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[cclib-svn] SF.net SVN: cclib: [27] trunk/src/cclib/parser
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From: <bao...@us...> - 2006-03-18 21:43:55
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Revision: 27 Author: baoilleach Date: 2006-03-18 13:43:47 -0800 (Sat, 18 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=27&view=rev Log Message: ----------- Adding the GAMESS parser. Currently passes simple unit tests. Modified Paths: -------------- trunk/src/cclib/parser/__init__.py Added Paths: ----------- trunk/src/cclib/parser/gamessparser.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-03-18 21:42:45 UTC (rev 26) +++ trunk/src/cclib/parser/__init__.py 2006-03-18 21:43:47 UTC (rev 27) @@ -1 +1,2 @@ from g03parser import G03 +from gamessparser import GAMESS Added: trunk/src/cclib/parser/gamessparser.py =================================================================== --- trunk/src/cclib/parser/gamessparser.py (rev 0) +++ trunk/src/cclib/parser/gamessparser.py 2006-03-18 21:43:47 UTC (rev 27) @@ -0,0 +1,270 @@ +""" +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 GAMESS(Logfile): + """A GAMESS log file.""" + SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] + def __init__(self,*args): + + # Call the __init__ method of the superclass + super(GAMESS, self).__init__(logname="GAMESS",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "GAMESS log file %s" % (self.filename) + + def __repr__(self): + """Return a representation of the object.""" + return 'GAMESS("%s")' % (self.filename) + + def parse(self): + """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 + + + endofopt = False + + for line in inputfile: + + if self.progress and random.random()<0.05: + + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step) + oldstep = step + + if line.find("OPTTOL")>=0: + # Two possibilities: + # OPTTOL = 1.000E-04 RMIN = 1.500E-03 + # INPUT CARD> $STATPT OPTTOL=0.0001 NSTEP=100 $END + if not hasattr(self,"geotargets"): + self.logger.info("Creating attribute geotargets[]") + temp = line.split() + for i,x in enumerate(temp): + if x.find("OPTTOL")>=0: + if x=="OPTTOL": + opttol = float(temp[i+2]) + else: + 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 not hasattr(self,"scfenergies"): + self.logger.info("Creating attribute scfenergies[]") + self.scfenergies = [] +# Here is an example from Neil Berry: +# 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" + temp = line.split() + self.scfenergies.append(temp[temp.index("IS")+1]) + + if not endofopt and 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 line.find("ITER EX DEM")==1: +# This is the section with the SCF information + if not hasattr(self,"scfvalues"): + self.logger.info("Creating attribute scfvalues") + self.scfvalues = [] + line = inputfile.next() + den = [] + while line!='\n': +# The SCF information is terminated by a blank line + try: + temp = int(line[0:4]) + except ValueError: +# Occurs for: +# * * * INITIATING DIIS PROCEDURE * * * +# CONVERGED TO SWOFF, SO DFT CALCULATION IS NOW SWITCHED ON +# DFT CODE IS SWITCHING BACK TO THE FINER GRID + pass + else: + den.append(float(line.split()[5])) + line = inputfile.next() + self.scfvalues.append(den) + + if line.find("NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION")>=0: + # Start of the frequency section + self.logger.info("Creating attributes vibfreqs, vibirs") + self.vibfreqs = [] + self.vibirs = [] + + # Need to get past the list of atomic weights + hyphens = inputfile.next() + blank = inputfile.next() + line = inputfile.next() + blank = inputfile.next() + line = inputfile.next() + numAtom = 0 + while line!="\n": + 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() + 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() + self.vibirs.extend(map(float,irIntensity[2:])) + blank = inputfile.next() + # Skip XYZ data for each atom plus + # the Sayvetz stuff at the end + for j in range(numAtom*3+10): + line = inputfile.next() + blank = inputfile.next() + freqNo = inputfile.next() + self.vibfreqs = Numeric.array(self.vibfreqs,"f") + self.vibirs = Numeric.array(self.vibirs,"f") + + + if line.find("EIGENVECTORS")==10 or line.find("MOLECULAR OBRITALS")==10: + # The details returned come from the *final* report of evalues and + # the last list of symmetries in the log file + # This is fine for GeoOpt and SP, but may be weird for TD and Freq(?) + + # Take the last one of either in the file + if not hasattr(self,"moenergies"): + self.logger.info("Creating attributes moenergies, mosyms") + 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: + line = inputfile.next() # Eigenvector no + line = inputfile.next() + self.moenergies.extend(map(float,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: + if base==0: # Just do this the first time 'round + atomno=int(line.split()[2])-1 + # atomorb[atomno].append(int(line.split()[0])-1) + # What's the story with the previous line? + temp = line[15:] # Strip off the crud at the start + j = 0 + while j*11+4<len(temp): + self.mocoeffs[0,base+j,i] = float(temp[j*11:(j+1)*11]) + j+=1 + line = inputfile.next() + i+=1 + base+=5 + 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") + + if line.find("TOTAL NUMBER OF ATOMS")==1: + self.logger.info("Creating attribute natom") + self.natom = int(line.split()[-1]) + + if line.find("NUMBER OF CARTESIAN GAUSSIAN BASIS")==1 or line.find("TOTAL NUMBER OF BASIS FUNCTIONS")==1: + # The first is from Julien's Example and the second is from Alexander's + # I think it happens if you use a polar basis function instead of a cartesian one + self.logger.info("Creating attribute nbasis") + self.nbasis = int(line.split()[-1]) + + elif line.find("TOTAL NUMBER OF MOS IN VARIATION SPACE")==1: + # Note that this line is not always present, so by default + # NBsUse is set equal to NBasis (see below). + self.logger.info("Creating attribute nindep") + self.indep = int(line.split()[-1]) + + 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") + base = 0 + while base<self.nbasis: + blank = inputfile.next() + line = inputfile.next() # Basis fn number + blank = inputfile.next() + for i in range(self.nbasis-base): # Fewer lines each time + line = inputfile.next() + temp = line.split() + for j in range(4,len(temp)): + self.aooverlaps[base+j-4,i+base] = float(temp[j]) + self.aooverlaps[i+base,base+j-4] = float(temp[j]) + base+=5 + + inputfile.close() + + if not hasattr(self,"geotargets"): + self.logger.info("Creating attribute geotargets[] with default values") + opttol = 1e-4 + self.geotargets = Numeric.array([opttol,3./opttol]) + if not hasattr(self,"scftargets"): + self.logger.info("Creating attribute scftargets[] with default values") + self.scftargets = Numeric.array([1e-5]) + if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f") + if not hasattr(self,"nindep"): + self.logger.info("Creating attribute nindep with default value") + self.nindep = self.nbasis + + + +if __name__=="__main__": + import doctest,parser + doctest.testmod(parser,verbose=False) Property changes on: trunk/src/cclib/parser/gamessparser.py ___________________________________________________________________ Name: svn:executable + * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
