Re: [cclib-users] Gaussian 03 IRC parsing

[Adam T. <ate...@gm...>]

Hi Ramon,

Thank you for alerting us to these issues, and providing an example logfile
and patches. Just to clarify: you are willing to place the logfile in the
public domain?

Also, for cclib v1.3 (6-12 months?), I do plan on changing optdone from a
bool to a list of integers corresponding to the energy/atomcoords index of
when an optimization has finished. This would make it easy to select the
energies and coordinates that correspond to points on a IRC or relaxed PES.

Thanks again,

Adam



On Fri, Mar 28, 2014 at 3:35 AM, Ramon Crehuet <rc...@iq...> wrote:

> 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)
>
>
>
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