cclib-devel

[cclib-devel] cclib support for NWChem

[Jeff H. <jef...@gm...>]

Dear cclib developers,

I read your JCC article and felt very lame because I'm still using
'grep' to parse output files, despite knowing far better tools for the
purpose.  cclib would seem to mitigate my laziness, except that it
doesn't currently support NWChem, Aces or Dalton, three of the
programs I use most often.  Although I use a fourth code, PSI,
infrequently, but as it is the only GPLed quantum chemistry code that
compares to the commercial codes, perhaps you are interested in
supporting it as well.  It's also the only fully C/C++ QC code out
there and will likely overtake GAMESS as the de facto free code for
non-DOE (ie supercomputer) users.  While PSI and Aces are more for the
high-accuracy community, NWChem and Dalton are popular in the DFT
crowd, particularly for their extensibility (parallel and properties)
which is unrivaled by the codes you currently support.

I wonder if I can help you support these programs.  I don't have time
to learn all that is necessary to write the parser code for the MO
vectors, but I should be able to write a parser for all the scalers
and other simple stuff.  If someone wants to deal with the MO vectors
and related quantities, I would be happy to provide all manner of
output files and technical support to that end.  All these codes all
store MO vectors as binary data somewhere and should use a standard
format.  Dalton and Aces may be the same since they use the integral
code.  I don't know the internal format of NWChem but I'm a developer
so it would somewhat pathetic if I was not able to figure it out from
the source.

If you have any suggestions for how to proceed, please let me know.  I
can't say that I'm going to make progress in the next few weeks due to
ACS preparations, but I should have time for it after that.

Best,

Jeff

-- 
Jeff Hammond
The University of Chicago

Re: [cclib-devel] cclib support for NWChem

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

On 10/03/2008, Jeff Hammond <jef...@gm...> wrote:
> Dear cclib developers,
>
>  I read your JCC article and felt very lame because I'm still using
>  'grep' to parse output files, despite knowing far better tools for the
>  purpose.  cclib would seem to mitigate my laziness, except that it
>  doesn't currently support NWChem, Aces or Dalton, three of the
>  programs I use most often.  Although I use a fourth code, PSI,
>  infrequently, but as it is the only GPLed quantum chemistry code that
>  compares to the commercial codes, perhaps you are interested in
>  supporting it as well.  It's also the only fully C/C++ QC code out
>  there and will likely overtake GAMESS as the de facto free code for
>  non-DOE (ie supercomputer) users.  While PSI and Aces are more for the
>  high-accuracy community, NWChem and Dalton are popular in the DFT
>  crowd, particularly for their extensibility (parallel and properties)
>  which is unrivaled by the codes you currently support.
>
>  I wonder if I can help you support these programs.  I don't have time
>  to learn all that is necessary to write the parser code for the MO
>  vectors, but I should be able to write a parser for all the scalers
>  and other simple stuff.  If someone wants to deal with the MO vectors
>  and related quantities, I would be happy to provide all manner of
>  output files and technical support to that end.  All these codes all
>  store MO vectors as binary data somewhere and should use a standard
>  format.  Dalton and Aces may be the same since they use the integral
>  code.  I don't know the internal format of NWChem but I'm a developer
>  so it would somewhat pathetic if I was not able to figure it out from
>  the source.
>
>  If you have any suggestions for how to proceed, please let me know.  I
>  can't say that I'm going to make progress in the next few weeks due to
>  ACS preparations, but I should have time for it after that.

This sounds fantastic Jeff. Of course we're interested, and we'd
appreciate any help you can give. I'm up to my eyeballs until the ACS
also. Why don't we meet up there and have a chat? (cclib has blanket
coverage of the ACS this year with me at New Orleans, and Adam at
Philadelphia)

Noel


>  Best,
>
>  Jeff
>
>  --
>  Jeff Hammond
>  The University of Chicago
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  cclib-devel mailing list
>  ccl...@li...
>  https://lists.sourceforge.net/lists/listinfo/cclib-devel
>

