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)
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
#!/usr/bin/env python
import os
import sys
from Harmonics import *
file = sys.argv[1]
Kcos = []
Ksin = []
harmonic = Harmonics(5, Kcos, Ksin)
harmonic.fitPotential(file)
for i in range(5):
print harmonic.Kcos[i], harmonic.Ksin[i]
for i in range(5):
print harmonic.Kcos[i], " ", "%3.1f" % (float(i + 1))
for i in range(5):
print harmonic.Ksin[i], " ", "%3.1f" % (float(i + 1))
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
#!/usr/bin/env python
import os
import sys
from Harmonics import *
file = sys.argv[1]
Kcos=[]
Ksin =[]
harmonic = Harmonics(5,Kcos,Ksin)
harmonic.fitPotential(file)
for i in range(5):
print harmonic.Kcos[i], harmonic.Ksin[i]
for i in range(5):
print harmonic.Kcos[i], " ", "%3.1f"%(float(i+1))
for i in range(5):
print harmonic.Ksin[i], " ", "%3.1f"%(float(i+1))
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)
