[cclib-users] Gaussian 03 IRC parsing

[Ramon C. <rc...@iq...>]

Hi again,
I'll answer my own question, because I've already modified gaussianparser.py so 
that it deals with missing coordinates. I took the idea from the lines reading 
the Forces. I just changed a few lines from line 190. I attach the file in case 
it can be useful to the community.
I know I should create a pull request on github, but I'm still a bit of a newby 
in github. Next time...
Ramon

PS. This version of gaussianparser.py also includes my previous contribution 
where optdone attribute is a list of booleans, not a boolean.


On 28/03/14 10:20, ccl...@li... wrote:
> Dear all,
> I'm trying to parse Gaussian 03 IRC calculations and I face two problems:
> 1) My IRC had some instability at the end of the calculation, therefore some big
> numbers could not be properly formatted, and parsing the output gives an error
> (see attached file). Fair enough, but it would be good if I could still parse
> the file and get all the previous points. Would that be possible? Here is a line
> that gives an error:
>
>                             Z-Matrix orientation:
>     ---------------------------------------------------------------------
>     Center     Atomic     Atomic              Coordinates (Angstroms)
>     Number     Number      Type              X           Y           Z
>     ---------------------------------------------------------------------
>        1          6             0 42354.982772************93749.516872
>        2          1             0 42355.937399************93750.035409
>        3          1             0 42354.724535************93748.877845
>        4          8             0 42354.612001************93749.055343
>        5          8             0 42353.940461************93750.217216
>     ---------------------------------------------------------------------
>
> 2) If I parse an IRC I get the energy of all the points, either optimized or
> not. It would be useful to me to be able to get which points are the final
> points of the optimization (for example if data.optdone was a boolean array for
> all the points). For that, I have modified gaussianparser.py and data.py to work
> this way. I enclose the source files, as they can be useful to others or to the
> development team. However I have only tested them with my log file. They need
> further testing.
>
> Cheers,
> Ramon

-- 
Ramon Crehuet
Cientific Titular (Assistant Professor)
Institute of Advanced Chemistry of Catalonia
IQAC - CSIC
http://www.iqac.csic.es/qteor
https://twitter.com/rcrehuet
http://ramoncrehuet.wordpress.com/
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain)