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[cclib-svn] SF.net SVN: cclib: [124] trunk/test
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From: <bao...@us...> - 2006-05-18 08:39:10
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Revision: 124 Author: baoilleach Date: 2006-05-18 01:38:50 -0700 (Thu, 18 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=124&view=rev Log Message: ----------- Renamed G03 object to Gaussian, and changed name of parser from gaussian03 to gaussian. Modified Paths: -------------- trunk/src/cclib/parser/__init__.py trunk/src/cclib/parser/jaguarparser.py trunk/src/cclib/parser/logfileparser.py trunk/test/parseGaussian.py trunk/test/testGeoOpt.py trunk/test/testSP.py trunk/test/testSPun.py trunk/test/testall.py Added Paths: ----------- trunk/src/cclib/parser/gaussianparser.py Removed Paths: ------------- trunk/src/cclib/parser/g03parser.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/__init__.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,4 +1,4 @@ -from g03parser import G03 +from gaussianparser import Gaussian from gamessparser import GAMESS from adfparser import ADF from jaguarparser import Jaguar Deleted: trunk/src/cclib/parser/g03parser.py =================================================================== --- trunk/src/cclib/parser/g03parser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/g03parser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,581 +0,0 @@ -""" -cclib is a parser for computational chemistry log files. - -See http://cclib.sf.net for more information. - -Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt - - This program is free software; you can redistribute and/or modify it - under the terms of the GNU General Public License as published by the - Free Software Foundation; either version 2, or (at your option) any later - version. - - This program is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY, without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. - -Contributions (monetary as well as code :-) are encouraged. -""" -import re,time -import Numeric -import random # For sometimes running the progress updater -from logfileparser import Logfile,convertor - -class G03(Logfile): - """A Gaussian 98/03 log file""" - SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] - def __init__(self,*args): - - # Call the __init__ method of the superclass - super(G03, self).__init__(logname="G03",*args) - - def __str__(self): - """Return a string representation of the object.""" - return "Gaussian 03 log file %s" % (self.filename) - - def __repr__(self): - """Return a representation of the object.""" - return 'G03("%s")' % (self.filename) - - def normalisesym(self,label): - """Use standard symmetry labels instead of Gaussian labels. - - To normalise: - (1) replace any G or U by their lowercase equivalent - - >>> sym = G03("dummyfile").normalisesym - >>> labels = ['A1','AG','A1G'] - >>> map(sym,labels) - ['A1', 'Ag', 'A1g'] - """ - ans = label.replace("U","u").replace("G","g") - return ans - - def parse(self,fupdate=0.05,cupdate=0.002): - """Extract information from the logfile.""" - inputfile = open(self.filename,"r") - - if self.progress: - - inputfile.seek(0,2) #go to end of file - nstep=inputfile.tell() - inputfile.seek(0) - self.progress.initialize(nstep) - oldstep=0 - - optfinished = False # Flag that indicates whether it has reached the end of a geoopt - - for line in inputfile: - - if self.progress and random.random()<cupdate: - - step = inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Unsupported Information") - oldstep = step - - if line[1:8]=="NAtoms=": -# Find the number of atoms - if self.progress and random.random()<fupdate: - step = inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Attributes") - oldstep=step - - natom = int(line.split()[1]) - if hasattr(self,"natom"): - assert self.natom==natom - else: - # I wonder whether this code will ever be executed - self.natom = natom - self.logger.info("Creating attribute natom: %d" % self.natom) - - if line[1:23]=="Optimization completed": - optfinished = True - - if not optfinished and line[26:43]=="Input orientation": -# Extract the atomic numbers and coordinates of the atoms - if self.progress and random.random()<cupdate: - step = inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Attributes") - oldstep=step - - if not hasattr(self,"atomcoords"): - self.logger.info("Creating attribute atomcoords[]") - self.atomcoords = [] - - hyphens = inputfile.next() - colmNames = inputfile.next() - colmNames = inputfile.next() - hyphens = inputfile.next() - - atomnos = [] - atomcoords = [] - line = inputfile.next() - while line!