cclib-users — Help and support for cclib users

Re: [cclib-users] Forces from gaussian job (feature request)

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

In that case, for sure we'd welcome the code.

- Noel

2009/5/16 Hugh Chaffey-Millar <hug...@ch...>:
> On Friday 15 May 2009 15:01:09 Noel O'Boyle wrote:
>> Looking at http://cclib.sourceforge.net/wiki/index.php/Parsed_Data,
>> there's the hessian. Is this what you're looking for?
>
> No. I'm looking for the vector dE/dx, i.e. the first derivatives of the energy
> with respect to atomic coordinates.
>
> Regard
> Hugh
>

Re: [cclib-users] Forces from gaussian job (feature request)

[Hugh Chaffey-M. <hug...@ch...>]

On Friday 15 May 2009 15:01:09 Noel O'Boyle wrote:
> Looking at http://cclib.sourceforge.net/wiki/index.php/Parsed_Data,
> there's the hessian. Is this what you're looking for?

No. I'm looking for the vector dE/dx, i.e. the first derivatives of the energy 
with respect to atomic coordinates.

Regard
Hugh

Re: [cclib-users] Forces from gaussian job (feature request)

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

Looking at http://cclib.sourceforge.net/wiki/index.php/Parsed_Data,
there's the hessian. Is this what you're looking for?

- Noel

2009/5/15 Hugh Chaffey-Millar <hug...@ch...>:
> Dear CCLib
>
> as far as I can tell, there is no way to extract the forces from a Gaussian
> log file from a force calculation; that is, from a job with the "force"
> keyword.
>
> Is this correct?
>
> If so, I would happily code this feature (for gaussian).
>
> Regards
> Hugh Chaffey-Millar
>
> --
> _______________________________
> Hugh Chaffey-Millar, Dr.
> Alexander von Humboldt Fellow
>
> Technische Universität München
> Fachgebiet Molekulare Katalyse
> Department Chemie
>
> Lichtenbergstr. 4
> 85747 Garching b. München
>
> Tel: +49 (0)89 289 13072
> hug...@ch...
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables
> unlimited royalty-free distribution of the report engine
> for externally facing server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Forces from gaussian job (feature request)

[Hugh Chaffey-M. <hug...@ch...>]

Dear CCLib

as far as I can tell, there is no way to extract the forces from a Gaussian 
log file from a force calculation; that is, from a job with the "force" 
keyword.

Is this correct?

If so, I would happily code this feature (for gaussian).

Regards
Hugh Chaffey-Millar

-- 
_______________________________
Hugh Chaffey-Millar, Dr.
Alexander von Humboldt Fellow

Technische Universität München
Fachgebiet Molekulare Katalyse
Department Chemie

Lichtenbergstr. 4
85747 Garching b. München

Tel: +49 (0)89 289 13072
hug...@ch...

[cclib-users] 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

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

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

I've been invited to give a talk about cclib and GaussSum among other
topics at the meeting described below, so if you can make it be sure
to say hello.

Noel

---------- Forwarded message ----------
From: Jens Thomas <j.m...@dl...>
Date: 26 Feb 2008 11:09
Subject: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation
To: Openbabel-discuss List <ope...@li...>


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.

 There are a large number of graphical interfaces and associated tools
 for working with electronic structure and molecular mechanics/dynamics
 codes in use in the computational chemistry community today. Many of
 these tools do similar jobs, but all have their own specialities,
 strengths and weaknesses.

 The aim of this meeting is to bring together the developers and users of
 these tools to:

 - raise awareness of the existing software tools and capabilities.
 - allow users to give the developers feedback on what is needed and
 which areas are not being sufficiently covered.
 - explore novel ways of visualising molecular data and other tasks.
 - provide an opportunity to discuss collaborations.

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

 The meeting will be held at the Holiday Inn in Runcorn, Cheshire, from
 11th-13th March (starting after lunch on the 11th and running through to
 lunch on the 13th). The afternoon of the 13th will be reserved for
 developers to run tutorials/practicals at Daresbury Laboratory.

 We still have some slots available for speakers, so if you are a code
 developer or user, and would be interested in speaking, then please
 contact: j.m...@dl...

 For registration information, please visit the meeting webpage at:

 http://www.ccp1.ac.uk/chemtoolsmeet

 We look forward to seeing you in March!

 --
 ===================================================================
 Jens Thomas,                email:  j.m...@dl...
 STFC Daresbury Lab,         tel:    +44-1925-603849
 Warrington,                 fax:    +44-1925-603634
 WA4 4AD,  UK.               http:   http://www.cse.scitech.ac.uk
 ===================================================================


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Re: [cclib-users] Problem with installation

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

On Tuesday 11 December 2007 12:14, Jean-Didier Mar=C3=A9chal wrote:
> Hi,
>
> Just a mistake: root =3D route:-)
>
> Cheers,
> JD

I see :)

=2D-=20
written by Karol Langner
wto, 11 gru 2007, 19:15:26 CET

Re: [cclib-users] Problem with installation

[Jean-Didier <jea...@ua...>]

Hi,

Just a mistake: root = route:-)

Cheers,
JD

On Mon, 2007-12-10 at 23:18 +0100, Karol Langner wrote:
> On Friday 30 November 2007 14:53, Noel O'Boyle wrote:
> > On 30/11/2007, Jean-Didier Maréchal <jea...@ua...> wrote:
> > > Well, I see that I could have done in four lines what I managed with
> > > twice more.
> > >
> > > One question though, is there any possibility to collect the root from
> > > the gaussian output?
> >
> > I'm afraid not. This seems to be true for both cclib and openbabel.
> 
> Hi jean and Noel. I think I'm missing part of the discussion here. What do yo 
> mean by 'root'?
> 
> Cheer,
> Karol
> 

Re: [cclib-users] Problem with installation

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

On 11/12/2007, Karol Langner <kar...@kn...> wrote:
> On Friday 30 November 2007 14:53, Noel O'Boyle wrote:
> > On 30/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrot=
e:
> > > Well, I see that I could have done in four lines what I managed with
> > > twice more.
> > >
> > > One question though, is there any possibility to collect the root fro=
m
> > > the gaussian output?
> >
> > I'm afraid not. This seems to be true for both cclib and openbabel.
>
> Hi jean and Noel. I think I'm missing part of the discussion here. What d=
o yo
> mean by 'root'?

It's just a typo: it should be "route", what Gaussian calls the
section at the start with the keywords.

> Cheer,
> Karol
>
> --
> written by Karol Langner
> pon, 10 gru 2007, 23:17:20 CET
>

Re: [cclib-users] Problem with installation

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

On Friday 30 November 2007 14:53, Noel O'Boyle wrote:
> On 30/11/2007, Jean-Didier Mar=C3=A9chal <jea...@ua...> wro=
te:
> > Well, I see that I could have done in four lines what I managed with
> > twice more.
> >
> > One question though, is there any possibility to collect the root from
> > the gaussian output?
>
> I'm afraid not. This seems to be true for both cclib and openbabel.

Hi jean and Noel. I think I'm missing part of the discussion here. What do =
yo=20
mean by 'root'?

Cheer,
Karol

=2D-=20
written by Karol Langner
pon, 10 gru 2007, 23:17:20 CET

Re: [cclib-users] Problem with installation

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

On 30/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrote:
> Well, I see that I could have done in four lines what I managed with
> twice more.
>
> One question though, is there any possibility to collect the root from
> the gaussian output?

I'm afraid not. This seems to be true for both cclib and openbabel.

