cclib-devel

[cclib-devel] Good vibes from tools meeting

[Noel O'B. <bao...@gm...>]

Hello all,

I will write in more detail later, but things went very well at the
tools meeting. It was really great to meet all these people, mainly
developers, who seemed to be interested in the same stuff.

GAMESS-UK developer Paul Sherwood and CCP1GUI developer Jens Thomas
are interested in using cclib as a front end to their code. CCP1GUI
actually does some pretty cool visualisations and is GPL to boot. It's
a well kept secret, it seems. Basically, the only thing holding them
back is how we handle gbasis. We're going to work with them to sort it
out, and maybe we can get them to help with other codes too (but one
step at a time). Basically, the problem is handling of Cartesian as
well as spherical basis functions, and also, it seems that the order
of the basis functions needs to be standardised (I'm a bit hazy on
this, but they seemed to be quite clear on the necessity for this).

Someone pointed me to a UK calculation farm which might give me access
to a variety of codes. I haven't chased this up - it may/may not be
possible.

At the meeting, there was also a consensus that we should contact all
QM codes and ask for a formal description of their machine readable
formats. If any QM codes respond, both ourselves and OpenBabel will
then add support.

Plugins are good. I'm thinking very strongly we should go down the
plugin route. It would allow upgrades to the latest parser simply by
dropping a new parser into a particular directory. This is especially
useful for programs that use cclib. It could just be a trivial change.

This is basically a brain dump, above. I will probably think of more,
and maybe write a blog post or two too. Any actual work on my part
I'll have to put off till after the ACS, though.

Regards,
   Noel

Re: [cclib-devel] Good vibes from tools meeting

[Grant H. <Hi...@Ca...>]

Firstly, congrats on the paper guys.


On Fri, 2008-03-14 at 19:58 +0000, Noel O'Boyle wrote:

> Someone pointed me to a UK calculation farm which might give me access
> to a variety of codes. I haven't chased this up - it may/may not be
> possible.

Is that NSCCS? I've had pretty good experiences with them so far,
although it's been for more "traditional" uses. Grant proposals could be
reasonably short and we heard back within a couple of weeks. Nice piece
of iron too.


> At the meeting, there was also a consensus that we should contact all
> QM codes and ask for a formal description of their machine readable
> formats. If any QM codes respond, both ourselves and OpenBabel will
> then add support.

The new version of Molpro (shouldn't be too far off) looks like it'll be
dumping xml'ised output by default, or certainly with very little
effort. While this should make the output easy to parse there will still
be the Molpro scripting capabilities stumbling block. Assuming you guys
can put up with some very naive questions I may be able to take a look
at adding something to cclib to parse the xml output in at least simple
cases. That, of course, depends on my free time and learning enough
Python to make it happen. Despite my best intentions I'm only half way
through the O'Reilly Learning Python.

Regards,

Grant

Re: [cclib-devel] Good vibes from tools meeting

[Noel O'B. <bao...@gm...>]

On 18/03/2008, Grant Hill <Hi...@ca...> wrote:
> Firstly, congrats on the paper guys.
>
>
>
>  On Fri, 2008-03-14 at 19:58 +0000, Noel O'Boyle wrote:
>
>  > Someone pointed me to a UK calculation farm which might give me access
>  > to a variety of codes. I haven't chased this up - it may/may not be
>  > possible.
>
>
> Is that NSCCS? I've had pretty good experiences with them so far,
>  although it's been for more "traditional" uses. Grant proposals could be
>  reasonably short and we heard back within a couple of weeks. Nice piece
>  of iron too.
It is. My requirements are quite different from the usual user, e.g.
typical jobs should run in less than 5 minutes. As I said, I have
still to look into this. I hope they will look kindly on a project
which attempts to serve the broader community.

>  > At the meeting, there was also a consensus that we should contact all
>  > QM codes and ask for a formal description of their machine readable
>  > formats. If any QM codes respond, both ourselves and OpenBabel will
>  > then add support.
>
>
> The new version of Molpro (shouldn't be too far off) looks like it'll be
>  dumping xml'ised output by default, or certainly with very little
>  effort. While this should make the output easy to parse there will still
>  be the Molpro scripting capabilities stumbling block. Assuming you guys
>  can put up with some very naive questions I may be able to take a look
>  at adding something to cclib to parse the xml output in at least simple
>  cases. That, of course, depends on my free time and learning enough
>  Python to make it happen. Despite my best intentions I'm only half way
>  through the O'Reilly Learning Python.

As you are possibly aware (?), Peter Knowles of Molpro was at the
meeting in Runcorn and spoke about the XML developments, which I was
very much in favour of. We do currently have some support for Molpro.
For sure the scripting capabilities mean that the general problem is
intractable, but if we can extract the relevant data from the most
common types of jobs, we will be happy. We welcome any help we can
get, so feel free to start asking naive questions at the first
opportunity.

Also, as I said, along with OpenBabel, Avogadro, GAMESS-UK and others,
we are going to start pushing for QM codes to release a specification
of their machine-readable formats (which I assume that Molpro also
has). This should be a more tractable problem.

Noel

>  Regards,
>
>  Grant
>
>
>
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Re: [cclib-devel] Good vibes from tools meeting

[Grant H. <Hi...@ca...>]

On 20 Mar 2008, at 16:17, Noel O'Boyle wrote:
> As you are possibly aware (?), Peter Knowles of Molpro was at the
> meeting in Runcorn and spoke about the XML developments, which I was
> very much in favour of. We do currently have some support for Molpro.
> For sure the scripting capabilities mean that the general problem is
> intractable, but if we can extract the relevant data from the most
> common types of jobs, we will be happy. We welcome any help we can
> get, so feel free to start asking naive questions at the first
> opportunity.

I knew Peter was at the meeting, I'm glad you managed to get a word in  
with him as he obviously knows a lot more about the xml than I do.  
I'll certainly _try_ to see if I can help with parsing some of it soon.

> Also, as I said, along with OpenBabel, Avogadro, GAMESS-UK and others,
> we are going to start pushing for QM codes to release a specification
> of their machine-readable formats (which I assume that Molpro also
> has). This should be a more tractable problem.

Molpro can dump several different machine readable files, although one  
is probably much more interesting than the others. I don't personally  
know the format for them but there are other devs down the corridor  
who can probably tell me. I'll have a chat with them when I get back  
from vacation in a weeks time.


Grant