cclib-devel — Developer's mailing list

Re: [cclib-devel] PBC in Gaussian09

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

There are no mocoeffs in the G09 file. There are in the G03 file, and
we appear to parse them.

- Noel

On 29 March 2010 17:39, Nuno A. G. Bandeira <nun...@is...> wrote:
> The previous one was run with G03 rev. E, this one is G09.
>
>
> --
> Nuno A. G. Bandeira, AMRSC
> Laboratoire de Chimie LR6
> Ecole Normale Superieure de Lyon
> 46, Allee d'Italie
> 69364 Lyon Cedex 07 - France
> http://cqb.fc.ul.pt/intheochem/nuno/
> --
>
>
>

Re: [cclib-devel] PBC in Gaussian09

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

Hi Nuno,

Your file does not contain molecular orbital coefficients.

- Noel

On 26 March 2010 16:19, Nuno A. G. Bandeira <nun...@is...> wrote:
> Dear developers,
>
> CClib does not correctly parse the information from G09 PBC calculations.
> The error message goes :
>
>>>> analysis.calculate()
> [MPA Gaussian log file /cygdrive/c/neoprene.out ERROR] Missing mocoeffs
> False
>>>>
>
> So attached is the same tutorial file they have in the manual.
>
> Also can I ask how can I update the cclib libraries in QMForge in Windows ?
> The program is immensely outdated but it would suit me for my purposes
> rather than using cumbersome command lines.
>
> I've tried to simply replace the cclib contents in the library.zip file but
> no luck so far it seems.
>
>
> --
> Nuno A. G. Bandeira, AMRSC
> Laboratoire de Chimie LR6
> Ecole Normale Superieure de Lyon
> 46, Allee d'Italie
> 69364 Lyon Cedex 07 - France
> http://cqb.fc.ul.pt/intheochem/nuno/
> --
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

Re: [cclib-devel] [POSSIBLE VIRUS:###] PBC in Gaussian09

[Adam T. <ate...@gm...>]

 Hi Nuno (and others),

I'm the (busy? bad?) maintainer of QMForge. Unfortunately, I haven't
figured out an easy way to upgrade its cclib libraries without
completely rebuilding the binary Windows distribution. Which is
complicated because last time I was working on QMForge (yes, years
ago), I was porting to a newer version of Qt (or PyQt) which had
changed enough that it actually broke parts of QMForge.

If you are feeling adventurous, you can download and install the most
recent versions of PyQt, PyOpenGL, openbabel, cclib, and the source
distribution of QMForge. I can try to troubleshoot any of your
problems via email. I'll also try to move working on cclib/QMForge to
the top of my list of things to do, but it definitely won't be ready
for at least a couple of weeks.

Sorry for the trouble,

Adam

On Fri, Mar 26, 2010 at 8:19 AM, Nuno A. G. Bandeira
<nun...@is...> wrote:
> Dear developers,
>
> CClib does not correctly parse the information from G09 PBC calculations.
> The error message goes :
>
>>>> analysis.calculate()
> [MPA Gaussian log file /cygdrive/c/neoprene.out ERROR] Missing mocoeffs
> False
>>>>
>
> So attached is the same tutorial file they have in the manual.
>
> Also can I ask how can I update the cclib libraries in QMForge in Windows ?
> The program is immensely outdated but it would suit me for my purposes
> rather than using cumbersome command lines.
>
> I've tried to simply replace the cclib contents in the library.zip file but
> no luck so far it seems.
>
>
> --
> Nuno A. G. Bandeira, AMRSC
> Laboratoire de Chimie LR6
> Ecole Normale Superieure de Lyon
> 46, Allee d'Italie
> 69364 Lyon Cedex 07 - France
> http://cqb.fc.ul.pt/intheochem/nuno/
> --
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

[cclib-devel] ANN: cclib 1.0 now available

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

Hello everyone,

cclib 1.0 is now available for download from http://cclib.sf.net. It's
been some time since the last release, so we recommend you to upgrade
to this version.

Changes since cclib-0.9:

Features:
	* Handle PBC calculations from Gaussian
	* Updates to handle Gaussian09
	* Support TDDFT calculations from ADF
	* A number of improvements for GAMESS support
	* ccopen now supports any file-like object with a read() method, so it
	can parse across HTTP

Bugfixes:
	* Many many additional files parsed thanks to bugs reported by users

Remember to cite cclib if you use it to obtain results for
publication. This encourages us to keep doing what we do.

Regards,
   The cclib development team

Re: [cclib-devel] [cclib-users] GAMESS-US and mpenergies

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

This is now fixed. Thanks again. Keep sending any failures.