> I'd like to generate an input file recovering the optimized geometry and
> the keywords.
>
> All the best,
> JD
>
>
> On Fri, 2007-11-30 at 10:08 +0000, Noel O'Boyle wrote:
> > On 29/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrot=
e:
> > > > Glad to hear. Let us know if you have any problems; also, we are
> > > > interested to know what you are using cclib for...
> > >
> > > I have different  projects I hope cclib to help me with (Well, once
I'll
> > > have understood how to use it (:-)). To get use to your module, the
> > > first thing I want to do is to generate gaussian inputs extracting th=
e
> > > optimized geometry from a previous gaussian output. I know that sound=
s
> > > ruin but truth is that I work on systems with a lot of conformations
and
> > > which size oblige me to optimize in gas phase. So, I want to perform
> > > post calculations separately afterward. Scripting the generation of
this
> > > inputs will be of great help for me.
> > >
> > > Thanks a lot,
> > >
> > > JD
> >
> > Although cclib can help you with this, our functionality overlaps a
> > little bit with another Python library, OpenBabel.
> >
> > Here is an example of reading the output file with cclib, and creating
> > a Gaussian input file with OpenBabel:
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> > import pybel
> >
> > from cclib.parser import ccopen
> > from cclib.bridge import makeopenbabel
> >
> > t =3D ccopen("dvb_gopt.out")
> > d =3D t.parse()
> >
> > obmol =3D makeopenbabel(d.atomcoords[-1], d.atomnos, d.charge, d.mult)
> > mol =3D pybel.Molecule(obmol)
> > print mol.write("gau")
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >
> > However, OpenBabel can also read Gaussian output files, so in this
> > case it's easier just to do:
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> > import pybel
> >
> > mol =3D pybel.readfile("g03", "dvb_gopt.out").next()
> > print mol.write("gau")
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >
> > cclib has the advantage of giving you access to lots of other
> > information, it can read output files from more computational
> > chemistry packages, and it provides implementations of several
> > computational chemistry algorithms. OpenBabel can read and write a
> > very large number of molecular file formats, and provides access to
> > several algorithms for manipulating chemical structures.
> >
> > It's easy to interconvert data from one to the other, so you can
> > easily use them both.
> >
> > Noel
>
>

Re: [cclib-users] Problem with installation

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

On 29/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrote:
> > Glad to hear. Let us know if you have any problems; also, we are
> > interested to know what you are using cclib for...
>
> I have different  projects I hope cclib to help me with (Well, once I'll
> have understood how to use it (:-)). To get use to your module, the
> first thing I want to do is to generate gaussian inputs extracting the
> optimized geometry from a previous gaussian output. I know that sounds
> ruin but truth is that I work on systems with a lot of conformations and
> which size oblige me to optimize in gas phase. So, I want to perform
> post calculations separately afterward. Scripting the generation of this
> inputs will be of great help for me.
>
> Thanks a lot,
>
> JD

Although cclib can help you with this, our functionality overlaps a
little bit with another Python library, OpenBabel.

Here is an example of reading the output file with cclib, and creating
a Gaussian input file with OpenBabel:
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
import pybel

from cclib.parser import ccopen
from cclib.bridge import makeopenbabel

t =3D ccopen("dvb_gopt.out")
d =3D t.parse()

obmol =3D makeopenbabel(d.atomcoords[-1], d.atomnos, d.charge, d.mult)
mol =3D pybel.Molecule(obmol)
print mol.write("gau")
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

However, OpenBabel can also read Gaussian output files, so in this
case it's easier just to do:
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
import pybel

mol =3D pybel.readfile("g03", "dvb_gopt.out").next()
print mol.write("gau")
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

cclib has the advantage of giving you access to lots of other
information, it can read output files from more computational
chemistry packages, and it provides implementations of several
computational chemistry algorithms. OpenBabel can read and write a
very large number of molecular file formats, and provides access to
several algorithms for manipulating chemical structures.

It's easy to interconvert data from one to the other, so you can
easily use them both.

Noel

Re: [cclib-users] Problem with installation

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

On 28/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrote:
> Hi,
>
> I found the problem. As you mention in your e-mail, things should have
> been setup correctly. So, I began to scratch on permissions and python
> variables.
>
> I found that my user does not have the PYTHONPATH variable defined at
> all and that without this python was not even able to import the os
> module! (I guess this problem comes from the recent creation of a root
> user on my ubuntu box; I am sure that I did not have any problem with
> python before that)

As I understand, Ubuntu does not need a root user. Just prepend "sudo"
to the command you wish to run as root, and when prompted for the
password use "root".

> Anyway, after generating the correct PYTHONPATH I managed to have cclib
> working!

Glad to hear. Let us know if you have any problems; also, we are
interested to know what you are using cclib for...

