Re: [cclib-devel] Patch for extraction of scan data from gaussian output files

[Edward H. <hol...@ca...>]

Hi Adam,

1) Yes, this is an over sight on my behalf, i can easily add this.

2) AS you mention this is some what complicated. 

The for rigid scan case the calculation is basically a series of single point energies, and cclib correctly collects these coordinates in the atom coords section. For this case i suggest we copy the atomcoords array to a scancoords array for clarity and completeness.

The situation for a relaxed scan is much more complicated. 
Gaussian outputs the geometries as values for a z-matrix. While it is fairly simple to extract these values converting them into xyz coordinates this would require parsing the input z matrix and converting the z-matrix with open babel (i guess)
As the scan is now a series of optimisations cclib does not correctly collect all geometries as the parser halts after the first optimisation has completed.

I think the best solution for the relaxed scan problem is to avoid converting the z-mat and extent the code that searches for geometries to look for more than 1 optimisation step in scan jobs. My reasoning for choosing this option is that it avoids additional dependancies (open babel) and the coded would also be useful for other jobs that are expected to be a series of optimisations (IRC jobs for example).

I'll probably have some time over the next weekend to work on this code.

Yours

Ed Holland 
 
On 21 Jan 2012, at 18:06, Adam Tenderholt wrote:

> Hi Ed,
> 
> Thanks for the patch. Your changes look pretty straight-forward. A
> couple of questions:
> 
> 1) Do you think the names of the variables should also be stored? This
> would probably be important if it's a multi-dimensional scan.
> 2) Do you have interest in trying to parse the final xyz coordinates
> at each point? If I remember correctly, this is somewhat complicated
> but something that cclib should probably handle.
> 
> Thanks again,
> 
> Adam
> 
> 
> On Wed, Jan 18, 2012 at 7:14 AM, Edward Holland <hol...@ca...> wrote:
>> helps if i attach the file!!
>> 
>> 
>> 
>> On 18 Jan 2012, at 15:13, Edward Holland wrote:
>> 
>>> Hi All,
>>> 
>>> I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch.
>>> 
>>> I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time.
>>> 
>>> Yours
>>> 
>>> Ed Holland
>> 
>> 
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