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[cclib-svn] SF.net SVN: cclib: [12] trunk/src/cclib/parser/g03parser.py
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From: <bao...@us...> - 2006-03-09 09:04:26
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Revision: 12 Author: baoilleach Date: 2006-03-09 01:03:51 -0800 (Thu, 09 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=12&view=rev Log Message: ----------- Changed half of the attribute names to the new names. Modified Paths: -------------- trunk/src/cclib/parser/g03parser.py Modified: trunk/src/cclib/parser/g03parser.py =================================================================== --- trunk/src/cclib/parser/g03parser.py 2006-03-08 17:12:33 UTC (rev 11) +++ trunk/src/cclib/parser/g03parser.py 2006-03-09 09:03:51 UTC (rev 12) @@ -22,23 +22,8 @@ from logfileparser import Logfile # import the superclass class G03(Logfile): - """A Gaussian 03 log file - - Attributes: - filename -- the name of the log file - logger -- a logging object - NAtoms -- the number of atoms in the molecule - atomicNo[] -- the atomic numbers of the atoms - - scfenergy[] -- the SCF energies - - Class Methods: - float(a) -- convert a string to a float - - Methods: - parse() -- extract general info from the logfile - """ - SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftarget[] + """A Gaussian 98/03 log file""" + SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] def __init__(self,filename): # Call the __init__ method of the superclass @@ -63,67 +48,60 @@ return 'G03("%s")' % (self.filename) def parse(self): - """Extract general info from the logfile. - - Creates the following instance attributes: - NAtoms, atomicNo[], - scfProgress[], SCF_target_rms, SCF_target_energy, SCF_target_max, - geoProgress[], scfenergy[] - evalue [[]] - """ + """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=": # Find the number of atoms - NAtoms = int(line.split()[1]) - if hasattr(self,"NAtoms"): - assert self.NAtoms==NAtoms + natom = int(line.split()[1]) + if hasattr(self,"natom"): + assert self.natom==natom else: # I wonder whether this code will ever be executed - self.NAtoms = NAtoms - self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms) + self.natom = natom + self.logger.info("Creating attribute natom: %d" % self.natom) - if not hasattr(self,"atomicNo") and (line.find("Z-Matrix orientation")>=0 + if not hasattr(self,"atomnos") and (line.find("Z-Matrix orientation")>=0 or line[25:45]=="Standard orientation" or line[26:43]=="Input orientation"): # Extract the atomic numbers of the atoms - self.logger.info("Creating attribute atomicNo[]") - self.atomicNo = [] + self.logger.info("Creating attribute atomnos[]") + self.atomnos = [] hyphens = inputfile.next() colmNames = inputfile.next(); colmNames = inputfile.next() hyphens = inputfile.next() line = inputfile.next() while line!=hyphens: - self.atomicNo.append(int(line.split()[1])) + self.atomnos.append(int(line.split()[1])) line = inputfile.next() - NAtoms = len(self.atomicNo) - if hasattr(self,"NAtoms"): - assert self.NAtoms==NAtoms + natom = len(self.atomnos) + if hasattr(self,"natom"): + assert self.natom==natom else: - self.NAtoms = NAtoms - self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms) + self.natom = natom + self.logger.info("Creating attribute natom: %d" % self.natom) # Find the targets for the SCF convergence (QM calcs) # We assume that the targets don't change, although it's # easy enough to store all of the targets if line[1:44]=='Requested convergence on RMS density matrix': - if not hasattr(self,"scftarget"): - self.logger.info("Creating attribute scftarget[]") - self.scftarget = [None]*3 - self.scftarget[G03.SCFRMS] = self.float(line.split('=')[1].split()[0]) + if not hasattr(self,"scftargets"): + self.logger.info("Creating attribute scftargets[]") + self.scftargets = [None]*3 + self.scftargets[G03.SCFRMS] = self.float(line.split('=')[1].split()[0]) if line[1:44]=='Requested convergence on MAX density matrix': - self.scftarget[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) + self.scftargets[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) if line[1:44]=='Requested convergence on energy': - self.scftarget[G03.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) + self.scftargets[G03.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) if line[1:10]=='Cycle 1': # Extract SCF convergence information (QM calcs) - if not hasattr(self,"scfvalue"): - self.logger.info("Creating attribute scfvalue[[]]") - self.scfvalue = [] - newlist = [ [] for x in self.scftarget ] + if not hasattr(self,"scfvalues"): + self.logger.info("Creating attribute scfvalues[[]]") + self.scfvalues = [] + newlist = [ [] for x in self.scftargets ] line = inputfile.next() while line.find("SCF Done")==-1: if line.find(' E=')==0: @@ -147,18 +125,18 @@ line = inputfile.next() except StopIteration: # May be interupted by EOF break - self.scfvalue.append(newlist) + self.scfvalues.append(newlist) if line[1:4]=='It=': # Extract SCF convergence information (AM1 calcs) - self.logger.info("Creating attributes scftarget[],scfvalue[[]]") - self.scftarget = [1E-7] # This is the target value for the rms - self.scfvalue = [[]] + self.logger.info("Creating attributes scftargets[],scfvalues[[]]") + self.scftargets = [1E-7] # This is the target value for the rms + self.scfvalues = [[]] line = inputfile.next() while