> Thanks for the e-mail,
>
> JD
>
> On Wed, 2007-11-28 at 19:50 +0200, Noel O'Boyle wrote:
> > On 28/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrot=
e:
> > > Hello,
> > >
> > > I have been stuck with the installation of cclib on unbuntu 7.10 for =
few
> > > days now, and I wonder what I am doing wrong. Initially, I had proble=
ms
> > > with python and in particular with the numeric module. Being solved
> > > this, I am stuck once again.
> > >
> > > Basically, when I run the -  python setup.py build - command, I
> > > systematically receive the following answer:
> > >
> > >         'import site' failed; use -v for traceback
> > >         Traceback (most recent call last):
> > >           File "setup.py", line 56, in ?
> > >             setup_cclib()
> > >           File "setup.py", line 29, in setup_cclib
> > >             from distutils.core import setup
> > >         ImportError: No module named distutils.core
> >
> > Very strange. If you installed Python using your package manager, then
> > there would be no problem finding "distutils.core" which a central
> > part of the Python installation on Ubuntu 7.10. As you can see from
> > the following search for "core.py", it's included in the "python2.4"
> > package:
> > http://packages.ubuntu.com/cgi-bin/search_contents.pl?word=3Dcore.py&se=
archmode=3Dsearchfiles&case=3Dinsensitive&version=3Dgutsy&arch=3Di386
> >
> > You should not have had any problems with numeric either. We have
> > switched to numpy, which is available in the Ubuntu distribution also.
> >
> > Hope this helps. Our installation instructions are at the following add=
ress:
> > http://cclib.sourceforge.net/wiki/index.php/Install
> >
> > Noel
> >
> > > What do I miss?
> > >
> > > Cheers
> > > JD
> > >
> > >
> > >         --
> > >         Dr. Jean-Didier Mar=E9chal
> > >         Assistant Professor
> > >         Computational Bioorganic and Bioinorganic Chemistry @Transmet
> > >         Unitat de Qu=EDmica F=EDsica
> > >         Departament de Qu=EDmica
> > >         Universitat Aut=F2noma de Barcelona
> > >         08193 Bellaterra, Spain
> > >         Tel: +34.(0)1935814936
> > >         Fax: +34.(0)1935812920
> > >         e-mail:jea...@ua...
> > >
> > >
> > >
>
>

Re: [cclib-users] Problem with installation

[Jean-Didier <jea...@ua...>]

Hi,

I found the problem. As you mention in your e-mail, things should have
been setup correctly. So, I began to scratch on permissions and python
variables. 

I found that my user does not have the PYTHONPATH variable defined at
all and that without this python was not even able to import the os
module! (I guess this problem comes from the recent creation of a root
user on my ubuntu box; I am sure that I did not have any problem with
python before that) 

Anyway, after generating the correct PYTHONPATH I managed to have cclib
working! 

Thanks for the e-mail,

JD

On Wed, 2007-11-28 at 19:50 +0200, Noel O'Boyle wrote:
> On 28/11/2007, Jean-Didier Maréchal <jea...@ua...> wrote:
> > Hello,
> >
> > I have been stuck with the installation of cclib on unbuntu 7.10 for few
> > days now, and I wonder what I am doing wrong. Initially, I had problems
> > with python and in particular with the numeric module. Being solved
> > this, I am stuck once again.
> >
> > Basically, when I run the -  python setup.py build - command, I
> > systematically receive the following answer:
> >
> >         'import site' failed; use -v for traceback
> >         Traceback (most recent call last):
> >           File "setup.py", line 56, in ?
> >             setup_cclib()
> >           File "setup.py", line 29, in setup_cclib
> >             from distutils.core import setup
> >         ImportError: No module named distutils.core
> 
> Very strange. If you installed Python using your package manager, then
> there would be no problem finding "distutils.core" which a central
> part of the Python installation on Ubuntu 7.10. As you can see from
> the following search for "core.py", it's included in the "python2.4"
> package:
> http://packages.ubuntu.com/cgi-bin/search_contents.pl?word=core.py&searchmode=searchfiles&case=insensitive&version=gutsy&arch=i386
> 
> You should not have had any problems with numeric either. We have
> switched to numpy, which is available in the Ubuntu distribution also.
> 
> Hope this helps. Our installation instructions are at the following address:
> http://cclib.sourceforge.net/wiki/index.php/Install
> 
> Noel
> 
> > What do I miss?
> >
> > Cheers
> > JD
> >
> >
> >         --
> >         Dr. Jean-Didier Maréchal
> >         Assistant Professor
> >         Computational 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...
> >
> >
> >

