184
alpha2 = 2 * math.pi * delV2 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[1].imagFreq)
if (alpha1 < alpha2):
rate[j] *= Eckart.computeTunnelingCorrection(
delV1, Temp[j], alpha1, alpha2)
else:
# reverse the direction: pass delV2 and alpha1 in place of alpha2
rate[j] *= Eckart.computeTunnelingCorrection(
delV2, Temp[j], alpha2, alpha1)
elif (data.ReacType == 'Bimol'):
#rate[j] = (1.381e-23*Temp[j]/6.626e-34)*(82.05746*Temp[j]/1.0)*math.exp((Entropy[2*len(Temp)+j]-Entropy[len(Temp)+j]-Entropy[j])/1.9872)*math.exp(-(data.MoleculeList[2].Energy - data.MoleculeList[0].Energy - data.MoleculeList[1].Energy)*627.5095*1.0e3/1.9872/Temp[j])
kbT_hC = (1.381e-23 * Temp[j] / 6.626e-34) * (82.05746 * Temp[j] /
1.0)
G_TS = Thermal[2 * len(Temp) + j] * 1e3 + data.MoleculeList[
2].Energy * 627.5095 * 1e3 - Temp[j] * Entropy[2 * len(Temp) +
j]
G_react1 = Thermal[len(Temp) + j] * 1e3 + data.MoleculeList[
1].Energy * 627.5095 * 1e3 - Temp[j] * Entropy[len(Temp) + j]
G_react2 = Thermal[j] * 1e3 + data.MoleculeList[
0].Energy * 627.5095 * 1e3 - Temp[j] * Entropy[j]
rate[j] = kbT_hC * math.exp(
-(G_TS - G_react1 - G_react2) / 1.9872 / Temp[j])
#wigner correction
#rate[j] *= 1.0 + 1.0/24.0 * (1.44*data.MoleculeList[2].imagFreq/Temp[j])**2
#Tunneling:
#Wigner - need imaginary frequency + temperature
if data.TunnelType == 'Wigner':
rate[j] *= 1.0 + 1.0 / 24.0 * (
1.44 * data.MoleculeList[2].imagFreq / Temp[j])**2
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react)
elif data.TunnelType == 'sEckart':
delV1 = data.MoleculeList[2].E0 - data.MoleculeList[
0].E0 - data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2 * math.pi * delV1 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[2].imagFreq)
alpha2 = alpha1
rate[j] *= Eckart.computeTunnelingCorrection(
delV1, Temp[j], alpha1, alpha2)
#Symmetric Eckart - need imaginary frequency + temperature + (E0_TS - E_react) + (E0_TS - E_prod)
elif data.TunnelType == 'aEckart':
delV1 = data.MoleculeList[2].E0 - data.MoleculeList[
0].E0 - data.MoleculeList[1].E0
delV1 = delV1 / 6.022e23 * 4184
alpha1 = 2 * math.pi * delV1 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[2].imagFreq)
if data.numProds == 1:
delV2 = data.MoleculeList[2].E0 - data.MoleculeList[3].E0
else:
delV2 = data.MoleculeList[2].E0 - data.MoleculeList[
3].E0 - data.MoleculeList[4].E0
delV2 = delV2 / 6.022e23 * 4184
alpha2 = 2 * math.pi * delV2 / 6.626e-34 / 3.00e10 / (
-1 * data.MoleculeList[2].imagFreq)
if (alpha1 < alpha2):
rate[j] *= Eckart.computeTunnelingCorrection(
delV1, Temp[j], alpha1, alpha2)
else:
# reverse the direction: pass delV2 and alpha1 in place of alpha2
rate[j] *= Eckart.computeTunnelingCorrection(
delV2, Temp[j], alpha2, alpha1)
A[j, :] = mat([1.0, math.log(Temp[j]), -1.0 / 1.9872 / Temp[j]])
y[j] = log(rate[j])
A1[j, :] = mat([1.0, -1.0 / 1.9872 / Temp[j]])
b = linalg.inv(transpose(A) * A) * (transpose(A) * y)
b1 = linalg.inv(transpose(A1) * A1) * (transpose(A1) * y)
oFile.write('\n\nRate Data: Modified Arrhenius format\n')
oFile.write('r = A*(T/1000)^n*exp(-Ea/R/T)' + '%12.2e' %
(exp(b[0]) * 1000.0**float(b[1])) + '%6.2f' % b[1] + '%12.2f' %
(b[2] / 1.0e3) + '\n')
oFile.write('r = A*T^n*exp(-Ea/R/T)' + '%12.2e' % (exp(b[0])) +
'%6.2f' % b[1] + '%12.2f' % (b[2] / 1.0e3) + '\n')
oFile.write('%12s' % 'Temperature' + '%12s' % 'Rate' +
'%12s\n' % 'Fit Rate')
for j in range(len(Temp)):
fitrate = exp(b[0]) * Temp[j]**float(b[1]) * exp(
-b[2] / 1.9872 / Temp[j])
oFile.write('%12.2f' % Temp[j] + '%12.2e' % rate[j] +
'%12.2e\n' % fitrate)
oFile.write('\n\n')
oFile.write('Rate Data: Arrhenius format\n')
oFile.write('r = A*exp(-Ea/R/T)' + '%12.2e' % (exp(b1[0])) + '%12.2f' %
(b1[1] / 1.0e3) + '\n')
oFile.write('%12s' % 'Temperature' + '%12s' % 'Rate' +
'%12s\n' % 'Fit Rate')
for j in range(len(Temp)):
fitrate2 = exp(b1[0]) * exp(-b1[1] / 1.9872 / Temp[j])
oFile.write('%12.2f' % Temp[j] + '%12.2e' % rate[j] +
'%12.2e\n' % fitrate2)
oFile.write('\n\n')
oFile.close()