Re: [cclib-devel] cclib support for NWChem

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

On Monday 10 March 2008 15:20, Noel O'Boyle wrote:
> On 10/03/2008, Jeff Hammond <jef...@gm...> wrote:
> > Dear cclib developers,
> >
> >  I read your JCC article and felt very lame because I'm still using
> >  'grep' to parse output files, despite knowing far better tools for the
> >  purpose.  cclib would seem to mitigate my laziness, except that it
> >  doesn't currently support NWChem, Aces or Dalton, three of the
> >  programs I use most often.  Although I use a fourth code, PSI,
> >  infrequently, but as it is the only GPLed quantum chemistry code that
> >  compares to the commercial codes, perhaps you are interested in
> >  supporting it as well.  It's also the only fully C/C++ QC code out
> >  there and will likely overtake GAMESS as the de facto free code for
> >  non-DOE (ie supercomputer) users.  While PSI and Aces are more for the
> >  high-accuracy community, NWChem and Dalton are popular in the DFT
> >  crowd, particularly for their extensibility (parallel and properties)
> >  which is unrivaled by the codes you currently support.
> >
> >  I wonder if I can help you support these programs.  I don't have time
> >  to learn all that is necessary to write the parser code for the MO
> >  vectors, but I should be able to write a parser for all the scalers
> >  and other simple stuff.  If someone wants to deal with the MO vectors
> >  and related quantities, I would be happy to provide all manner of
> >  output files and technical support to that end.  All these codes all
> >  store MO vectors as binary data somewhere and should use a standard
> >  format.  Dalton and Aces may be the same since they use the integral
> >  code.  I don't know the internal format of NWChem but I'm a developer
> >  so it would somewhat pathetic if I was not able to figure it out from
> >  the source.
> >
> >  If you have any suggestions for how to proceed, please let me know.  I
> >  can't say that I'm going to make progress in the next few weeks due to
> >  ACS preparations, but I should have time for it after that.
>
> This sounds fantastic Jeff. Of course we're interested, and we'd
> appreciate any help you can give. I'm up to my eyeballs until the ACS
> also. Why don't we meet up there and have a chat? (cclib has blanket
> coverage of the ACS this year with me at New Orleans, and Adam at
> Philadelphia)

Jeff & Noel,

 I'd help out with NWChem, since I sometimes use it also. I've just created a 
working branch for it in our SVN repository. When I get the newest version 
(NWChem5.1 is it?) and the time I'll add some test jobs.

Cheers,
Karol

-- 
written by Karol Langner
Fri Mar 21 14:20:59 CET 2008

Re: [cclib-devel] cclib support for NWChem

[Jeff H. <jef...@gm...>]

Karol,

That sounds good.  It might work well to add the test jobs that come
with NWChem in the QA (quality assurance) directory.  Those tests are
up-to-date - unlike those in the examples directory - and are already
parsed by an included Perl script, hence one need only translate Perl
to Python if that is the easiest route.

The biggest changes from 5.0 to 5.1 other than bug fixes and tuning
are the inclusion of property codes (primarily polarizabilities).
Since this was my contribution to 5.1, I'm going to start there with
respect to adding parsing features to CCLib.  Thus, it is not
necessary to get 5.1 if you don't otherwise need it.

Best,

Jeff

On Fri, Mar 21, 2008 at 8:21 AM, Karol M. Langner
<kar...@gm...> wrote:
>   I'd help out with NWChem, since I sometimes use it also. I've just created a
>  working branch for it in our SVN repository. When I get the newest version
>  (NWChem5.1 is it?) and the time I'll add some test jobs.
>
>  Cheers,
>  Karol
>
>  --
>  written by Karol Langner
>  Fri Mar 21 14:20:59 CET 2008
>



-- 
Jeff Hammond
The University of Chicago

Re: [cclib-devel] cclib support for NWChem

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

Jeff,

 I've installed 5.1 already. This is a good occasion to stir things up with 
cclib again, since the project has been dormant for some time now :)

 I think the idea behind the cclib test suite is to have tests as similiar as 
possible for all the parsers. So the first thing would be to create and run 
jobs in NWChem that correspond to the tests that already exist for the other 
parsers. For example, yesterday I added single-point Hartree-Fock and DFT 
inputs/outputs (for divinylbenzene like for all our supported programs).

 There is also a regression system in cclib. That is the place to add QA jobs 
shipped with NWChem - at least those that are not parsed satisfactorily when 
the parser is up and running.

 I guess Noel or Adam might have something to add to that, and perhaps some 
general comments about the future of cclib?

Cheers,
Karol

On Monday 31 March 2008 16:10, Jeff Hammond wrote:
> Karol,
>
> That sounds good.  It might work well to add the test jobs that come
> with NWChem in the QA (quality assurance) directory.  Those tests are
> up-to-date - unlike those in the examples directory - and are already
> parsed by an included Perl script, hence one need only translate Perl
> to Python if that is the easiest route.
>
> The biggest changes from 5.0 to 5.1 other than bug fixes and tuning
> are the inclusion of property codes (primarily polarizabilities).
> Since this was my contribution to 5.1, I'm going to start there with
> respect to adding parsing features to CCLib.  Thus, it is not
> necessary to get 5.1 if you don't otherwise need it.
>
> Best,
>
> Jeff
>
> On Fri, Mar 21, 2008 at 8:21 AM, Karol M. Langner
>
> <kar...@gm...> wrote:
> >   I'd help out with NWChem, since I sometimes use it also. I've just
> > created a working branch for it in our SVN repository. When I get the
> > newest version (NWChem5.1 is it?) and the time I'll add some test jobs.
> >
> >  Cheers,
> >  Karol
> >
> >  --
> >  written by Karol Langner
> >  Fri Mar 21 14:20:59 CET 2008

-- 
written by Karol Langner
Mon Mar 31 18:16:51 CEST 2008

Re: [cclib-devel] cclib support for NWChem

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

I met with Jeff at the ACS and we had a good discussion. I took him
through the basics of parsing, and we discussed what exactly he wants
to get from cclib. One of the things he is keen on, is to be able to
handle jobs consisting of multiple runs.