=hyphens: - broken = line.split() - atomnos.append(int(broken[1])) - atomcoords.append(map(float,broken[3:6])) - line = inputfile.next() - self.atomcoords.append(atomcoords) - if not hasattr(self,"natom"): - self.atomnos = Numeric.array(atomnos,'i') - self.logger.info("Creating attribute atomnos[]") - self.natom = len(self.atomnos) - self.logger.info("Creating attribute natom: %d" % self.natom) - - if line[1:44]=='Requested convergence on RMS density matrix': -# Find the targets for SCF convergence (QM calcs) - if not hasattr(self,"scftargets"): - self.logger.info("Creating attribute scftargets[]") - self.scftargets = Numeric.array([0.0,0.0,0.0],'f') - self.scftargets[G03.SCFRMS] = self.float(line.split('=')[1].split()[0]) - if line[1:44]=='Requested convergence on MAX density matrix': - self.scftargets[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) - if line[1:44]=='Requested convergence on energy': - 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,"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 self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"QM Convergence") - oldstep=step - - if line.find(' E=')==0: - self.logger.debug(line) - if line.find(" RMSDP")==0: - parts = line.split() - newlist[G03.SCFRMS].append(self.float(parts[0].split('=')[1])) - newlist[G03.SCFMAX].append(self.float(parts[1].split('=')[1])) - energy = 1.0 - if len(parts)>4: - energy = parts[2].split('=')[1] - if energy=="": - energy = self.float(parts[3]) - else: - energy = self.float(energy) - # I moved the following line back a TAB to see the effect - # (it was originally part of the above "if len(parts)") - newlist[G03.SCFENERGY].append(energy) - try: - line = inputfile.next() - except StopIteration: # May be interupted by EOF - break - self.scfvalues.append(newlist) - - if line[1:4]=='It=': -# Extract SCF convergence information (AM1 calcs) - - self.logger.info("Creating attributes scftargets, scfvalues") - self.scftargets = Numeric.array([1E-7],"f") # This is the target value for the rms - self.scfvalues = [[]] - line = inputfile.next() - while line.find(" Energy")==-1: - - if self.progress: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"AM1 Convergence") - oldstep=step - - parts = line.strip().split() - self.scfvalues[0].append(self.float(parts[-1][:-1])) - line = inputfile.next() - - if line[1:9]=='SCF Done': -# Note: this needs to follow the section where 'SCF Done' is used to terminate -# a loop when extracting SCF convergence information - if not hasattr(self,"scfenergies"): - self.logger.info("Creating attribute scfenergies[]") - self.scfenergies = [] - self.scfenergies.append(self.float(line.split()[4])) - - if line[49:59]=='Converged?': -# Extract Geometry convergence information - if not hasattr(self,"geotargets"): - self.logger.info("Creating attributes geotargets[],geovalues[[]]") - self.geovalues = [] - self.geotargets = Numeric.array( [0.0,0.0,0.0,0.0],"f") - newlist = [0]*4 - for i in range(4): - line = inputfile.next() - self.logger.debug(line) - parts = line.split() - try: - value = self.float(parts[2]) - except ValueError: - self.logger.error("Problem parsing the value for geometry optimisation: %s is not a number." % parts[2]) - else: - newlist[i] = value - self.geotargets[i] = self.float(parts[3]) - self.geovalues.append(newlist) - - if line[1:19]=='Orbital symmetries' and not hasattr(self,"mosyms"): -# Extracting orbital symmetries - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"MO Symmetries") - oldstep=step - - self.logger.info("Creating attribute mosyms[[]]") - self.mosyms = [[]] - line = inputfile.next() - unres = False - if line.find("Alpha Orbitals")==1: - unres = True - line = inputfile.next() - i = 0 - while len(line)>18 and line[17]=='(': - if line.find('Virtual')>=0: - self.homos = Numeric.array([i-1],"i") # 'HOMO' indexes the HOMO in the arrays - self.logger.info("Creating attribute homos[]") - parts = line[17:].split() - for x in parts: - self.mosyms[0].append(self.normalisesym(x.strip('()'))) - i+= 1 - line = inputfile.next() - if unres: - line = inputfile.next() - # Repeat with beta orbital information - i = 0 - self.mosyms.append([]) - while len(line)>18 and line[17]=='(': - if line.find('Virtual')>=0: - self.homos.resize([2]) # Extend the array to two elements - self.homos[1] = i-1 # 'HOMO' indexes the HOMO in the arrays - parts = line[17:].split() - for x in parts: - self.mosyms[1].append(self.normalisesym(x.strip('()'))) - i+= 1 - line = inputfile.next() - - if line[1:6]=="Alpha" and line.find("eigenvalues")>=0: -# Extract the alpha electron eigenvalues - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Eigenvalues") - oldstep=step - - 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.moenergies[0])-1 - if hasattr(self,"homos"): - assert HOMO==self.homos[0] - else: - self.logger.info("Creating attribute homos[]") - self.homos = Numeric.array([HOMO],"i") - part = line[28:] - i = 0 - while i*10+4<len(part): - x = part[i*10:(i+1)*10] - self.moenergies[0].append(convertor(self.float(x),"hartree","eV")) - i += 1 - line = inputfile.next() - if line.find('Beta')==2: - 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.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? - assert HOMO==self.homos[1] - else: - self.homos.resize([2]) - self.homos[1] = HOMO - part = line[28:] - i = 0 - while i*10+4<len(part): - x = part[i*10:(i+1)*10] - self.moenergies[1].append(convertor(self.float(x),"hartree","eV")) - i += 1 - line = inputfile.next() - self.moenergies = Numeric.array(self.moenergies,"f") - - if line[1:14]=="Harmonic freq": -# Start of the IR/Raman frequency section - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Frequency Information") - oldstep=step - - self.vibsyms = [] - self.vibirs = [] - self.vibfreqs = [] - 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 - line = inputfile.next() - line = inputfile.next() # The line with symmetries - while len(line[:15].split())==0: - self.logger.debug(line) - self.vibsyms.extend(line.split()) # Adding new symmetry - line = inputfile.next() - 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,"vibramans"): - self.vibramans = [] - self.logger.info("Creating attribute vibramans[]") - line = inputfile.next() - self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities - line = inputfile.next() - while len(line[:15].split())>0: - line = inputfile.next() - line = inputfile.next() # Should be the line with symmetries - self.vibfreqs = Numeric.array(self.vibfreqs,"f") - self.vibirs = Numeric.array(self.vibirs,"f") - if hasattr(self,"vibramans"): self.vibramans = Numeric.array(self.vibramans,"f") - - if line[1:14]=="Excited State": -# Extract the electronic transitions - if not hasattr(self,"etenergy"): - 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.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() - - p = re.compile("(\d+)") - CIScontrib = [] - while line.find(" ->")>=0: # This is a contribution to the transition - parts = line.split("->") - self.logger.debug(parts) - # Has to deal with lines like: - # 32 -> 38 0.04990 - # 35A -> 45A 0.01921 - frommoindex = 0 # For restricted or alpha unrestricted - fromMO = parts[0].strip() - if fromMO[-1]=="B": - frommoindex = 1 # For beta unrestricted - fromMO = int(p.match(fromMO).group()) # extract the number - - t = parts[1].split() - tomoindex = 0 - toMO = t[0] - if toMO[-1]=="B": - tomoindex = 1 - toMO = int(p.match(toMO).group()) - - percent = self.float(t[1]) - sqr = percent**2*2 # The fractional contribution of this CI - if percent<0: - sqr = -sqr - CIScontrib.append([(fromMO,frommoindex),(toMO,tomoindex),sqr]) - line = inputfile.next() - self.etsecs.append(CIScontrib) - self.etenergies = Numeric.array(self.etenergies,"f") - self.etoscs = Numeric.array(self.etoscs,"f") - - if line[1:52]=="<0|r|b> * <b|rxdel|0> (Au), Rotatory Strengths (R)": -# Extract circular dichroism data - self.etrotats = [] - self.logger.info("Creating attribute etrotats[]") - inputfile.next() - inputfile.next() - line = inputfile.next() - parts = line.strip().split() - while len(parts)==5: - try: - R = self.float(parts[-1]) - except ValueError: - # nan or -nan if there is no first excited state - # (for unrestricted calculations) - pass - else: - self.etrotats.append(R) - line = inputfile.next() - temp = line.strip().split() - parts = line.strip().split() - self.etrotats = Numeric.array(self.etrotats,"f") - - if line[1:7]=="NBasis" or line[4:10]=="NBasis": -# Extract the number of basis sets - nbasis = int(line.split('=')[1].split()[0]) - # Has