Re: [cclib-users] Problem with installation

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

On 28/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrote:
> Hello,
>
> I have been stuck with the installation of cclib on unbuntu 7.10 for few
> days now, and I wonder what I am doing wrong. Initially, I had problems
> with python and in particular with the numeric module. Being solved
> this, I am stuck once again.
>
> Basically, when I run the -  python setup.py build - command, I
> systematically receive the following answer:
>
>         'import site' failed; use -v for traceback
>         Traceback (most recent call last):
>           File "setup.py", line 56, in ?
>             setup_cclib()
>           File "setup.py", line 29, in setup_cclib
>             from distutils.core import setup
>         ImportError: No module named distutils.core

Very strange. If you installed Python using your package manager, then
there would be no problem finding "distutils.core" which a central
part of the Python installation on Ubuntu 7.10. As you can see from
the following search for "core.py", it's included in the "python2.4"
package:
http://packages.ubuntu.com/cgi-bin/search_contents.pl?word=3Dcore.py&search=
mode=3Dsearchfiles&case=3Dinsensitive&version=3Dgutsy&arch=3Di386

You should not have had any problems with numeric either. We have
switched to numpy, which is available in the Ubuntu distribution also.

Hope this helps. Our installation instructions are at the following address=
:
http://cclib.sourceforge.net/wiki/index.php/Install

Noel

> What do I miss?
>
> Cheers
> JD
>
>
>         --
>         Dr. Jean-Didier Mar=E9chal
>         Assistant Professor
>         Computational Bioorganic and Bioinorganic Chemistry @Transmet
>         Unitat de Qu=EDmica F=EDsica
>         Departament de Qu=EDmica
>         Universitat Aut=F2noma de Barcelona
>         08193 Bellaterra, Spain
>         Tel: +34.(0)1935814936
>         Fax: +34.(0)1935812920
>         e-mail:jea...@ua...
>
>
>

[cclib-users] ANN: cclib 0.8 now available for download

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

cclib 0.8 is now available for download from http://cclib.sf.net.

cclib is an open source library, written in Python, for parsing and
interpreting the results of computational chemistry packages. It
currently parses output files from ADF, GAMESS (US), GAMESS-UK,
Gaussian, Jaguar, Molpro and PC GAMESS.

Among other data, cclib extracts:

    * coordinates and energies
    * information about geometry optimization
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation

(For a complete list see http://cclib.sf.net/wiki/index.php/Parsed_Data).

cclib also provides some calculation methods for interpreting the
electronic properties of molecules using analyses such as:

    * Mulliken and Lowdin population analyses
    * Overlap population analysis
    * Calculation of Mayer's bond orders.

(For a complete list see
http://cclib.sf.net/wiki/index.php/Calculation_Methods).

For information on how to use cclib, see
      http://cclib.sf.net/wiki/index.php/Using_cclib.

If you need help, find a bug, want new features or have any questions,
please send an email to our mailing list:
	https://lists.sourceforge.net/lists/listinfo/cclib-users

Regards,

 The cclib development team

[cclib-users] ANN: cclib 0.8 beta now available for download

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

Dear cclib users,

The beta version of cclib 0.8 is now available for download from our
project page at:
http://sourceforge.net/project/showfiles.php?group_id=161285&package_id=181681&release_id=546598

The website is currently being updated for this release.

