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[cclib-svn] SF.net SVN: cclib: [13] trunk/src/cclib/parser/g03parser.py
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From: <bao...@us...> - 2006-03-09 09:54:09
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Revision: 13 Author: baoilleach Date: 2006-03-09 01:54:04 -0800 (Thu, 09 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=13&view=rev Log Message: ----------- Updated all of the variable names in the G03 parser. (Need to fix the variable types next...) Modified Paths: -------------- trunk/src/cclib/parser/g03parser.py Modified: trunk/src/cclib/parser/g03parser.py =================================================================== --- trunk/src/cclib/parser/g03parser.py 2006-03-09 09:03:51 UTC (rev 12) +++ trunk/src/cclib/parser/g03parser.py 2006-03-09 09:54:04 UTC (rev 13) @@ -183,7 +183,7 @@ while len(line)>18 and line[17]=='(': if line.find('Virtual')>=0: self.homos = [i-1] # 'HOMO' indexes the HOMO in the arrays - self.logger.info("Creating attribute HOMO[]") + self.logger.info("Creating attribute homos[]") parts = line[17:].split() for x in parts: self.mosyms[0].append(x.strip('()')) @@ -205,14 +205,14 @@ if line[1:6]=="Alpha" and line.find("eigenvalues")>=0: # Extract the alpha electron eigenvalues - self.logger.info("Creating attribute evalue[[]]") - self.evalue = [[]] + self.logger.info("Creating attribute moenergies[[]]") + self.moenergies = [[]] HOMO = -2 while line.find('Alpha')==1: if line.split()[1]=="virt." and HOMO==-2: # If there aren't any symmetries, # this is a good way to find the HOMO - HOMO = len(self.evalue[0])-1 + HOMO = len(self.moenergies[0])-1 if hasattr(self,"homos"): assert HOMO==self.homos[0] else: @@ -222,17 +222,17 @@ i = 0 while i*10+4<len(part): x = part[i*10:(i+1)*10] - self.evalue[0].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV + self.moenergies[0].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV i += 1 line = inputfile.next() if line.find('Beta')==2: - self.evalue.append([]) + self.moenergies.append([]) HOMO = -2 while line.find('Beta')==2: if line.split()[1]=="virt." and HOMO==-2: # If there aren't any symmetries, # this is a good way to find the HOMO - HOMO = len(self.evalue[1])-1 + HOMO = len(self.moenergies[1])-1 if len(self.homos)==2: # It already has a self.homos (with the Alpha value) # but does it already have a Beta value? @@ -243,7 +243,7 @@ i = 0 while i*10+4<len(part): x = part[i*10:(i+1)*10] - self.evalue[1].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV + self.moenergies[1].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV i += 1 line = inputfile.next() @@ -251,7 +251,7 @@ # Start of the IR/Raman frequency section self.vibsyms = [] self.vibirs = [] - self.vibfreq = [] + self.vibfreqs = [] self.logger.info("Creating attribute vibsyms[]") self.logger.info("Creating attribute vibfreqs[]") self.logger.info("Creating attribute vibirs[]") @@ -264,15 +264,15 @@ self.logger.debug(line) self.vibsyms.extend(line.split()) # Adding new symmetry line = inputfile.next() - self.vibfreq.extend(map(self.float,line[15:].split())) # Adding new frequencies + self.vibfreqs.extend(map(self.float,line[15:].split())) # Adding new frequencies [inputfile.next() for i in [0,1]] # Skip two lines line = inputfile.next() self.vibirs.extend(map(self.float,line[15:].split())) # Adding IR intensities line = inputfile.next() if line.find("Raman")>=0: - if not hasattr(self,"raman"): + if not hasattr(self,"vibramans"): self.vibramans = [] - self.logger.info("Creating attribute raman[]") + self.logger.info("Creating attribute vibramans[]") line = inputfile.next() self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities line = inputfile.next() @@ -283,23 +283,20 @@ if line[1:14]=="Excited State": # Extract the electronic transitions if not hasattr(self,"etenergy"): - self.etenergy = [] - self.etwavelen = [] - self.etosc = [] - self.etsym = [] - self.etcis = [] - self.logger.info("Creating attributes etenergy[], etwavelen[], etosc[], etsym[], etcis[]") + self.etenergies = [] + self.etoscs = [] + self.etsyms = [] + self.etsecs = [] + self.logger.info("Creating attributes etenergies[], etoscs[], etsyms[], etsecs[]") # Need to deal with lines like: # (restricted calc) # Excited State 1: Singlet-BU 5.3351 eV 232.39 nm f=0.1695 # (unrestricted calc) (first excited state is 2!) # Excited State 2: ?Spin -A 0.1222 eV 10148.75 nm f=0.0000 parts = line[36:].split() - self.logger.debug(parts) - self.etenergy.append(convertor(self.float(parts[0]),"eV","cm-1")) - self.etwavelen.append(self.float(parts[2])) - self.etosc.append(self.float(parts[4].split("=")[1])) - self.etsym.append(line[21:36].split()) + self.etenergies.append(convertor(self.float(parts[0]),"eV","cm-1")) + self.etoscs.append(self.float(parts[4].split("=")[1])) + self.etsyms.append(line[21:36].split()) line = inputfile.next() @@ -330,13 +327,13 @@ sqr = -sqr CIScontrib.append([(fromMO,frommoindex),(toMO,tomoindex),sqr]) line = inputfile.next() - self.etcis.append(CIScontrib) + self.etsecs.append(CIScontrib) if line[1:52]=="<0|r|b> * <b|rxdel|0> (Au), Rotatory Strengths (R)": # Extract