cclib-devel — Developer's mailing list

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...>]

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] Problem with parsing Jaguar run.

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

Could you provide the input file that causes this problem in an attachment
or online somewhere? Also, which version of cclib are you using?

Cheers,
Karol

On Thu, Apr 3, 2008 at 5:57 PM, Noel O'Boyle <bao...@gm...> wrote:

> Unfortunately, I'm about to go to the ACS for the next week, but
> perhaps my co-developers can help you in the meanwhile...
>
> Noel
>
> On 03/04/2008, Jean-Didier Maréchal <jea...@ua...> wrote:
> > Dear Noel,
> >
> >  I have a problem that seems to be related with the geometry parsing of
> a
> >  jaguar run. Could you tell me what I do wrong?
> >
> >  I run:
> >
> >  >>> import cclib
> >  >>> myfile=cclib.parser.ccopen('ptnh3_2h2o_2plus.out')
> >  >>> myfile.parse()
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute charge: 2
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute mult: 1
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute nbasis: 104
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute atomcoords[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute atomnos[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute natom: 12
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute nmo: 104
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute homos[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scfvalues[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scftargets[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scfenergies[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute moenergies[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute geovalues[]
> >  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute geotargets[]
> >  Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py",
> >  line 142, in parse
> >     self.extract(inputfile, line)
> >   File "/usr/lib/python2.5/site-packages/cclib/parser/jaguarparser.py",
> >  line 155, in extract
> >     if line[41] == "(":
> >  IndexError: string index out of range
> >
> >
> >  All the best
> >  JD
> >
> >  --
> >  Dr. Jean-Didier Maréchal
> >  Assistant Professor
> >  Computational Medicinal Bioorganic and Bioinorganic Chemistry @Transmet
> >  Unitat de Química Física
> >  Departament de Química
> >  Universitat Autònoma de Barcelona
> >  08193 Bellaterra, Spain
> >  Tel: +34.(0)1935814936
> >  Fax: +34.(0)1935812920
> >  e-mail:jea...@ua... <e-mail%3Aj...@ua...>
> >
> >
>
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Re: [cclib-devel] Problem with parsing Jaguar run.

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

Unfortunately, I'm about to go to the ACS for the next week, but
perhaps my co-developers can help you in the meanwhile...

Noel

On 03/04/2008, Jean-Didier Maréchal <jea...@ua...> wrote:
> Dear Noel,
>
>  I have a problem that seems to be related with the geometry parsing of a
>  jaguar run. Could you tell me what I do wrong?
>
>  I run:
>
>  >>> import cclib
>  >>> myfile=cclib.parser.ccopen('ptnh3_2h2o_2plus.out')
>  >>> myfile.parse()
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute charge: 2
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute mult: 1
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute nbasis: 104
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute atomcoords[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute atomnos[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute natom: 12
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute nmo: 104
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute homos[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scfvalues[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scftargets[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute scfenergies[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute moenergies[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute geovalues[]
>  [Jaguar ptnh3_2h2o_2plus.out INFO] Creating attribute geotargets[]
>  Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py",
>  line 142, in parse
>     self.extract(inputfile, line)
>   File "/usr/lib/python2.5/site-packages/cclib/parser/jaguarparser.py",
>  line 155, in extract
>     if line[41] == "(":
>  IndexError: string index out of range
>
>
>  All the best
>  JD
>
>  --
>  Dr. Jean-Didier Maréchal
>  Assistant Professor
>  Computational Medicinal Bioorganic and Bioinorganic Chemistry @Transmet
>  Unitat de Química Física
>  Departament de Química
>  Universitat Autònoma de Barcelona
>  08193 Bellaterra, Spain
>  Tel: +34.(0)1935814936
>  Fax: +34.(0)1935812920
>  e-mail:jea...@ua...
>
>

[cclib-devel] Presentation on cclib at ChemToolsMeet

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

I recently gave a presentation on cclib and related software at
ChemToolsMeet. The PDF of the talk is now available at:
http://www.ccp1.ac.uk/chemtoolsmeet/presentations/NoelOBoyle.pdf

(Note that QMForge is accidentally omitted from the list of Python QM
software near the start.)

