Re: [cclib-devel] parser-refactoring

[Karol L. <kar...@kn...>]

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