to deal with lines like: - # 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 - else: - 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 - nmo = int(line.split('=')[1].split()[0]) - if hasattr(self,"nmo"): - assert nmo==self.nmo - else: - self.nmo = nmo - self.logger.info("Creating attribute nmo: %d" % self.nmo) - - if line[7:22]=="basis functions,": -# For AM1 calculations, set nbasis by a second method -# (nmo 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) - - if line[1:4]=="***" and (line[5:12]=="Overlap" - or line[8:15]=="Overlap"): -# Extract the molecular orbital overlap matrix - # Has to deal with lines such as: - # *** Overlap *** - # ****** Overlap ****** - self.logger.info("Creating attribute aooverlaps[x,y]") - 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: - - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Overlap") - oldstep=step - - 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+1].replace("D","E")) - self.aooverlaps[base+j,i+base] = k - self.aooverlaps[i+base,base+j] = k - base += 5 - colmNames = inputfile.next() - self.aooverlaps = Numeric.array(self.aooverlaps,"f") - - - if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients": - if line[5:40]=="Beta Molecular Orbital Coefficients": - beta = True - # Need to add an extra dimension to self.mocoeffs - self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nmo,nbasis)) - else: - beta = False - self.logger.info("Creating attributes aonames[], mocoeffs[][]") - self.aonames = [] - self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float") - - base = 0 - for base in range(0,nmo,5): - - if self.progress: - step=inputfile.tell() - if step!=oldstep and random.random() < fupdate: - self.progress.update(step,"Coefficients") - oldstep=step - - colmNames = inputfile.next() - symmetries = inputfile.next() - eigenvalues = inputfile.next() - 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 - parts = line[:11].split() - if len(parts)>1: # New atom - atomname = "%s%s" % (parts[2],parts[1]) - orbital = line[11:20].strip() - 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.mocoeffs[1,base:base+len(part)/10,i] = temp - else: - self.mocoeffs[0,base:base+len(part)/10,i] = temp - - inputfile.close() - - if self.progress: - self.progress.update(nstep,"Done") - - if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f") - if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f") - if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues] - if hasattr(self,"atomcoords"): self.atomcoords = Numeric.array(self.atomcoords,"f") - self.parsed = True - - - -# Note to self: Needs to be added to the main parser - def extractTrajectory(self): - """Extract trajectory information from a Gaussian logfile.""" - inputfile = open(self.filename,"r") - self.traj = [] - self.trajSummary = [] - for line in inputfile: - if line.find(" Cartesian coordinates:")==0: - coords = [] - for i in range(self.natom): - line = inputfile.next() - parts = line.strip().split() - # Conversion from a.u. to Angstrom - coords.append([ self.float(x)*0.5292 for x in [parts[3],parts[5],parts[7]] ]) - self.traj.append(coords) - if line==" Trajectory summary\n": - # self.trajSummaryHeader = inputfile.next().strip().split() - header = inputfile.next() - line = inputfile.next() - while line.find("Max Error")==-1: - parts = line.strip().split(" ") - self.trajSummary.append(parts) - line = inputfile.next() - inputfile.close() - assert len(self.traj)==len(self.trajSummary) - -if __name__=="__main__": - import doctest,g03parser - doctest.testmod(g03parser,verbose=False) Copied: trunk/src/cclib/parser/gaussianparser.py (from rev 123, trunk/src/cclib/parser/g03parser.py) =================================================================== --- trunk/src/cclib/parser/gaussianparser.py (rev 0) +++ trunk/src/cclib/parser/gaussianparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -0,0 +1,581 @@ +""" +cclib is a parser for computational chemistry log files. + +See http://cclib.sf.net for more information. + +Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt + + This program is free software; you can redistribute and/or modify it + under the terms of the GNU General Public License as published by the + Free Software Foundation; either version 2, or (at your option) any later + version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY, without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + +Contributions (monetary as well as code :-) are encouraged. +""" +import re,time +import Numeric +import random # For sometimes running the progress updater +from logfileparser import Logfile,convertor + +class Gaussian(Logfile): + """A Gaussian 98/03 log file""" + SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] + def __init__(self,*args): + + # Call the __init__ method of the superclass + super(Gaussian, self).