line.find(" Energy")==-1: self.logger.debug(line) parts = line.strip().split() - self.scfvalue[0].append(self.float(parts[-1][:-1])) + self.scfvalues[0].append(self.float(parts[-1][:-1])) line = inputfile.next() if line[1:9]=='SCF Done': @@ -166,18 +144,18 @@ # a loop when extract SCF convergence information self.logger.debug(line) self.logger.debug("SCF Done") - if hasattr(self,"scfenergy"): - self.scfenergy.append(line.split()[4]) + if hasattr(self,"scfenergies"): + self.scfenergies.append(line.split()[4]) else: - self.scfenergy = [line.split()[4]] - self.logger.info("Creating attribute scfenergy[]") + self.scfenergies = [line.split()[4]] + self.logger.info("Creating attribute scfenergies[]") if line[49:59]=='Converged?': # Extract Geometry convergence information - if not hasattr(self,"geotarget"): - self.logger.info("Creating attributes geotarget[],geovalue[[]]") - self.geovalue = [] - self.geotarget = [None]*4 + if not hasattr(self,"geotargets"): + self.logger.info("Creating attributes geotargets[],geovalues[[]]") + self.geovalues = [] + self.geotargets = [None]*4 newlist = [0]*4 for i in range(4): line = inputfile.next() @@ -189,13 +167,13 @@ self.logger.error("Problem parsing the value for geometry optimisation: %s is not a number." % parts[2]) else: newlist[i] = value - self.geotarget[i] = self.float(parts[3]) - self.geovalue.append(newlist) + self.geotargets[i] = self.float(parts[3]) + self.geovalues.append(newlist) - if line[1:19]=='Orbital symmetries' and not hasattr(self,"orbsym"): + if line[1:19]=='Orbital symmetries' and not hasattr(self,"mosyms"): # Extracting orbital symmetries - self.logger.info("Creating attribute orbsym[[]]") - self.orbsym = [[]] + self.logger.info("Creating attribute mosyms[[]]") + self.mosyms = [[]] line = inputfile.next() unres = False if line.find("Alpha Orbitals")==1: @@ -204,24 +182,24 @@ i = 0 while len(line)>18 and line[17]=='(': if line.find('Virtual')>=0: - self.HOMO = [i-1] # 'HOMO' indexes the HOMO in the arrays + self.homos = [i-1] # 'HOMO' indexes the HOMO in the arrays self.logger.info("Creating attribute HOMO[]") parts = line[17:].split() for x in parts: - self.orbsym[0].append(x.strip('()')) + self.mosyms[0].append(x.strip('()')) i+= 1 line = inputfile.next() if unres: line = inputfile.next() # Repeat with beta orbital information i = 0 - self.orbsym.append([]) + self.mosyms.append([]) while len(line)>18 and line[17]=='(': if line.find('Virtual')>=0: - self.HOMO.append(i-1) # 'HOMO' indexes the HOMO in the arrays + self.homos.append(i-1) # 'HOMO' indexes the HOMO in the arrays parts = line[17:].split() for x in parts: - self.orbsym[1].append(x.strip('()')) + self.mosyms[1].append(x.strip('()')) i+= 1 line = inputfile.next() @@ -235,11 +213,11 @@ # If there aren't any symmetries, # this is a good way to find the HOMO HOMO = len(self.evalue[0])-1 - if hasattr(self,"HOMO"): - assert HOMO==self.HOMO[0] + if hasattr(self,"homos"): + assert HOMO==self.homos[0] else: - self.logger.info("Creating attribute HOMO[]") - self.HOMO = [HOMO] + self.logger.info("Creating attribute homos[]") + self.homos = [HOMO] part = line[28:] i = 0 while i*10+4<len(part): @@ -255,12 +233,12 @@ # If there aren't any symmetries, # this is a good way to find the HOMO HOMO = len(self.evalue[1])-1 - if len(self.HOMO)==2: - # It already has a self.HOMO (with the Alpha value) + if len(self.homos)==2: + # It already has a self.homos (with the Alpha value) # but does it already have a Beta value? - assert HOMO==self.HOMO[1] + assert HOMO==self.homos[1] else: - self.HOMO.append(HOMO) + self.homos.append(HOMO) part = line[28:] i = 0 while i*10+4<len(part): @@ -271,12 +249,12 @@ if line[1:14]=="Harmonic freq": # Start of the IR/Raman frequency section - self.vibsym = [] - self.ir = [] + self.vibsyms = [] + self.vibirs = [] self.vibfreq = [] - self.logger.info("Creating attribute vibsym[]") - self.logger.info("Creating attribute vibfreq[]") - self.logger.info("Creating attribute ir[]") + self.logger.info("Creating attribute vibsyms[]") + self.logger.info("Creating attribute vibfreqs[]") + self.logger.info("Creating attribute vibirs[]") line = inputfile.next() while len(line[:15].split())>0: # Get past the three/four line title of the columns @@ -284,19 +262,19 @@ line = inputfile.next() # The line with symmetries while len(line[:15].split())==0: self.logger.debug(line) - self.vibsym.extend(line.split()) # Adding new symmetry + self.vibsyms.extend(line.split()) # Adding new symmetry line = inputfile.next() self.vibfreq.extend(map(self.float,line[15:].split())) # Adding new frequencies [inputfile.next() for i in [0,1]] # Skip two lines line = inputfile.next() - self.ir.extend(map(self.float,line[15:].split())) # Adding IR intensities + 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"): - self.raman = [] + self.vibramans = [] self.logger.info("Creating attribute raman[]") line = inputfile.next() - self.raman.extend(map(self.float,line[15:].split())) # Adding Raman intensities + self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities line = inputfile.next() while len(line[:15].split())>0: line = inputfile.next() @@ -482,7 +460,7 @@ for line in inputfile: if line.find(" Cartesian coordinates:")==0: coords = [] - for i in range(self.NAtoms): + for i in range(self.natom): line = inputfile.next() parts = line.strip().split() # Conversion from a.u. to Angstrom This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