Noel

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

[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

[cclib-devel] cclib paper

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

JCompChem have sent me a complimentary copy of the cclib issue (as I
call it :-). It makes me realise how long it's been since I actually
looked through a paper copy of a journal. Probably not since my PhD...

Noel

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] 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

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
>
>
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
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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

[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] 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
>

[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] Fwd: Wiley InterScience Article Publication Alert

[Adam T. <a-t...@st...>]

It also makes a wonderful present, officially coming out in print a  
day earlier than my birthday... :-)

On Feb 27, 2008, at 2:49 AM, Noel O'Boyle wrote:

> Wow - that was quick. :-)
>
> ---------- Forwarded message ----------
> From: Wiley InterScience <Pub...@in...>
> Date: 27 Feb 2008 10:42
> Subject: Wiley InterScience Article Publication Alert
> To: Noel O'Boyle <bao...@gm...>
>
>
> Dear Noel O'Boyle:
>
> We are pleased to inform you that your article has now been published
> online on Wiley InterScience with pagination:
>
> cclib: A library for package-independent computational chemistry  
> algorithms
> Noel M. O'boyle, Adam L. Tenderholt, Karol M. Langner
>
> Journal of Computational Chemistry
> Volume 29, Issue 5, Pages 839-845, 15 April 2008
> Online ISSN: 1096-987X
> Print ISSN: 0192-8651
> Copyright � 2008 Wiley Periodicals, Inc., A Wiley Company
>
> Published Online: Sep 11 2007  7:26AM
> DOI: 10.1002/jcc.20823
>
>
> If your institution holds a subscription to this journal, you will be
> able to view your article at
> http://www3.interscience.wiley.com/cgi-bin/abstract/116316435/ABSTRACT
>
> Please feel free to share this e-mail with your co-authors and
> colleagues who may be interested in your work or in this area of
> research.
>
> We look forward to your future submissions and invite you to visit
> our website at http://www.interscience.wiley.com/authors, where you
> will find valuable resources and tools to assist you in your research.
>
>
> Good luck with your future work.
>
>
> Sincerely,
> Wiley InterScience
>
>
> Notes:
> 1.  To create the link to this article from your homepage, take the
> DOI (digital object identifier) provided above and append it to
> "http://dx.doi.org/" as per following example: DOI 10.1002/cncr.21464,
> becomes http://dx.doi.org/10.1002/cncr.21464
>
> 2.  To include the DOI in a citation to this article, simply append
> it to the reference as follows:
> Oestreicher, N., The cost of adjuvant chemotherapy in patients with
> early-stage breast carcinoma, Cancer 10(1), pp. 2054 - 2062, DOI:
> 10.1002/cncr.21464
>
>
> -------------------------------------------------------------------------------------------------------------------------
> This is an automated e-mail; please do not reply to this message. If
> you have a query about your
> article, please contact the production editor of the journal.
> -------------------------------------------------------------------------------------------------------------------------
>
>
>
> Wiley InterScience is a division of:
> John Wiley & Sons, Inc.  |  111 River Street  |  Hoboken, NJ 07030
> Phone: 800-225-5945  |  Fax: 800-605-2665  |  www.wiley.com
> -------------------------------------------------------------------------
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Re: [cclib-devel] Fwd: Wiley InterScience Article Publication Alert

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

It might be a good idea to add a 'how to cite cclib' thingy to the wiki...

