Re: [cclib-users] read the log file after HESSIAN calculation by GAMESS

[Karol M. L. <kar...@gm...>]

Hi Chengju,

Thanks for the file and sorry for taking so long. Your file is parsed
correctly as of r951. Enjoy!

It seems GAMESS-US added some extra output to the normal coord. analysis,
including symmetry details which actually caused the problem. Note that
I just added a fix for the parser to not die on this output, but cclib
does not parser the symmetries.

Thanks for your feedback,
Karol

On Dec 17 2011, Chengju Wang wrote:
> Sure, thanks for the prompt response.
> 
> Attached please find the log file I've run into. Since this is a test case
> of water, you are free to do ANYTHING with it.
> 
> 
> Best regards and happy holidays!
> 
> Chengju
> 
> On Sat, Dec 17, 2011 at 2:51 PM, Karol M. Langner
> <kar...@gm...>wrote:
> 
> > Hi Chengju,
> >
> > Could you make the log file available?
> >
> > We need it to test the fix, and we need your consent to redistribute
> > it with our regression suite.
> >
> > If you provide us with the file, there is a good chance the
> > problem will be fixed.
> >
> > Best,
> > Karol
> >
> > On Dec 16 2011, Chengju Wang wrote:
> > > *Hi, everyone.*
> > > *
> > > *
> > > *I'm new to cclib. I just found a 'problem' with cclib. *
> > > *
> > > *
> > > *After run this n_water.inp*
> > >
> > > *!   File created by MacMolPlt 7.4.2*
> > > * $CONTRL SCFTYP=RHF RUNTYP=HESSIAN MAXIT=60 MULT=1 $END*
> > > * $SYSTEM TIMLIM=525600 MWORDS=9000 $END*
> > > * $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END*
> > > * $SCF DIRSCF=.TRUE. $END*
> > > * $STATPT OPTTOL=0.0001 NSTEP=2000 HSSEND=.t. PROJCT=.FALSE. $END*
> > > * $FORCE METHOD=ANALYTIC VIBANL=.TRUE. $END*
> > > * $DATA*
> > > *Test run of H2O*
> > > *CNV 2*
> > > *
> > > *
> > > *O     8.0     0.00000     0.00000     0.00000*
> > > *H     1.0    -0.75800     0.00000     0.54500*
> > > * $END*
> > >
> > > *I tried to open the log file using GaussSum, I got this message"cclib
> > has
> > > problems parsing n_water.log. If you .....".*
> > > *
> > > *
> > > *Then I go to Python to call cclib directly, I got this*
> > > *
> > > *
> > > *>>> from cclib.parser import ccopen*
> > > *>>> p=ccopen("n_water.log")*
> > > *>>> date=p.parse()*
> > > *[GAMESS n_water.log INFO] Creating attribute atomcoords[]*
> > > *[GAMESS n_water.log INFO] Creating attribute atomnos[]*
> > > *[GAMESS n_water.log INFO] Creating attribute gbasis[]*
> > > *[GAMESS n_water.log INFO] Creating attribute nbasis: 19*
> > > *[GAMESS n_water.log INFO] Creating attribute charge: 0*
> > > *[GAMESS n_water.log INFO] Creating attribute mult: 1*
> > > *[GAMESS n_water.log INFO] Creating attribute homos[]*
> > > *[GAMESS n_water.log INFO] Creating attribute natom: 3*
> > > *[GAMESS n_water.log INFO] Creating attribute scftargets[]*
> > > *[GAMESS n_water.log INFO] Creating attribute scfvalues[]*
> > > *[GAMESS n_water.log INFO] Creating attribute scfenergies[]*
> > > *[GAMESS n_water.log INFO] Creating attribute moenergies[]*
> > > *[GAMESS n_water.log INFO] Creating attribute mosyms[]*
> > > *[GAMESS n_water.log INFO] Creating attribute nmo: 19*
> > > *[GAMESS n_water.log INFO] Creating attribute mocoeffs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute atombasis[]*
> > > *[GAMESS n_water.log INFO] Creating attribute aonames[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibfreqs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibirs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibdisps[]*
> > > *[GAMESS n_water.log WARNING] This is not a stationary point on the
> > > molecularPES.*
> > > * The vibrational analysis is not valid.*
> > > *Traceback (most recent call last):*
> > > *  File "<stdin>", line 1, in ?*
> > > *  File "/usr/lib/python2.4/site-packages/cclib/parser/logfileparser.py",
> > > line 22*
> > > *1, in parse*
> > > *    self.extract(inputfile, line)*
> > > *  File "/usr/lib/python2.4/site-packages/cclib/parser/gamessparser.py",
> > > line 528*
> > > *, in extract*
> > > *    newfreq.append(float(x))*
> > > *ValueError: invalid literal for float(): MASSES*
> > >
> > > *Thank you for your suggestion to read my log file w/ cclib.*
> > > *
> > > *
> > > *Best and happy holidays!*
> > > *
> > > *
> > > *Frank*
> >
> > >
> > ------------------------------------------------------------------------------
> > > Learn Windows Azure Live!  Tuesday, Dec 13, 2011
> > > Microsoft is holding a special Learn Windows Azure training event for
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> > it
> > > provides. You can attend the event by watching it streamed LIVE online.
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> >
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> >
> >
> > --
> > written by Karol M. Langner
> > Sat Dec 17 20:48:58 CET 2011
> >



-- 
written by Karol Langner
Thu Jan 19 15:50:44 CET 2012