The changelog is as follows:

Features:
	* New parser: cclib can now parse Molpro files
	* Separation of parser and data objects: Parsed data is now returned
	as a ccData object that can be pickled, and converted to and from JSON
	* Parsers: multiple files can be parsed with one parse command
	* NumPy support: Dropped Numeric support in favour of NumPy
	* API addition: 'charge' for molecular charge
	* API addition: 'mult' for spin multiplicity
	* API addition: 'atombasis' for indices of atom orbitals on each atom
	* API addition: 'nocoeffs' for Natural Orbital (NO) coefficients
	* GAMESS-US parser: added 'etoscs' (CIS calculations)
	* Jaguar parser: added 'mpenergies' (LMP2 calcualtions)
	* Jaguar parser: added 'etenergies' and 'etoscs' (CIS calculations)
	* New method: Lowdin Population Analysis (LPA)
	* Tests: unittests can be run from the Python interpreter, and for
	a single parser; the number of "passed" tests is also counted and shown

Bugfixes:
	* Several parsing errors were fixed
	* Fixed some methods to work with different numbers of alpha and beta
	MO coefficients in mocoeffs (MPA, CSPA, OPA)

Regards,
    Noel on behalf of the cclib development team

Re: [cclib-users] How to use cclib

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

cclib is a Python library, so you need to write a Python script, for example:

from cclib import ccopen
p = ccopen("myoutputfile.log")
p.parse()
print p.atomcoords[0]

This program prints the atom coordinates of the first atom in the molecule.

Noel

On 11/10/2007, Alexis Otero Calvi <ao...@is...> wrote:
> Dear cclib user
> I am a new user of the code and I need help.
> How I can obtain the requested information to cclib?
> For example. How I can print the atom coordinates or the result of MPA.
>
> Thank you
> Alexis
>
>
>
>
> -------------------------------------------------------------------------
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Re: [cclib-users] How to use cclib

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

Hi Alexis,

There is a wiki for cclib. Specifically, you can find a tutorial at  
http://cclib.sourceforge.net/wiki/index.php/Using_cclib. Hopefully  
you find the information there useful.

Adam

On Oct 11, 2007, at 1:02 PM, Alexis Otero Calvi wrote:

> Dear cclib user
> I am a new user of the code and I need help.
> How I can obtain the requested information to cclib?
> For example. How I can print the atom coordinates or the result of  
> MPA.
>
> Thank you
> Alexis
>
>
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a  
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[cclib-users] How to use cclib

[Alexis O. C. <ao...@is...>]

Dear cclib user
I am a new user of the code and I need help.
How I can obtain the requested information to cclib?
For example. How I can print the atom coordinates or the result of MPA.

Thank you
Alexis

Re: [cclib-users] request: CDA in cclib 0.7

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

Hi Pradeep,

It looks like you are missing the overlap matrix in your output  
files. To do this in Gaussian, you need to use iop(3/33=1) for at  
least the calculation of the entire molecule. I don't remember if you  
need an overlap matrix for the fragments. Hope this helps,

Adam

On Sep 30, 2007, at 9:41 PM, venkata pradeep indrakanti wrote:

> Hi all,
> I am trying to analyze the electron donation interactions between  
> CO2 and TiO2. I have computed geometries of the cluster at the  
> B3LYP/6-31+G(d) level and also have single point calculations for  
> the (fixed geometry) individual fragments. When I run cda, I get  
> the following error:   
> ********************************************************************** 
> *************
> Traceback (most recent call last):
>  File "cda.py" line 31,in ?
>   cda.calculate([frag1,frag2])
>  File "c:\python24\Lib\site-packages\cclib\method\cda.py",line 82,  
> in calculate
>   donations[spin][i] += 2*occs * self.mocoeffs[spin][i,k] \
> AttributeError: 'CDA' object has no attribute 'fooverlaps'
> ********************************************************************** 
> *************
> I am a newbie to Python and so do not know how to fix this  
> (appropriate classes not loaded ?). I am attaching the longer  
> version of the output with this email. Can anyone kindly tell me  
> why I am getting this error ?
> Thanks,
> Pradeep
> p.s.
> The output files are simply single point calculations at the B3LYP/ 
> 6-31+G(d) level using the optimized cluster geometry.
> I run $ python cda.py A.out A1.out A2.out
> I used the following (modified) script: (from http:// 
> cclib.sourceforge.net/wiki/index.php/Charge_Decomposition_Analysis )
> from cclib.parser import ccopen
> from cclib.method import CDA
> import sys
> clus_name = sys.argv[1]
> f1_name = sys.argv[2]
> f2_name = sys.argv[3]
> #print "Molecule file name is:",clus_name
> #print f1_name
> #print f2_name
> molecule = ccopen(clus_name)
> frag1 = ccopen(f1_name)
> frag2 = ccopen(f2_name)
> molecule.parse()
> frag1.parse()
> frag2.parse()
> cda = CDA(molecule)
> cda.calculate([frag1, frag2])
> <log.txt>
> ---------------------------------------------------------------------- 
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[cclib-users] request: CDA in cclib 0.7