First of all, we need to get you up and running as a developer. You'll
have to create a sourceforge (SF) account, and send us your username.
Next we need to get a working parser set up with failing tests. Karol
has started this. I'll get it set up to fail some tests. We also need
several test files to get started - we've a list of the files we need
on the wiki (I will update this in the next few minutes):
http://cclib.sourceforge.net/wiki/index.php?title=Tests

That should be enough to get you going, right?

Noel

Re: [cclib-devel] cclib support for NWChem

[Jeff H. <jef...@gm...>]

Noel,

This is my sourceforge account: jeff_science.

Thanks for all your help at the ACS.  I'll let you know when I make
some progress.

Best,

On Tue, Apr 15, 2008 at 10:18 AM, Noel O'Boyle <bao...@gm...> wrote:
> I met with Jeff at the ACS and we had a good discussion. I took him
>  through the basics of parsing, and we discussed what exactly he wants
>  to get from cclib. One of the things he is keen on, is to be able to
>  handle jobs consisting of multiple runs.
>
>  First of all, we need to get you up and running as a developer. You'll
>  have to create a sourceforge (SF) account, and send us your username.
>  Next we need to get a working parser set up with failing tests. Karol
>  has started this. I'll get it set up to fail some tests. We also need
>  several test files to get started - we've a list of the files we need
>  on the wiki (I will update this in the next few minutes):
>  http://cclib.sourceforge.net/wiki/index.php?title=Tests
>
>  That should be enough to get you going, right?
>
>  Noel
>



-- 
Jeff Hammond
The University of Chicago

Re: [cclib-devel] cclib support for NWChem

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

OK - welcome to cclib! I'll start sorting out the parser...

Noel

On 15/04/2008, Jeff Hammond <jef...@gm...> wrote:
> Noel,
>
>  This is my sourceforge account: jeff_science.
>
>  Thanks for all your help at the ACS.  I'll let you know when I make
>  some progress.
>
>  Best,
>
>
>  On Tue, Apr 15, 2008 at 10:18 AM, Noel O'Boyle <bao...@gm...> wrote:
>  > I met with Jeff at the ACS and we had a good discussion. I took him
>  >  through the basics of parsing, and we discussed what exactly he wants
>  >  to get from cclib. One of the things he is keen on, is to be able to
>  >  handle jobs consisting of multiple runs.
>  >
>  >  First of all, we need to get you up and running as a developer. You'll
>  >  have to create a sourceforge (SF) account, and send us your username.
>  >  Next we need to get a working parser set up with failing tests. Karol
>  >  has started this. I'll get it set up to fail some tests. We also need
>  >  several test files to get started - we've a list of the files we need
>  >  on the wiki (I will update this in the next few minutes):
>  >  http://cclib.sourceforge.net/wiki/index.php?title=Tests
>  >
>  >  That should be enough to get you going, right?
>  >
>  >  Noel
>  >
>
>
>
>
> --
>  Jeff Hammond
>  The University of Chicago
>

Re: [cclib-devel] cclib support for NWChem

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

OK, Jeff, the NWChem parser is ready to rock.

The work flow is something like:
(1) Add some code to the nwchemparser.py
(2) Run "python setup.py install"
(3) Run "python testSP.py NWChem" (or just "python testSP.py")
(4) "svn commit"

Keep repeating until all the tests pass. :-) The SP is for single
point. These are the only test files that are currently uploaded.

Noel

On 17/04/2008, Noel O'Boyle <bao...@gm...> wrote:
> OK - welcome to cclib! I'll start sorting out the parser...
>
>
>  Noel
>
>
>  On 15/04/2008, Jeff Hammond <jef...@gm...> wrote:
>  > Noel,
>  >
>  >  This is my sourceforge account: jeff_science.
>  >
>  >  Thanks for all your help at the ACS.  I'll let you know when I make
>  >  some progress.
>  >
>  >  Best,
>  >
>  >
>  >  On Tue, Apr 15, 2008 at 10:18 AM, Noel O'Boyle <bao...@gm...> wrote:
>  >  > I met with Jeff at the ACS and we had a good discussion. I took him
>  >  >  through the basics of parsing, and we discussed what exactly he wants
>  >  >  to get from cclib. One of the things he is keen on, is to be able to
>  >  >  handle jobs consisting of multiple runs.
>  >  >
>  >  >  First of all, we need to get you up and running as a developer. You'll
>  >  >  have to create a sourceforge (SF) account, and send us your username.
>  >  >  Next we need to get a working parser set up with failing tests. Karol
>  >  >  has started this. I'll get it set up to fail some tests. We also need
>  >  >  several test files to get started - we've a list of the files we need
>  >  >  on the wiki (I will update this in the next few minutes):
>  >  >  http://cclib.sourceforge.net/wiki/index.php?title=Tests
>  >  >
>  >  >  That should be enough to get you going, right?
>  >  >
>  >  >  Noel
>  >  >
>  >
>  >
>  >
>  >
>  > --
>  >  Jeff Hammond
>  >  The University of Chicago
>  >
>