Re: [cclib-devel] parser-refactoring

[Adam T. <a-t...@st...>]

Minor problem with Rev. 509 and ADF files:

 >>> from cclib.parser import ccopen
 >>> from cclib.progress import TextProgress
 >>> progress = TextProgress()
 >>> import logging
 >>> parser = ccopen("dvb_sp.adfout", progress, logging.ERROR)
 >>> parser.parse()
[=========-]  97%    Unsupported informationTraceback (most recent  
call last):
   File "<stdin>", line 1, in ?
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/cclib/parser/logfileparser.py", line 223, in  
parse
     self.progress.update(nstep, "Done")
NameError: global name 'nstep' is not defined

I haven't checked if it affects other calculation files yet. Just  
noticed it when I was using PyMOlyze this morning on an ADF file... ;o)

Adam


On Feb 4, 2007, at 3:25 AM, Karol Langner wrote:

> On Sunday 04 of February 2007 00:24, Adam Tenderholt wrote:
>> Hi Karol,
>>
>> I found a couple of problems:
>>
>> 1) Gaussian object has no attribute optfinished (line 77 in _extract)
>> when I run PyMOlyze (and ccget) on trunk/data/Gaussian/Gaussian03/
>> Mo4OSibdt2-opt.log.bz2.
>
> That's strange, I don't get that error:
>
>>>> import cclib
>>>> cclib.parser.gaussianparser.__revision__
> '$Revision: 509 $'
>>>> g = cclib.parser.ccopen("Mo4OSibdt2-opt.log.bz2")
>>>> g.parse()
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute atomcoords[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute atomnos[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute natom: 62
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute gbasis[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute nbasis: 581
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute nmo: 581
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute scftargets[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute scfvalues[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute  
> scfenergies[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute mosyms[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute homos[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute moenergies[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute aonames[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute mocoeffs[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute geovalues[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute geotargets[]
> [Gaussian Mo4OSibdt2-opt.log.bz2 INFO] Creating attribute  
> coreelectrons[]
>
> Everything looks fine here. Are you sure you're using revision 509  
> of the
> Gaussian parser? The attribute optfinished is set to False at the  
> beginning.
> Using ccget with the file also works for me, and all the regression  
> tests
> finish fine.
>
>> 2) nstep isn't defined when I try to open trunk/data/Gaussian/
>> basicGaussian03/dvb_gopt.out with PyMOlyze. Presumably, this isn't
>> seen in ccget because it doesn't use a progress class. This appears
>> to be a problem with a lot of the other dvb_gopt/sp files from ADF
>> and GAMESS calcs.
>
>> This is after completely removing cclib from python's site-packages
>> (remove all traces of trunk) and reinstalling cclib from revision 508
>> of your new branch. There's also a bunch of errors that I don't
>> recall seeing from trunk/test/regression.py.
>
> That's what I get for not reading mails to the end :) Could you try  
> out
> revision 509 from the branch? That's when I added minor fixes for  
> these
> attributes
>
> Karol
>
> -- 
> written by Karol Langner
> Sun Feb  4 12:14:55 CET 2007
>
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