[venkata p. i. <vx...@ps...>]

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KioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKio=

[cclib-users] Investment Enquiry

[Mr. S. Hadi. <sal...@gm...>]

Dear Sir=2C
 
With deep appreciation of your esteem contact I got from your company=2C I wish to introduce myself=3B I am Mr=2E Salah =2EA=2E Hadi Citizen of Iraq=2E Actually I will like to invest in your company=2E I will like to know the procedures of non-citizen investors=2E In investments=2C you have to look for a good company that the safety environmental condition of the foreign investor is guaranteed=2C actually after reading through your web-site=2C I decided to contact you=2E

I will be very much more delighted if you can give me details about your company=2C I am also looking forward to read your reply soon so as to detail you my background of my investment programme and how much fund that I am intending to invest and also the area that I would like to invest it after good negotiation=2E 

Thanks very much for taking time to go through to my e-mail=2C I shall be glad to reserve this respect and opportunity for you=2C if you so desire=2C but do urge you to give the matter your immediate attention it deserves=2E Respond to my private email=3A salahahadi=40najaf=2Ecc =3Cmailto=3Asalahahadi=40najaf=2Ecc=3E

 Regards
 
Mr=2E  Salah A=2EHadi=2E

Re: [cclib-users] Bug in reading MO values

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

Hello Jerome,

Thanks for reporting this.

Can you send us a .zip file containing the input and output files for
this calculation? Please note that we only fix bugs for files that are
in the public domain. If you are not happy with this, perhaps you
could create an example file with the same problem...

Regards,
   Noel

On 04/07/07, Jer...@sa...
<Jer...@sa...> wrote:
> Dear CCLib developpers,
>
> I noticed a bug when reading a gaussian log file when the energy of the d=
eepest orbital cannot fit in the formated 9 char .
> Maybe this is due to the 2 iodines in this molecule (di-iodophenyl) or to=
 the Dgauss DZVP basis set used.
>
> Of course the bug occures by the python command :
> float("**********"), in Logfile.parse.float(), line 188 of logfileparser.=
py
>
> Here is an extract of the gaussian output.
>  The electronic state is 1-A.
>  Alpha  occ. eigenvalues -- ********************-176.38175-176.37760-165.=
76438
>  Alpha  occ. eigenvalues -- -165.76230-165.76225-165.76023-165.75813-165.=
75807
>  Alpha  occ. eigenvalues --  -35.82446 -35.82036 -31.33591 -31.33183 -31.=
33009
>
> Kind regards.
> --
> J=E9r=F4me Kieffer (PhD)
> Molecular modeling @ RIC
> Sanofi-Aventis Sisteron
> Tel: +33 (0)4.92.33.31.98
>
>
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> Download DB2 Express C - the FREE version of DB2 express and take
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> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Bug in reading MO values

[<Jer...@sa...>]

Dear CCLib developpers,

I noticed a bug when reading a gaussian log file when the energy of the =
deepest orbital cannot fit in the formated 9 char .
Maybe this is due to the 2 iodines in this molecule (di-iodophenyl) or =
to the Dgauss DZVP basis set used.

Of course the bug occures by the python command :=20
float("**********"), in Logfile.parse.float(), line 188 of =
logfileparser.py
=20
Here is an extract of the gaussian output.
 The electronic state is 1-A.
 Alpha  occ. eigenvalues -- =
********************-176.38175-176.37760-165.76438
 Alpha  occ. eigenvalues -- =
-165.76230-165.76225-165.76023-165.75813-165.75807
 Alpha  occ. eigenvalues --  -35.82446 -35.82036 -31.33591 -31.33183 =
-31.33009

Kind regards.
--=20
J=E9r=F4me Kieffer (PhD)
Molecular modeling @ RIC=20
Sanofi-Aventis Sisteron
Tel: +33 (0)4.92.33.31.98