- Noel

On 6 March 2010 13:13, Paulo E. Abreu <pau...@ci...> wrote:
> Hello,
> There is still a problem with the mp2energies for non-restricted MP2
> calculation.
> I have attached files (which I put in the public domain) of example
> calculations:
> N2-RMP2.out (RHF MP2 calculation) is parsed correctly
> N2-UMP2.out (UHF MP2 calculation) is not parsed correctly
> N2-ROMP2.out (ROHF MP2 calculation) is not parsed correctly
> Hope this helps ironing these minor bugs.
> All the best,
> Paulo
>
> On Thu, Mar 4, 2010 at 3:49 PM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> This is now fixed in our development version. I'd appreciate if you
>> could test it and let us know if it's working fine for you.
>>
>> - Noel
>>
>> On 25 February 2010 15:47, Paulo E. Abreu <pau...@ci...> wrote:
>> > Hiya Noel,
>> > Attached you will find a MP2 calculation on water. Parsing this file
>> > with
>> > cclib I get
>> > [GAMESS h2o-mp2.out INFO] Creating attribute atomcoords[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute atomnos[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute gbasis[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute nbasis: 19
>> > [GAMESS h2o-mp2.out INFO] Creating attribute charge: 0
>> > [GAMESS h2o-mp2.out INFO] Creating attribute mult: 1
>> > [GAMESS h2o-mp2.out INFO] Creating attribute homos[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute natom: 3
>> > [GAMESS h2o-mp2.out INFO] Creating attribute scftargets[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute scfvalues[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute scfenergies[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute moenergies[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute mosyms[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute nmo: 19
>> > [GAMESS h2o-mp2.out INFO] Creating attribute mocoeffs[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute atombasis[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute aonames[]
>> > [GAMESS h2o-mp2.out INFO] Creating attribute coreelectrons[]
>> > No mpenergies are defined.
>> > And yes you can distribute this file.
>> > Hope this helps.
>> > Paulo
>> >
>> > On Thu, Feb 25, 2010 at 3:34 PM, Noel O'Boyle <bao...@gm...>
>> > wrote:
>> >>
>> >> Hello Paulo,
>> >>
>> >> Sounds like a bug.
>> >>
>> >> Could you provide us with a public domain test file? That is, this
>> >> should be a test file which you are happy for us to share with the
>> >> world.
>> >>
>> >> - Noel
>> >>
>> >> On 25 February 2010 12:16, Paulo E. Abreu <pau...@ci...> wrote:
>> >> > Hello,
>> >> > I have been using cclib for my parsers and just noticed something odd
>> >> > about
>> >> > GAMESS-US files with MP2 calculations.
>> >> > According to http://cclib.sourceforge.net/wiki/index.php/Parsed_Data
>> >> > and
>> >> >  http://cclib.sourceforge.net/wiki/index.php/Mpenergies
>> >> > this is available for GAMESS-US output files. The problem is that I
>> >> > cannot
>> >> > access this information. The logging after parsing the file
>> >> > does not show any mpenergies and consequently when I try to use it I
>> >> > get
>> >> > an
>> >> > error
>> >> > AttributeError: 'ccData' object has no attribute 'mpenergies'
>> >> > Is there something which I am missing here ?
>> >> > ===begin code snippet
>> >> > myfile = ccopen("mp2.out")
>> >> > data = myfile.parse()
>> >> > print data.mpenergies
>> >> > ===end code snippet
>> >> > Thanks a lot
>> >> > --
>> >> > Paulo E. Abreu
>> >> > Professor Auxiliar
>> >> > Departamento de Química
>> >> > Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Download Intel&#174; Parallel Studio Eval
>> >> > Try the new software tools for yourself. Speed compiling, find bugs
>> >> > proactively, and fine-tune applications for parallel performance.
>> >> > See why Intel Parallel Studio got high marks during beta.
>> >> > http://p.sf.net/sfu/intel-sw-dev
>> >> > _______________________________________________
>> >> > cclib-users mailing list
>> >> > ccl...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >> >
>> >> >
>> >
>> >
>> >
>> > --
>> > Paulo E. Abreu
>> > Professor Auxiliar
>> > Departamento de Química
>> > Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>> >
>
>
>
> --
> Paulo E. Abreu
> Professor Auxiliar
> Departamento de Química
> Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>

[cclib-devel] Fwd: [cclib-users] cclib-0.91 bug Gaussian parser does not parse Vibsyms correctly if T symm

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

---------- Forwarded message ----------
From: Klemens Noga <kn...@ch...>
Date: 5 March 2010 09:48
Subject: Re: [cclib-users] cclib-0.91 bug Gaussian parser does not
parse  Vibsyms correctly if T symm
To: Noel O'Boyle <bao...@gm...>


Dear Noel,

Feel free to place those files in the public domain.

