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[cclib-svn] SF.net SVN: cclib: [29] trunk/src/cclib/parser/gamessparser.py
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From: <bao...@us...> - 2006-03-19 19:53:06
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Revision: 29 Author: baoilleach Date: 2006-03-19 11:52:56 -0800 (Sun, 19 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=29&view=rev Log Message: ----------- Now the gamessparser can parse (correctly or not) all of the dvb test files. Modified Paths: -------------- trunk/src/cclib/parser/gamessparser.py Modified: trunk/src/cclib/parser/gamessparser.py =================================================================== --- trunk/src/cclib/parser/gamessparser.py 2006-03-19 19:51:04 UTC (rev 28) +++ trunk/src/cclib/parser/gamessparser.py 2006-03-19 19:52:56 UTC (rev 29) @@ -77,32 +77,28 @@ opttol = float(x.split('=')[1]) self.geotargets = Numeric.array([opttol,3./opttol]) - if line.find("EQUILIBRIUM GEOMETRY LOCATED")>=0: -# This is necessary if a frequency calculation follows a geometry optimisation - endofopt = True - - if not endofopt and line.find("FINAL")==1: + if line.find("FINAL")==1: if not hasattr(self,"scfenergies"): self.logger.info("Creating attribute scfenergies[]") self.scfenergies = [] -# Here is an example from Neil Berry: +# Has to deal with such lines as: # FINAL R-B3LYP ENERGY IS -382.0507446475 AFTER 10 ITERATIONS -# but in some cases the energy can be in position [3] not [4] so let's -# take the number after the "IS" +# FINAL ENERGY IS -379.7594673378 AFTER 9 ITERATIONS +# ...so take the number after the "IS" temp = line.split() self.scfenergies.append(temp[temp.index("IS")+1]) - if not endofopt and line.find("MAXIMUM GRADIENT")>0: + if line.find("MAXIMUM GRADIENT")>0: if not hasattr(self,"geovalues"): self.logger.info("Creating attribute geovalues[]") self.geovalues = [] temp = line.strip().split() self.geovalues.append([float(temp[3]),float(temp[7])]) - - if line.find("DENSITY CONV=")==5: - self.scftargets[0] = float(line.strip().split()[-1]) + if not hasattr(self,"scftargets"): + self.logger.info("Creating attribute scftargets") + self.scftargets = Numeric.array([float(line.strip().split()[-1])]) if line.find("ITER EX DEM")==1: # This is the section with the SCF information @@ -127,7 +123,38 @@ self.scfvalues.append(den) if line.find("NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION")>=0: - # Start of the frequency section +# GAMESS has... +# MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. +# +# FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2, +# REDUCED MASSES IN AMU. +# +# 1 2 3 4 5 +# FREQUENCY: 52.49 41.45 17.61 9.23 10.61 +# REDUCED MASS: 3.92418 3.77048 5.43419 6.44636 5.50693 +# IR INTENSITY: 0.00013 0.00001 0.00004 0.00000 0.00003 + +# whereas PC-GAMESS has... +# MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. +# +# FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2 +# +# 1 2 3 4 5 +# FREQUENCY: 5.89 1.46 0.01 0.01 0.01 +# IR INTENSITY: 0.00000 0.00000 0.00000 0.00000 0.00000 + +# If Raman is present we have (for PC-GAMESS)... +# MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. +# +# FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2 +# RAMAN INTENSITIES IN ANGSTROM**4/AMU, DEPOLARIZATIONS ARE DIMENSIONLESS +# +# 1 2 3 4 5 +# FREQUENCY: 5.89 1.46 0.04 0.03 0.01 +# IR INTENSITY: 0.00000 0.00000 0.00000 0.00000 0.00000 +# RAMAN INTENSITY: 12.675 1.828 0.000 0.000 0.000 +# DEPOLARIZATION: 0.750 0.750 0.124 0.009 0.750 + self.logger.info("Creating attributes vibfreqs, vibirs") self.vibfreqs = [] self.vibirs = [] @@ -143,22 +170,32 @@ numAtom += 1 line = inputfile.next() - # Print out the following lines which may contain some useful info: - # e.g. WARNING, MODE 7 HAS BEEN CHOSEN AS A VIBRATION line = inputfile.next() while line.find("FREQUENCIES IN CM**-1")==-1: line = inputfile.next() - line = inputfile.next() - - blank = inputfile.next() + while line!