__init__(logname="Gaussian",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "Gaussian log file %s" % (self.filename) + + def __repr__(self): + """Return a representation of the object.""" + return 'Gaussian("%s")' % (self.filename) + + def normalisesym(self,label): + """Use standard symmetry labels instead of Gaussian labels. + + To normalise: + (1) replace any G or U by their lowercase equivalent + + >>> sym = Gaussian("dummyfile").normalisesym + >>> labels = ['A1','AG','A1G'] + >>> map(sym,labels) + ['A1', 'Ag', 'A1g'] + """ + ans = label.replace("U","u").replace("G","g") + return ans + + def parse(self,fupdate=0.05,cupdate=0.002): + """Extract information from the logfile.""" + inputfile = open(self.filename,"r") + + if self.progress: + + inputfile.seek(0,2) #go to end of file + nstep=inputfile.tell() + inputfile.seek(0) + self.progress.initialize(nstep) + oldstep=0 + + optfinished = False # Flag that indicates whether it has reached the end of a geoopt + + for line in inputfile: + + if self.progress and random.random()<cupdate: + + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Unsupported Information") + oldstep = step + + if line[1:8]=="NAtoms=": +# Find the number of atoms + if self.progress and random.random()<fupdate: + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Attributes") + oldstep=step + + natom = int(line.split()[1]) + if hasattr(self,"natom"): + assert self.natom==natom + else: + # I wonder whether this code will ever be executed + self.natom = natom + self.logger.info("Creating attribute natom: %d" % self.natom) + + if line[1:23]=="Optimization completed": + optfinished = True + + if not optfinished and line[26:43]=="Input orientation": +# Extract the atomic numbers and coordinates of the atoms + if self.progress and random.random()<cupdate: + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Attributes") + oldstep=step + + if not hasattr(self,"atomcoords"): + self.logger.info("Creating attribute atomcoords[]") + self.atomcoords = [] + + hyphens = inputfile.next() + colmNames = inputfile.next() + colmNames = inputfile.next() + hyphens = inputfile.next() + + atomnos = [] + atomcoords = [] + line = inputfile.next() + while line!=hyphens: + broken = line.split() + atomnos.append(int(broken[1])) + atomcoords.append(map(float,broken[3:6])) + line = inputfile.next() + self.atomcoords.append(atomcoords) + if not hasattr(self,"natom"): + self.atomnos = Numeric.array(atomnos,'i') + self.logger.info("Creating attribute atomnos[]") + self.natom = len(self.atomnos) + self.logger.info("Creating attribute natom: %d" % self.natom) + + if line[1:44]=='Requested convergence on RMS density matrix': +# Find the targets for SCF convergence (QM calcs) + if not hasattr(self,"scftargets"): + self.logger.info("Creating attribute scftargets[]") + self.scftargets = Numeric.array([0.0,0.0,0.0],'f') + self.scftargets[Gaussian.SCFRMS] = self.float(line.split('=')[1].split()[0]) + if line[1:44]=='Requested convergence on MAX density matrix': + self.scftargets[Gaussian.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) + if line[1:44]=='Requested convergence on energy': + self.scftargets[Gaussian.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) + + if line[1:10]=='Cycle 1': +# Extract SCF convergence information (QM calcs) + + 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 self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"QM Convergence") + oldstep=step + + if line.find(' E=')==0: + self.logger.debug(line) + if line.find(" RMSDP")==0: + parts = line.split() + newlist[Gaussian.SCFRMS].append(self.float(parts[0].split('=')[1])) + newlist[Gaussian.SCFMAX].append(self.float(parts[1].split('=')[1])) + energy = 1.0 + if len(parts)>4: + energy = parts[2].split('=')[1] + if energy=="": + energy = self.float(parts[3]) + else: + energy = self.float(energy) + # I moved the following line back a TAB to see the effect + # (it was