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[cclib-svn] SF.net SVN: cclib: [142] trunk/src/cclib/parser/adfparser.py
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From: <bao...@us...> - 2006-05-22 10:44:26
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Revision: 142 Author: baoilleach Date: 2006-05-22 03:43:56 -0700 (Mon, 22 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=142&view=rev Log Message: ----------- Atomcoords is correctly parsed, at least from geoopt files. Modified Paths: -------------- trunk/src/cclib/parser/adfparser.py Modified: trunk/src/cclib/parser/adfparser.py =================================================================== --- trunk/src/cclib/parser/adfparser.py 2006-05-22 10:43:22 UTC (rev 141) +++ trunk/src/cclib/parser/adfparser.py 2006-05-22 10:43:56 UTC (rev 142) @@ -82,6 +82,10 @@ self.progress.initialize(nstep) oldstep=0 + # Used to avoid extracting the final geometry twice in a GeoOpt + NOTFOUND, GETLAST, NOMORE = range(3) + finalgeometry= NOTFOUND + for line in inputfile: if self.progress and random.random()<cupdate: @@ -109,23 +113,28 @@ if line[1:6]=="ATOMS": # Find the number of atoms and their atomic numbers +# Also extract the starting coordinates (for a GeoOpt anyway) 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.logger.info("Creating attribute atomnos[], atomcoords[]") self.atomnos=[] + self.atomcoords = [] underline=inputfile.next() #clear pointless lines label1=inputfile.next() # label2=inputfile.next() # line=inputfile.next() + atomcoords = [] while len(line)>1: #ensure that we are reading no blank lines info=line.split() self.atomnos.append(self.table.number[info[1]]) + atomcoords.append(map(float,info[2:5])) line=inputfile.next() + self.atomcoords.append(atomcoords) self.natom=len(self.atomnos) self.logger.info("Creating attribute natom: %d" % self.natom) @@ -171,43 +180,29 @@ if hasattr(self,"scfvalues"): self.scfvalues.append(newlist) -# 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[51:65]=="Final Geometry": + finalgeometry = GETLAST + + if line[1:24]=="Coordinates (Cartesian)" and finalgeometry in [NOTFOUND, GETLAST]: + # Get the coordinates from each step of the GeoOpt + if not hasattr(self,"atomcoords"): + self.logger.info("Creating attribute atomcoords") + self.atomcoords = [] + equals = inputfile.next() + blank = inputfile.next() + title = inputfile.next() + title = inputfile.next() + hyphens = inputfile.next() + atomcoords = [] + line = inputfile.next() + while line!=hyphens: + atomcoords.append(map(float,line.split()[5:])) + line = inputfile.next() + self.atomcoords.append(atomcoords) + if finalgeometry==GETLAST: # Don't get any more coordinates + finalgeometry = NOMORE + if line[1:27]=='Geometry Convergence Tests': # Extract Geometry convergence information if not hasattr(self,"geotargets"): @@ -652,13 +647,16 @@ 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] - self.parsed = True if hasattr(self,"moenergies"): self.nmo = len(self.moenergies[0]) + 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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