circular dichroism data - self.rotatory = [] - self.logger.info("Creating attribute rotatory[]") + self.etrotats = [] + self.logger.info("Creating attribute etrotats[]") inputfile.next() inputfile.next() line = inputfile.next() @@ -349,43 +346,43 @@ # (for unrestricted calculations) pass else: - self.rotatory.append(R) + self.etrotats.append(R) line = inputfile.next() temp = line.strip().split() parts = line.strip().split() if line[1:7]=="NBasis" or line[4:10]=="NBasis": # Extract the number of basis sets - NBasis = int(line.split('=')[1].split()[0]) + nbasis = int(line.split('=')[1].split()[0]) # Has to deal with lines like: - # NBasis= 434 NAE= 97 NBE= 97 NFC= 34 NFV= 0 + # NBasis = 434 NAE= 97 NBE= 97 NFC= 34 NFV= 0 # NBasis = 148 MinDer = 0 MaxDer = 0 # Although the former is in every file, it doesn't occur before # the overlap matrix is printed - if hasattr(self,"NBasis"): - assert NBasis==self.NBasis + if hasattr(self,"nbasis"): + assert nbasis==self.nbasis else: - self.NBasis = NBasis - self.logger.info("Creating attribute NBasis: %d" % self.NBasis) + self.nbasis= nbasis + self.logger.info("Creating attribute nbasis: %d" % self.nbasis) if line[1:7]=="NBsUse": # Extract the number of linearly-independent basis sets - NBsUse = int(line.split('=')[1].split()[0]) - if hasattr(self,"NBsUse"): - assert NBsUse==self.NBsUse + nindep = int(line.split('=')[1].split()[0]) + if hasattr(self,"nindep"): + assert nindep==self.nindep else: - self.NBsUse = NBsUse - self.logger.info("Creating attribute NBsUse: %d" % self.NBsUse) + self.nindep = nindep + self.logger.info("Creating attribute nindep: %d" % self.nindep) if line[7:22]=="basis functions,": -# For AM1 calculations, set NBasis by a second method -# (NBsUse may not always be explicitly stated) - NBasis = int(line.split()[0]) - if hasattr(self,"NBasis"): - assert NBasis==self.NBasis +# For AM1 calculations, set nbasis by a second method +# (nindep may not always be explicitly stated) + nbasis = int(line.split()[0]) + if hasattr(self,"nbasis"): + assert nbasis==self.nbasis else: - self.NBasis = NBasis - self.logger.info("Creating attribute NBasis: %d" % self.NBasis) + self.nbasis = nbasis + self.logger.info("Creating attribute nbasis: %d" % self.nbasis) if line[1:4]=="***" and (line[5:12]=="Overlap" or line[8:15]=="Overlap"): @@ -393,20 +390,20 @@ # Has to deal with lines such as: # *** Overlap *** # ****** Overlap ****** - self.logger.info("Creating attribute overlap[x,y]") + self.logger.info("Creating attribute aooverlaps[x,y]") import time; oldtime = time.time() - self.overlap = Numeric.zeros( (self.NBasis,self.NBasis), "float") - # Overlap integrals for basis fn#1 are in overlap[0] + self.aooverlaps = Numeric.zeros( (self.nbasis,self.nbasis), "float") + # Overlap integrals for basis fn#1 are in aooverlaps[0] base = 0 colmNames = inputfile.next() - while base<self.NBasis: - for i in range(self.NBasis-base): # Fewer lines this time + while base<self.nbasis: + for i in range(self.nbasis-base): # Fewer lines this time line = inputfile.next() parts = line.split() for j in range(len(parts)-1): # Some lines are longer than others k = float(parts[j].replace("D","E")) - self.overlap[base+j,i+base] = k - self.overlap[i+base,base+j] = k + self.aooverlaps[base+j,i+base] = k + self.aooverlaps[i+base,base+j] = k base += 5 colmNames = inputfile.next() self.logger.info("Took %f seconds" % (time.time()-oldtime)) @@ -415,20 +412,20 @@ import time; oldtime = time.time() if line[5:40]=="Beta Molecular Orbital Coefficients": beta = True - # Need to add an extra dimension to self.mocoeff - self.mocoeff = Numeric.resize(self.mocoeff,(2,NBsUse,NBasis)) + # Need to add an extra dimension to self.mocoeffs + self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nindep,nbasis)) else: beta = False - self.logger.info("Creating attributes orbitals[], mocoeff[][]") - self.orbitals = [] - self.mocoeff = Numeric.zeros((NBsUse,NBasis),"float") + self.logger.info("Creating attributes aonames[], mocoeffs[][]") + self.aonames = [] + self.mocoeffs = Numeric.zeros((nindep,nbasis),"float") base = 0 - for base in range(0,NBsUse,5): + for base in range(0,nindep,5): colmNames = inputfile.next() symmetries = inputfile.next() eigenvalues = inputfile.next() - for i in range(NBasis): + for i in range(nbasis): line = inputfile.next() if base==0 and not beta: # Just do this the first time 'round # Changed below from :12 to :11 to deal with Elmar Neumann's example @@ -436,18 +433,17 @@ if len(parts)>1: # New atom atomname = "%s%s" % (parts[2],parts[1]) orbital = line[11:20].strip() - self.orbitals.append("%s_%s" % (atomname,orbital)) + self.aonames.append("%s_%s" % (atomname,orbital)) part = line[21:].replace("D","E").rstrip() temp = [] for j in range(0,len(part),10): temp.append(float(part[j:j+10])) if beta: - self.mocoeff[1,base:base+len(part)/10,i] = temp + self.mocoeffs[1,base:base+len(part)/10,i] = temp else: - self.mocoeff[base:base+len(part)/10,i] = temp + self.mocoeffs[base:base+len(part)/10,i] = temp self.logger.info("Took %f seconds" % (time.time()-oldtime)) - inputfile.close() This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