originally part of the above "if len(parts)") + newlist[Gaussian.SCFENERGY].append(energy) + try: + line = inputfile.next() + except StopIteration: # May be interupted by EOF + break + self.scfvalues.append(newlist) + + if line[1:4]=='It=': +# Extract SCF convergence information (AM1 calcs) + + self.logger.info("Creating attributes scftargets, scfvalues") + self.scftargets = Numeric.array([1E-7],"f") # This is the target value for the rms + self.scfvalues = [[]] + line = inputfile.next() + while line.find(" Energy")==-1: + + if self.progress: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"AM1 Convergence") + oldstep=step + + parts = line.strip().split() + self.scfvalues[0].append(self.float(parts[-1][:-1])) + line = inputfile.next() + + if line[1:9]=='SCF Done': +# Note: this needs to follow the section where 'SCF Done' is used to terminate +# a loop when extracting SCF convergence information + if not hasattr(self,"scfenergies"): + self.logger.info("Creating attribute scfenergies[]") + self.scfenergies = [] + self.scfenergies.append(self.float(line.split()[4])) + + if line[49:59]=='Converged?': +# Extract Geometry convergence information + if not hasattr(self,"geotargets"): + self.logger.info("Creating attributes geotargets[],geovalues[[]]") + self.geovalues = [] + self.geotargets = Numeric.array( [0.0,0.0,0.0,0.0],"f") + newlist = [0]*4 + for i in range(4): + line = inputfile.next() + self.logger.debug(line) + parts = line.split() + try: + value = self.float(parts[2]) + except ValueError: + self.logger.error("Problem parsing the value for geometry optimisation: %s is not a number." % parts[2]) + else: + newlist[i] = value + self.geotargets[i] = self.float(parts[3]) + self.geovalues.append(newlist) + + if line[1:19]=='Orbital symmetries' and not hasattr(self,"mosyms"): +# Extracting orbital symmetries + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"MO Symmetries") + oldstep=step + + self.logger.info("Creating attribute mosyms[[]]") + self.mosyms = [[]] + line = inputfile.next() + unres = False + if line.find("Alpha Orbitals")==1: + unres = True + line = inputfile.next() + i = 0 + while len(line)>18 and line[17]=='(': + if line.find('Virtual')>=0: + self.homos = Numeric.array([i-1],"i") # 'HOMO' indexes the HOMO in the arrays + self.logger.info("Creating attribute homos[]") + parts = line[17:].split() + for x in parts: + self.mosyms[0].append(self.normalisesym(x.strip('()'))) + i+= 1 + line = inputfile.next() + if unres: + line = inputfile.next() + # Repeat with beta orbital information + i = 0 + self.mosyms.append([]) + while len(line)>18 and line[17]=='(': + if line.find('Virtual')>=0: + self.homos.resize([2]) # Extend the array to two elements + self.homos[1] = i-1 # 'HOMO' indexes the HOMO in the arrays + parts = line[17:].split() + for x in parts: + self.mosyms[1].append(self.normalisesym(x.strip('()'))) + i+= 1 + line = inputfile.next() + + if line[1:6]=="Alpha" and line.find("eigenvalues")>=0: +# Extract the alpha electron eigenvalues + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Eigenvalues") + oldstep=step + + 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.moenergies[0])-1 + if hasattr(self,"homos"): + assert HOMO==self.homos[0] + else: + self.logger.info("Creating attribute homos[]") + self.homos = Numeric.array([HOMO],"i") + part = line[28:] + i = 0 + while i*10+4<len(part): + x = part[i*10:(i+1)*10] + self.moenergies[0].append(convertor(self.float(x),"hartree","eV")) + i += 1 + line = inputfile.next() + if line.find('Beta')==2: + 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.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? + assert HOMO==self.homos[1] + else: + self.homos.resize([2]) + self.homos[1] = HOMO + part = line[28:] + i = 0 + while i*10+4<len(part): + x = part[i*10:(i+1)*10] + self.moenergies[1].append(convertor(self.float(x),"hartree","eV")) + i += 1 + line = inputfile.next() + self.moenergies = Numeric.array(self.moenergies,"f") + + if line[1:14]=="Harmonic freq": +# Start of the IR/Raman frequency section + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Frequency Information") + oldstep=step + + self.vibsyms = [] + self.vibirs = [] + self.vibfreqs = [] + 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 + line = inputfile.next() + line = inputfile.next() # The line with symmetries + while len(line[:15].split())==0: + self.logger.debug(line) + self.vibsyms.extend(line.split()) # Adding new symmetry + line = inputfile.next() + 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,"vibramans"): + self.vibramans = [] + self.logger.info("Creating attribute vibramans[]") + line = inputfile.next() + self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities + line = inputfile.next() + while len(line[:15].split())>0: + line = inputfile.next() + line = inputfile.next() # Should be the line with symmetries + self.vibfreqs = Numeric.array(self.vibfreqs,"f") + self.vibirs = Numeric.array(self.vibirs,"f") + if hasattr(self,"vibramans"): self.vibramans = Numeric.array(self.vibramans,"f") + + if line[1:14]=="Excited State": +# Extract the electronic transitions + if not hasattr(self,"etenergy"): + 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.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() + + p = re.compile("(\d+)") + CIScontrib = [] + while line.find(" ->")>=0: # This is a contribution to the transition + parts = line.split("->") + self.logger.debug(parts) + # Has to deal with lines like: + # 32 -> 38 0.04990 + # 35A -> 45A 0.01921 + frommoindex = 0 # For restricted or alpha unrestricted + fromMO = parts[0].strip() + if fromMO[-1]=="B": + frommoindex = 1 # For beta unrestricted + fromMO = int(p.match(fromMO).group()) # extract the number + + t = parts[1].split() + tomoindex = 0 + toMO = t[0] + if toMO[-1]=="B": + tomoindex = 1 + toMO = int(p.match(toMO).group()) + + percent = self.float(t[1]) + sqr = percent**2*2 # The fractional contribution of this CI + if percent<0: + sqr = -sqr + CIScontrib.append([(fromMO,frommoindex),(toMO,tomoindex),sqr]) + line = inputfile.next() + self.etsecs.append(CIScontrib) + self.etenergies = Numeric.array(self.etenergies,"f") + self.etoscs = Numeric.array(self.etoscs,"f") + + if line[1:52]=="<0|r|b> * <b|rxdel|0> (Au), Rotatory Strengths (R)": +# Extract circular dichroism data + self.etrotats = [] + self.logger.info("Creating attribute etrotats[]") + inputfile.next() + inputfile.next() + line = inputfile.next() + parts = line.strip().split() + while len(parts)==5: + try: + R = self.float(parts[-1]) + except ValueError: + # nan or -nan if there is no first excited state + # (for unrestricted calculations) + pass + else: + self.etrotats.append(R) + line = inputfile.next() + temp = line.strip().split() + parts = line.strip().split() + self.etrotats = Numeric.array(self.etrotats,"f") + + if line[1:7]=="NBasis" or line[4:10]=="NBasis": +# Extract the number of basis sets + nbasis = int(line.split('=')[1].split()[0]) + # Has to deal with lines like: + # 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 + else: + 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 + nmo = int(line.split('=')[1].split()[0]) + if hasattr(self,"nmo"): + assert nmo==self.nmo + else: + self.nmo = nmo + self.logger.info("Creating attribute nmo: %d" % self.nmo) + + if line[7:22]=="basis functions,": +# For AM1 calculations, set nbasis by a second method +# (nmo 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) + + if line[1:4]=="***" and (line[5:12]=="Overlap" + or line[8:15]=="Overlap"): +# Extract the molecular orbital overlap matrix + # Has to deal with lines such as: + # *** Overlap *** + # ****** Overlap ****** + self.logger.info("Creating attribute aooverlaps[x,y]") + 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: + + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Overlap") + oldstep=step + + 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+1].replace("D","E")) + self.aooverlaps[base+j,i+base] = k + self.aooverlaps[i+base,base+j] = k + base += 5 + colmNames = inputfile.next() + self.aooverlaps = Numeric.array(self.aooverlaps,"f") + + + if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients": + if line[5:40]=="Beta Molecular Orbital Coefficients": + beta = True + # Need to add an extra dimension to self.mocoeffs + self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nmo,nbasis)) + else: + beta = False + self.logger.info("Creating attributes aonames[], mocoeffs[][]") + self.aonames = [] + self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float") + + base = 0 + for base in range(0,nmo,5): + + if self.progress: + step=inputfile.tell() + if step!