Re: [cclib-devel] Bug in cclib's orcaparser

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

Dear Xaver,

 Looks like an easy one to fix. But could you provide us with a
log file that recreates this bug, in the Public Domain?

Cheers,
Karol 

On Mon, Mar 28, 2011 at 12:38:11PM +0200, Xaver W. wrote:
> Hi,
> in case of dummy atoms, orcaparser can't read the atoms. Consider:
> 
> >>> cclibdata = cfile.parse()
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "cclib/parser/logfileparser.py", line 221, in parse
>     self.extract(inputfile, line)
>   File "cclib/parser/orcaparser.py", line 196, in extract
>     atomnos.append(self.table.number[broken[0]])
> KeyError: '-'
> 
> I think the lines which orcaparser is trying to read are (sth like):
> 
>   138 ---------------------------------
>   139 CARTESIAN COORDINATES (ANGSTROEM)
>   140 ---------------------------------
>   141   Fe     0.000000    0.000000    0.000660
>   142   O     -0.592830    1.741600   -0.806850
>   143   O      0.592830   -1.741600   -0.806850
>   144   C      0.000000    2.934410   -0.176690
>   145   C      0.000000   -2.934410   -0.176690
>   146   H     -0.018170    3.765540   -0.884740
>   147   H      0.018170   -3.765540   -0.884740
>   148   C      1.428890    2.563280    0.175900
>   149   C     -1.428890   -2.563280    0.175900
>   150   H      2.069080    2.492180   -0.707270
>   151   H     -2.069080   -2.492180   -0.707270
>   152   O      1.366300    1.233000    0.806640
>   153   O     -1.366300   -1.233000    0.806640
>   154   H     -0.593730    3.184280    0.706460
>   155   H      0.593730   -3.184280    0.706460
>   156   H      1.849370    3.280780    0.883620
>   157   H     -1.849370   -3.280780    0.883620
>   158   H     -1.264360    1.976320   -1.465620
>   159   H      1.264360   -1.976320   -1.465620
>   160   H      2.067340    1.111470    1.465270
>   161   H     -2.067340   -1.111470    1.465270
>   162   -      0.408688    1.481601    0.017975
>   163   -     -0.442210   -1.472899    0.045583
> 
> (line numbers by "vi", ignore)
> 
> The two last lines are the coordinates of two dummy atoms. They turn up as 
> "DA" in the input, but apparently as " - " in the coordinate blocks of the 
> output.
> 
> Drop me a line if you need more info.
> 
> Regards,
> Xaver W.
> (for ccwatcher.sourceforge.net)
> 
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-- 
written by Karol M. Langner
Mon Mar 28 12:46:01 CEST 2011