On Wednesday 27 February 2008 11:49, Noel O'Boyle wrote:
> Wow - that was quick. :-)
>
> ---------- Forwarded message ----------
> From: Wiley InterScience <Pub...@in...>
> Date: 27 Feb 2008 10:42
> Subject: Wiley InterScience Article Publication Alert
> To: Noel O'Boyle <bao...@gm...>
>
>
> Dear Noel O'Boyle:
>
>  We are pleased to inform you that your article has now been published
> online on Wiley InterScience with pagination:
>
>  cclib: A library for package-independent computational chemistry
> algorithms Noel M. O'boyle, Adam L. Tenderholt, Karol M. Langner
>
>  Journal of Computational Chemistry
>  Volume 29, Issue 5, Pages 839-845, 15 April 2008
>  Online ISSN: 1096-987X
>  Print ISSN: 0192-8651
>  Copyright � 2008 Wiley Periodicals, Inc., A Wiley Company
>
>  Published Online: Sep 11 2007  7:26AM
>  DOI: 10.1002/jcc.20823
>
>
>  If your institution holds a subscription to this journal, you will be
> able to view your article at
>  http://www3.interscience.wiley.com/cgi-bin/abstract/116316435/ABSTRACT
>
>  Please feel free to share this e-mail with your co-authors and
> colleagues who may be interested in your work or in this area of
> research.
>
>  We look forward to your future submissions and invite you to visit
> our website at http://www.interscience.wiley.com/authors, where you
> will find valuable resources and tools to assist you in your research.
>
>
>  Good luck with your future work.
>
>
>  Sincerely,
>  Wiley InterScience
>
>
>  Notes:
>  1.  To create the link to this article from your homepage, take the
> DOI (digital object identifier) provided above and append it to
> "http://dx.doi.org/" as per following example: DOI 10.1002/cncr.21464,
> becomes http://dx.doi.org/10.1002/cncr.21464
>
>  2.  To include the DOI in a citation to this article, simply append
> it to the reference as follows:
>  Oestreicher, N., The cost of adjuvant chemotherapy in patients with
> early-stage breast carcinoma, Cancer 10(1), pp. 2054 - 2062, DOI:
> 10.1002/cncr.21464

-- 
written by Karol Langner
Wed Feb 27 23:47:08 CET 2008

[cclib-devel] Fwd: Wiley InterScience Article Publication Alert

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

Wow - that was quick. :-)

---------- Forwarded message ----------
From: Wiley InterScience <Pub...@in...>
Date: 27 Feb 2008 10:42
Subject: Wiley InterScience Article Publication Alert
To: Noel O'Boyle <bao...@gm...>


Dear Noel O'Boyle:

 We are pleased to inform you that your article has now been published
online on Wiley InterScience with pagination:

 cclib: A library for package-independent computational chemistry algorithms
 Noel M. O'boyle, Adam L. Tenderholt, Karol M. Langner

 Journal of Computational Chemistry
 Volume 29, Issue 5, Pages 839-845, 15 April 2008
 Online ISSN: 1096-987X
 Print ISSN: 0192-8651
 Copyright � 2008 Wiley Periodicals, Inc., A Wiley Company

 Published Online: Sep 11 2007  7:26AM
 DOI: 10.1002/jcc.20823


 If your institution holds a subscription to this journal, you will be
able to view your article at
 http://www3.interscience.wiley.com/cgi-bin/abstract/116316435/ABSTRACT

 Please feel free to share this e-mail with your co-authors and
colleagues who may be interested in your work or in this area of
research.

 We look forward to your future submissions and invite you to visit
our website at http://www.interscience.wiley.com/authors, where you
will find valuable resources and tools to assist you in your research.


 Good luck with your future work.


 Sincerely,
 Wiley InterScience


 Notes:
 1.  To create the link to this article from your homepage, take the
DOI (digital object identifier) provided above and append it to
"http://dx.doi.org/" as per following example: DOI 10.1002/cncr.21464,
becomes http://dx.doi.org/10.1002/cncr.21464

 2.  To include the DOI in a citation to this article, simply append
it to the reference as follows:
 Oestreicher, N., The cost of adjuvant chemotherapy in patients with
early-stage breast carcinoma, Cancer 10(1), pp. 2054 - 2062, DOI:
10.1002/cncr.21464


 -------------------------------------------------------------------------------------------------------------------------
 This is an automated e-mail; please do not reply to this message. If
you have a query about your
 article, please contact the production editor of the journal.
 -------------------------------------------------------------------------------------------------------------------------



 Wiley InterScience is a division of:
 John Wiley & Sons, Inc.  |  111 River Street  |  Hoboken, NJ 07030
 Phone: 800-225-5945  |  Fax: 800-605-2665  |  www.wiley.com

Re: [cclib-devel] Fwd: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation

[Adam T. <a-t...@st...>]

>>> Yes - indeed, sorry for the surprise. It was just arranged in the  
>>> last
>> week. I said I would talk about cclib, GaussSum, pybel, and some CCDC
>> stuff too - it's only 30 minutes long so I'll see what I can squeeze
>> in that's relevant to QM.
>
> That's great, more advertisement for cclib :)

Excellent. :-) I'd like to see a copy of your talk at some point  
(either before or after you give the talk).

