def main():
logFile = open(sys.argv[1], 'r')
file = logFile
inertiaFile = open('inertia.dat', 'r')
(geom, Mass) = readGeomFc.readGeom(logFile)
(rotors) = readGeomFc.readGeneralInertia(inertiaFile)
D = calculateD(geom, Mass, rotors)
(l, v) = linalg.eigh(D)
print(l, linalg.det(D))
def main():
logFile = open(sys.argv[1],'r')
file = logFile
inertiaFile = open('inertia.dat','r')
(geom,Mass)=readGeomFc.readGeom(logFile)
(rotors)= readGeomFc.readGeneralInertia(inertiaFile)
#D=calculateI23(geom,Mass,rotors)
D=calculateD(geom,Mass,rotors)
(l,v)= linalg.eigh(D)
print l, linalg.det(D)
#initialize parameters
#seed = 200
numIter = 20000
theory = ' b3lyp/6-31G(d) '
numprocessors = 8
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):
def __init__(self,file, isTS):
self.Freq = []
self.Harmonics = []
self.hindFreq = []
self.bonds = []
self.Etype = ''
self.TS = isTS
self.E0 = []
#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
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() == "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 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() == 'G3'):
self.Etype = 'g3'
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() == 'G3'):
self.Etype = 'g3'
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 = int(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()
#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() == '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 = ['1220.log','0120.log','1000.log','1120.log','2101.log','2120.log']
inputFiles = ['022.log','112.log','012.log','120.log']
#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 = []
#initialize parameters
#seed = 200
numIter = 20000
theory = ' b3lyp/6-31G(d) '
numprocessors = 8
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)):
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 = ['1220.log','0120.log','1000.log','1120.log','2101.log','2120.log']
inputFiles = ['022.log', '112.log', '012.log', '120.log']
#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 = []