Best regards,

Klemens

On 5 Mar 2010, at 10:39, Noel O'Boyle wrote:

> Hello Klemens,
>
> Thanks for letting us know. To fix bugs we need public domain test
> files - are you happy to place your attached files in the public
> domain? If not, we'd appreciate if you could generate some small test
> files that reproduce the problem.
>
> I've leave the others to discuss Turbomole.
>
> - Noel
>
> On 5 March 2010 07:32, Klemens Noga <kn...@ch...> wrote:
>>
>> Dear all,
>>
>> My name is Klemens Noga and I'm PhD student in Theoretical Chemistry at
>> Jagiellonian University in Krakow, Poland. I've started using cclib to parse
>> data from GAMESS and Gaussian output files and I probably found bug. When
>> there are vibrations with T symmetry they aren't parsed into vibsyms list
>> correctly. You could check it in attached example files. Is there any simple
>> solution?
>> Secondly, I'm interested in parsing data from Turbomole outputs. I've heard
>> that cclib development team is working at this issue but i've found only
>> very old information and I'm curious about progress.
>>
>> Best regads,
>>
>> Klemens
>>
>>
>>
>>
>>
>> Klemens Noga
>> Ph.D. student
>> Department of Theoretical Chemistry
>> Faculty of Chemistry, Jagiellonian University
>> Ingardena st. 3, 30-060 Krakow, Poland
>> tel. +48-12-6632023
>> e.mail: kn...@ch...
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>

Klemens Noga
Ph.D. student
Department of Theoretical Chemistry
Faculty of Chemistry, Jagiellonian University
Ingardena st. 3, 30-060 Krakow, Poland
tel. +48-12-6632023
e.mail: kn...@ch...

[cclib-devel] cclib 1.0 this weekend

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

Dear Adam and Karol,

It's been 18 months or so since the last cclib release, and so it's
time to get out another one. I know Adam's working on some new
features on a branch, and I still have to integrate a patch sent by a
user, so we'll have another release in a month or two. But right now,
I'd appreciate if you could check the cclib-1.0b release on
SourceForge and make any updates to the CHANGELOG etc that you feel
necessary.

- Noel

Re: [cclib-devel] [cclib-users] GAMESS-US and mpenergies

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

This is now fixed in our development version. I'd appreciate if you
could test it and let us know if it's working fine for you.

- Noel

On 25 February 2010 15:47, Paulo E. Abreu <pau...@ci...> wrote:
> Hiya Noel,
> Attached you will find a MP2 calculation on water. Parsing this file with
> cclib I get
> [GAMESS h2o-mp2.out INFO] Creating attribute atomcoords[]
> [GAMESS h2o-mp2.out INFO] Creating attribute atomnos[]
> [GAMESS h2o-mp2.out INFO] Creating attribute gbasis[]
> [GAMESS h2o-mp2.out INFO] Creating attribute nbasis: 19
> [GAMESS h2o-mp2.out INFO] Creating attribute charge: 0
> [GAMESS h2o-mp2.out INFO] Creating attribute mult: 1
> [GAMESS h2o-mp2.out INFO] Creating attribute homos[]
> [GAMESS h2o-mp2.out INFO] Creating attribute natom: 3
> [GAMESS h2o-mp2.out INFO] Creating attribute scftargets[]
> [GAMESS h2o-mp2.out INFO] Creating attribute scfvalues[]
> [GAMESS h2o-mp2.out INFO] Creating attribute scfenergies[]
> [GAMESS h2o-mp2.out INFO] Creating attribute moenergies[]
> [GAMESS h2o-mp2.out INFO] Creating attribute mosyms[]
> [GAMESS h2o-mp2.out INFO] Creating attribute nmo: 19
> [GAMESS h2o-mp2.out INFO] Creating attribute mocoeffs[]
> [GAMESS h2o-mp2.out INFO] Creating attribute atombasis[]
> [GAMESS h2o-mp2.out INFO] Creating attribute aonames[]
> [GAMESS h2o-mp2.out INFO] Creating attribute coreelectrons[]
> No mpenergies are defined.
> And yes you can distribute this file.
> Hope this helps.
> Paulo
>
> On Thu, Feb 25, 2010 at 3:34 PM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> Hello Paulo,
>>
>> Sounds like a bug.
>>
>> Could you provide us with a public domain test file? That is, this
>> should be a test file which you are happy for us to share with the
>> world.
>>
>> - Noel
>>
>> On 25 February 2010 12:16, Paulo E. Abreu <pau...@ci...> wrote:
>> > Hello,
>> > I have been using cclib for my parsers and just noticed something odd
>> > about
>> > GAMESS-US files with MP2 calculations.
>> > According to http://cclib.sourceforge.net/wiki/index.php/Parsed_Data and
>> >  http://cclib.sourceforge.net/wiki/index.php/Mpenergies
>> > this is available for GAMESS-US output files. The problem is that I
>> > cannot
>> > access this information. The logging after parsing the file
>> > does not show any mpenergies and consequently when I try to use it I get
>> > an
>> > error
>> > AttributeError: 'ccData' object has no attribute 'mpenergies'
>> > Is there something which I am missing here ?
>> > ===begin code snippet
>> > myfile = ccopen("mp2.out")
>> > data = myfile.parse()
>> > print data.mpenergies
>> > ===end code snippet
>> > Thanks a lot
>> > --
>> > Paulo E. Abreu
>> > Professor Auxiliar
>> > Departamento de Química
>> > Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Download Intel&#174; Parallel Studio Eval
>> > Try the new software tools for yourself. Speed compiling, find bugs
>> > proactively, and fine-tune applications for parallel performance.
>> > See why Intel Parallel Studio got high marks during beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>> >
>
>
>
> --
> Paulo E. Abreu
> Professor Auxiliar
> Departamento de Química
> Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>