=blank: + line = inputfile.next() + freqNo = inputfile.next() while freqNo.find("SAYVETZ")==-1: freq = inputfile.next().strip().split() self.vibfreqs.extend(map(float,freq[1:])) - reducedMass = inputfile.next() - irIntensity = inputfile.next().strip().split() + line = inputfile.next() + if line.find("REDUCED")>=0: # skip the reduced mass (not always present) + line = inputfile.next() + irIntensity = line.strip().split() self.vibirs.extend(map(float,irIntensity[2:])) - blank = inputfile.next() + line = inputfile.next() + if line.find("RAMAN")>=0: + if not hasattr(self,"vibramans"): + self.logger.info("Creating attribute vibramans") + self.vibramans = [] + ramanIntensity = line.strip().split() + self.vibramans.extend(map(float,ramanIntensity[2:])) + depolar = inputfile.next() + line = inputfile.next() + assert line==blank + # Skip XYZ data for each atom plus # the Sayvetz stuff at the end for j in range(numAtom*3+10): @@ -177,24 +214,22 @@ # Take the last one of either in the file if not hasattr(self,"moenergies"): self.logger.info("Creating attributes moenergies, mosyms") - self.moenergies = [] + self.moenergies = [[]] self.mosyms = [] if not hasattr(self,"nindep"): self.logger.info("Creating attribute nindep with default value") self.nindep = self.nbasis self.mocoeffs = Numeric.zeros((1,self.nindep,self.nbasis),"f") line = inputfile.next() - blank = inputfile.next() # blank line - base = 0 - while line.find("END OF RHF")==-1: + for base in range(0,self.nindep,5): + blank = inputfile.next() line = inputfile.next() # Eigenvector no line = inputfile.next() - self.moenergies.extend(map(float,line.split())) + self.moenergies[0].extend([convertor(float(x),"hartree","eV") for x in line.split()]) line = inputfile.next() self.mosyms.extend(line.split()) - line = inputfile.next() - i=0 - while line!=blank and line.find("END OF RHF")==-1: + for i in range(self.nbasis): + line = inputfile.next() if base==0: # Just do this the first time 'round atomno=int(line.split()[2])-1 # atomorb[atomno].append(int(line.split()[0])-1) @@ -204,16 +239,46 @@ while j*11+4<len(temp): self.mocoeffs[0,base+j,i] = float(temp[j*11:(j+1)*11]) j+=1 + line = inputfile.next() + if line.find("END OF RHF")==-1: # implies unrestricted +# If it's restricted we have +# ...... END OF RHF CALCULATION ...... +# If it's unrestricted we have... +# +# ----- BETA SET ----- +# +# ------------ +# EIGENVECTORS +# ------------ +# +# 1 2 3 4 5 + + self.mocoeffs.resize((2,self.nindep,self.nbasis)) + for i in range(5): line = inputfile.next() - i+=1 - base+=5 + for base in range(0,self.nindep,5): + blank = inputfile.next() + line = inputfile.next() # Eigenvector no + line = inputfile.next() + self.moenergies.extend(map(float,line.split())) + line = inputfile.next() + self.mosyms.extend(line.split()) + for i in range(self.nbasis): + line = inputfile.next() + temp = line[15:] # Strip off the crud at the start + j = 0 + while j*11+4<len(temp): + self.mocoeffs[1,base+j,i] = float(temp[j*11:(j+1)*11]) + j+=1 + line = inputfile.next() + assert line.find("END OF")>=0 self.moenergies = Numeric.array(self.moenergies,"f") if line.find("NUMBER OF OCCUPIED ORBITALS")>=0: if not hasattr(self,"homos"): self.logger.info("Creating attribute homos") temp = line.strip().split('=') - self.homos = Numeric.array(int(temp[-1])-1,"d") + self.homos = Numeric.array([int(temp[-1])-1],"i") if line.find("TOTAL NUMBER OF ATOMS")==1: self.logger.info("Creating attribute natom") @@ -234,8 +299,11 @@ elif line.find("OVERLAP MATRIX")==0 or line.find("OVERLAP MATRIX")==1: # The first is for PC-GAMESS, the second for GAMESS # Read 1-electron overlap matrix - self.logger.info("Creating attribute aooverlaps") - self.aooverlaps = Numeric.zeros((self.nbasis,self.nbasis), "f") + if not hasattr(self,"aooverlaps"): + self.logger.info("Creating attribute aooverlaps") + self.aooverlaps = Numeric.zeros((self.nbasis,self.nbasis), "f") + else: + self.logger.info("Reading additional aooverlaps...") base = 0 while base<self.nbasis: blank = inputfile.next() This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