Adam

Re: [cclib-devel] Fwd: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation

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

On Monday 25 February 2008 23:31, Noel O'Boyle wrote:
> On 25/02/2008, Karol M. Langner <kar...@gm...> wrote:
> > ----------  Forwarded Message  ----------
> >
> >  Subject: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and
> >  Visualisation
> >  Date: Monday 25 February 2008 15:46
> >  From: "Jens Thomas j.m.h.thomas a dl.ac.uk" <own...@cc...>
> >  To: "Langner, Karol M. -id#497-" <kar...@gm...>
> >
> >  Sent to CCL by: Jens Thomas [j.m.h.thomas],[dl.ac.uk]
> >  Molecular Modelling: Tools, GUIs and Visualisation
> >
> >  11th - 13th March 2008
> >
> >  This is to announce a CCP1 meeting looking at graphical interfaces,
> >  visualisation and tools for molecular modelling in general, but with the
> >  focus towards electronic structure.
> >
> >  (...)
> >
> >  We already have speakers confirmed from projects including OpenBabel,
> >  Avogadro, Molekel, Molpro, cclib, GaussSum, The CCP1GUI, GAMESS, and
> >  GAMESS-UK.
> >
> >  (...)
> >
> >  -----------------------------------------------
> >
> >  Hi guys,
> >
> >   Are you going to be speaking at that meeting, Noel?
>
> Yes - indeed, sorry for the surprise. It was just arranged in the last
> week. I said I would talk about cclib, GaussSum, pybel, and some CCDC
> stuff too - it's only 30 minutes long so I'll see what I can squeeze
> in that's relevant to QM.

That's great, more advertisement for cclib :)

- Karol

-- 
written by Karol Langner
Mon Feb 25 23:43:16 CET 2008

Re: [cclib-devel] Fwd: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation

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

On 25/02/2008, Karol M. Langner <kar...@gm...> wrote:
> ----------  Forwarded Message  ----------
>
>  Subject: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and
>  Visualisation
>  Date: Monday 25 February 2008 15:46
>  From: "Jens Thomas j.m.h.thomas a dl.ac.uk" <own...@cc...>
>  To: "Langner, Karol M. -id#497-" <kar...@gm...>
>
>  Sent to CCL by: Jens Thomas [j.m.h.thomas],[dl.ac.uk]
>  Molecular Modelling: Tools, GUIs and Visualisation
>
>  11th - 13th March 2008
>
>  This is to announce a CCP1 meeting looking at graphical interfaces,
>  visualisation and tools for molecular modelling in general, but with the
>  focus towards electronic structure.
>
>  (...)
>
>  We already have speakers confirmed from projects including OpenBabel,
>  Avogadro, Molekel, Molpro, cclib, GaussSum, The CCP1GUI, GAMESS, and
>  GAMESS-UK.
>
>  (...)
>
>  -----------------------------------------------
>
>  Hi guys,
>
>   Are you going to be speaking at that meeting, Noel?

Yes - indeed, sorry for the surprise. It was just arranged in the last
week. I said I would talk about cclib, GaussSum, pybel, and some CCDC
stuff too - it's only 30 minutes long so I'll see what I can squeeze
in that's relevant to QM.

Noel

>  - Karol
>
>  --
>  written by Karol Langner
>  Mon Feb 25 19:01:27 CET 2008
>
>  -------------------------------------------------------------------------
>  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
>

[cclib-devel] Fwd: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation

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

----------  Forwarded Message  ----------

Subject: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and 
Visualisation
Date: Monday 25 February 2008 15:46
From: "Jens Thomas j.m.h.thomas a dl.ac.uk" <own...@cc...>
To: "Langner, Karol M. -id#497-" <kar...@gm...>

Sent to CCL by: Jens Thomas [j.m.h.thomas],[dl.ac.uk]
Molecular Modelling: Tools, GUIs and Visualisation

11th - 13th March 2008

This is to announce a CCP1 meeting looking at graphical interfaces,
visualisation and tools for molecular modelling in general, but with the
focus towards electronic structure.

(...)

We already have speakers confirmed from projects including OpenBabel,
Avogadro, Molekel, Molpro, cclib, GaussSum, The CCP1GUI, GAMESS, and
GAMESS-UK.

