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[cclib-svn] SF.net SVN: cclib: [40] trunk/src/cclib/parser
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From: <ate...@us...> - 2006-03-22 22:57:51
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Revision: 40 Author: atenderholt Date: 2006-03-22 14:57:48 -0800 (Wed, 22 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=40&view=rev Log Message: ----------- Started work on ADF parser Modified Paths: -------------- trunk/src/cclib/parser/logfileparser.py Added Paths: ----------- trunk/src/cclib/parser/adfparser.py Added: trunk/src/cclib/parser/adfparser.py =================================================================== --- trunk/src/cclib/parser/adfparser.py (rev 0) +++ trunk/src/cclib/parser/adfparser.py 2006-03-22 22:57:48 UTC (rev 40) @@ -0,0 +1,543 @@ +""" +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 ADF(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(ADF, self).__init__(logname="ADF",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "ADF log file %s" % (self.filename) + + def __repr__(self): + """Return a representation of the object.""" + return 'ADF("%s")' % (self.filename) + + 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 + + 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.find("INPUT FILE")>=0: +#check to make sure we aren't parsing Create jobs + line2=inputfile.next() + while line: + if line.find("Create")<0: + break + + if self.progress and random.random()<cupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Unsupported Information") + oldstep=step + + + if line[1:6]=="ATOMS": +# Find the number of atoms and their atomic numbers + if self.progress and random.random()<cupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Attributes") + oldstep=step + + self.logger.info("Creating attribute atomnos[]") + self.atomnos=[] + + underline=inputfile.next() #clear pointless lines + label1=inputfile.next() # + label2=inputfile.next() # + line=inputfile.next() + while len(line)>1: #ensure that we are reading no blank lines + info=line.split() + self.atomnos.append(self.table.number[info[1]]) + line=inputfile.next() + + 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 self.progress and random.random()<fupdate: +# step=inputfile.tell() +# if step!=oldstep: +# self.progress.update(step,"QM Convergence") +# oldstep=step +# +# 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: +# 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) +# if self.progress: +# step=inputfile.tell() +# if step!=oldstep: +# self.progress.update(step,"AM1 Convergence") +# oldstep=step +# +# 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: +# 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(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(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 +# nindep = int(line.split('=')[1].split()[0]) +# if hasattr(self,"nindep"): +# assert nindep==self.nindep +# else: +# 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 +# # (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) +# +# 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].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,nindep,nbasis)) +# else: +# beta = False +# self.logger.info("Creating attributes aonames[], mocoeffs[][]") +# self.aonames = [] +# self.mocoeffs = Numeric.zeros((1,nindep,nbasis),"float") +# +# base = 0 +# for base in range(0,nindep,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(self.scftargets,"f") + + + +# 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,parser + doctest.testmod(parser,verbose=False) Property changes on: trunk/src/cclib/parser/adfparser.py ___________________________________________________________________ Name: svn:executable + * Modified: trunk/src/cclib/parser/logfileparser.py =================================================================== --- trunk/src/cclib/parser/logfileparser.py 2006-03-22 01:42:16 UTC (rev 39) +++ trunk/src/cclib/parser/logfileparser.py 2006-03-22 22:57:48 UTC (rev 40) @@ -94,6 +94,7 @@ self.progress = progress self.loglevel = loglevel self.logname = logname + self.table = PeriodicTable() # Set up the logger self.logger = logging.getLogger('%s %s' % (self.logname,self.filename)) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