=oldstep and random.random() < fupdate: + self.progress.update(step,"Coefficients") + oldstep=step + + colmNames = inputfile.next() + symmetries = inputfile.next() + eigenvalues = inputfile.next() + 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 + parts = line[:11].split() + if len(parts)>1: # New atom + atomname = "%s%s" % (parts[2],parts[1]) + orbital = line[11:20].strip() + 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.mocoeffs[1,base:base+len(part)/10,i] = temp + else: + self.mocoeffs[0,base:base+len(part)/10,i] = temp + + inputfile.close() + + if self.progress: + self.progress.update(nstep,"Done") + + if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f") + if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f") + if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues] + if hasattr(self,"atomcoords"): self.atomcoords = Numeric.array(self.atomcoords,"f") + self.parsed = True + + + +# Note to self: Needs to be added to the main parser + def extractTrajectory(self): + """Extract trajectory information from a Gaussian logfile.""" + inputfile = open(self.filename,"r") + self.traj = [] + self.trajSummary = [] + for line in inputfile: + if line.find(" Cartesian coordinates:")==0: + coords = [] + for i in range(self.natom): + line = inputfile.next() + parts = line.strip().split() + # Conversion from a.u. to Angstrom + coords.append([ self.float(x)*0.5292 for x in [parts[3],parts[5],parts[7]] ]) + self.traj.append(coords) + if line==" Trajectory summary\n": + # self.trajSummaryHeader = inputfile.next().strip().split() + header = inputfile.next() + line = inputfile.next() + while line.find("Max Error")==-1: + parts = line.strip().split(" ") + self.trajSummary.append(parts) + line = inputfile.next() + inputfile.close() + assert len(self.traj)==len(self.trajSummary) + +if __name__=="__main__": + import doctest,gaussianparser + doctest.testmod(gaussianparser,verbose=False) Modified: trunk/src/cclib/parser/jaguarparser.py =================================================================== --- trunk/src/cclib/parser/jaguarparser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/jaguarparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -169,5 +169,5 @@ self.parsed = True if __name__=="__main__": - import doctest,g03parser - doctest.testmod(g03parser,verbose=False) + import doctest,jaguarparser + doctest.testmod(jaguarparser,verbose=False) Modified: trunk/src/cclib/parser/logfileparser.py =================================================================== --- trunk/src/cclib/parser/logfileparser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/logfileparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -54,7 +54,7 @@ """Abstract class for logfile objects. Subclasses: - G03 + ADF, GAMESS, Gaussian, Jaguar Attributes: aonames -- "Ru_3p" (list) Modified: trunk/test/parseGaussian.py =================================================================== --- trunk/test/parseGaussian.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/parseGaussian.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os -from cclib.parser import G03 +from cclib.parser import Gaussian os.chdir(os.path.join("..","data","Gaussian")) @@ -7,7 +7,7 @@ for file in ["dvb_gopt.out","dvb_sp.out","dvb_ir.out","dvb_raman.out", "dvb_un_sp.out"]: - t = G03(file) + t = Gaussian(file) t.parse() Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/testGeoOpt.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os, unittest -from cclib.parser import GAMESS,G03,ADF,Jaguar +from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile @@ -43,7 +43,7 @@ class GaussianGeoOptTest(GenericGeoOptTest): def setUp(self): - self.data = getfile(G03,"basicGaussian03","dvb_gopt.out") + self.data = getfile(Gaussian,"basicGaussian03","dvb_gopt.out") class GamessUSGeoOptTest(GenericGeoOptTest): def setUp(self): Modified: trunk/test/testSP.py =================================================================== --- trunk/test/testSP.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/testSP.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os, unittest -from cclib.parser import GAMESS,G03,ADF,Jaguar +from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile @@ -15,7 +15,7 @@ class GaussianSPTest(GenericSPTest): def setUp(self): - self.data = getfile(G03,"basicGaussian03","dvb_sp.out") + self.data = getfile(Gaussian,"basicGaussian03","dvb_sp.out") class GamessUSSPTest(GenericSPTest): def setUp(self): Modified: trunk/test/testSPun.py ===================... 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