(...)

-----------------------------------------------

Hi guys,

 Are you going to be speaking at that meeting, Noel?

- Karol

-- 
written by Karol Langner
Mon Feb 25 19:01:27 CET 2008

Re: [cclib-devel] Point-Group Symmetry Codes

[Geoffrey H. <ge...@ge...>]

On Nov 28, 2007, at 9:41 AM, Noel O'Boyle wrote:

> In GaussView there is a setting for how 'strict' the point group
> detection software is. Is there some similar 'epsilon' value you can
> set for Sergei's code?

Yes. There are a variety of options, including how many "optimization"  
steps you can make.

The problem seems to be in the initial recognition phase. I'm going to  
continue to play with it, but I'm worried when benzene shows up as Cs  
and it doesn't even find any plausible C2 axes or other mirror planes.

A Google search this morning did turn up some code in GAMGI, which  
I'll examine.

Cheers,
-Geoff

Re: [cclib-devel] Point-Group Symmetry Codes

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

In GaussView there is a setting for how 'strict' the point group
detection software is. Is there some similar 'epsilon' value you can
set for Sergei's code?

On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote:
> I was hoping that Sergei's code would do the job as this would be a
> really useful capability. My only suggestion is to trawl through known
> open source codes, e.g.:
>
> http://www.google.com/codesearch?q=C2v+D3h&hl=en&btnG=Search+Code
>
> :-/
>
> Noel
>
> On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote:
> > Geoff is interested in point group symmetry code...
> >
> > ---------- Forwarded message ----------
> > From: Geoffrey Hutchison <ge...@pi...>
> >
> > Hi guys,
> >
> > I've been toying around with the point group symmetry code that was
> > GPL'ed by Dr. Serguei Patchkovskii
> > http://www.cobalt.chem.ucalgary.ca/ps/symmetry/
> >
> > I've found that while it looks like it has great capabilities (strange
> > higher-order symmetry like C7 and S7 rotations), it doesn't work very
> > well. For example, I drew benzene in Avogadro, ran an optimization and
> > saved it. The molecule is in the Z=0 plane, but slightly out of center
> > and not aligned to the X or Y axes. (In short, a typical aromatic
> > benzene with equal bond lengths.)
> >
> > All it finds is the mirror plane along Z=0.
> >
> > So I'm curious to ask you two: as part of the cclib work, whether
> > you've come across some *robust* point group symmetry recognition code?
> >
> > Thanks,
> > -Geoff
> >
> > -------------------------------------------
> > Geoff Hutchison
> > Assistant Professor
> > University of Pittsburgh, Department of Chemistry
> > 219 Parkman Avenue
> > Pittsburgh, PA 15260
> >
>

Re: [cclib-devel] Point-Group Symmetry Codes

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

I was hoping that Sergei's code would do the job as this would be a
really useful capability. My only suggestion is to trawl through known
open source codes, e.g.:

http://www.google.com/codesearch?q=C2v+D3h&hl=en&btnG=Search+Code

:-/

Noel

On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote:
> Geoff is interested in point group symmetry code...
>
> ---------- Forwarded message ----------
> From: Geoffrey Hutchison <ge...@pi...>
>
> Hi guys,
>
> I've been toying around with the point group symmetry code that was
> GPL'ed by Dr. Serguei Patchkovskii
> http://www.cobalt.chem.ucalgary.ca/ps/symmetry/
>
> I've found that while it looks like it has great capabilities (strange
> higher-order symmetry like C7 and S7 rotations), it doesn't work very
> well. For example, I drew benzene in Avogadro, ran an optimization and
> saved it. The molecule is in the Z=0 plane, but slightly out of center
> and not aligned to the X or Y axes. (In short, a typical aromatic
> benzene with equal bond lengths.)
>
> All it finds is the mirror plane along Z=0.
>
> So I'm curious to ask you two: as part of the cclib work, whether
> you've come across some *robust* point group symmetry recognition code?
>
> Thanks,
> -Geoff
>
> -------------------------------------------
> Geoff Hutchison
> Assistant Professor
> University of Pittsburgh, Department of Chemistry
> 219 Parkman Avenue
> Pittsburgh, PA 15260
>