Re: [cclib-devel] Analysis of scan results

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

Hi Ed,

Sorry for not answering sooner, I was bogged down with work.

On Nov 07 2011, Edward Holland wrote:
> I managed to run two fairly simple, and representative jobs over the weekend. They aren't very interesting jobs but the correctly illustrate the type of data that will need to be parsed.
>  The key parts are headed with "Summary of Optimized Potential Surface Scan" or "Summary of the potential surface scan".
> as you will be able to see the non optimised jobs will be much simpler to parse as there is no need to store a complete set of geometry data for each step.
> One complicated i can see if translating the z matrix variables given by the output into xyz coordinates as normally expected within cclib. 

So, could you provide the output file(s) you would liked parsed for this? With something to work, it oculd be easy to implement what you want.

> Another idea i've had is a boolean that stores if a output file has terminated	at an expected point, or been cut short.
> I suspect this would be useful for people hoping to make their job submission scripts more intelligent.

I'm afraid I don't understand this idea, and you need to explain in more detail what you mean.

Best regards,
Karol

> On 3 Nov 2011, at 13:08, Noel O'Boyle wrote:
> 
> > Hi Ed,
> > 
> > Sounds like an interesting project.
> > 
> > Regarding the scans, your're right - currently we don't support this.
> > Can you provide an example? (Preferably a small test case.) Then we'll
> > be able to discuss this a bit more.
> > 
> > - Noel
> > 
> > On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote:
> >> Hi all,
> >> 
> >>        I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way!
> >> 
> >>        Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least.
> >> 
> >>        Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about.

-- 
written by Karol M. Langner
Thu Dec 15 20:24:17 CET 2011