Re: [cclib-devel] Modifications to cclib 1.0

[Karol M. L. <km...@mm...>]

Hi!

Great. I added the file to our regression suite. I used the parts of your 
patch that fix scfenergies and homos, so that the regression parses 
correctly.

As far as adding new attributes and the MOPAC parser, I suppose we need to 
discuss that a bit more. Basically three issues I see here:
1) Do we want to add the MOPAC parser now? Probably should be as a separate 
branch.
2) Do we add the molmass attribute? Perhaps it would be more usefull to add an 
atomicmass attribute; more information and can be easily summed.
3) Do we want to add the rotation constants and symmetries now? I don't know 
if and how these things are printed in other programs (GAMESS, ADF).

Thanks again for the contribution,
Karol

On Tuesday 06 April 2010 22:08:06 Gregory Magoon wrote:
> 1. I have no objections to your use of the Gaussian log file.
>
> 2. I use the rotational constants as part of the rotational partition
> function for computing gas-phase thermodynamic quantities (entropy,
> enthalpy, heat capacity). I suppose I could instead calculate the moments
> of inertia based on the atomic coordinates and masses, but it is easier to
> just read in the result that Gaussian/MOPAC calculates. (For rotational
> symmetry number, I actually don't end up using the value from the Gaussian
> log file since it is often underestimated by Gaussian...I have instead been
> using a program called SYMMETRY which allows point group calculation within
> a user-specified tolerance: http://www.cobalt.chem.ucalgary.ca/ps/symmetry/
> ).
>
> 3. I have written some Python scripts that provide an interface between
> the Java
> code and cclib (I haven't included them in the public version of RMG yet).
> The Python scripts are executed from the Java code using
> Runtime.getRuntime().exec() and the Python script produces output read in
> by the Java code in a particular format. I have the Java code interface
> with RDKit
> in a similar way. (For what it's worth, there is also a Python version
> of RMG in
> development: http://github.com/GreenGroup/RMG-Py )
>
> Greg
>
> Quoting Noel O'Boyle <bao...@gm...>:
> > Thanks for the patch Greg and the positive comments.
> >
> > We'll look into integrating this as soon as possible - in particular,
> > it would be great to beef up our MOPAC support. We'll probably have
> > more questions later but right now, I've got three that spring to
> > mind:
> > (1) Are you happy to place the attached log file in the public domain?
> > (This is a requirement for our test suite)
> > (2) Why are you interested in parsing the rotational data?
> > (3) RMG looks like a nice project, but how are you using cclib given
> > that it's a Java/FORTRAN project?
> >
> > - Noel
> >
> > On 6 April 2010 19:51, Gregory Magoon <gm...@mi...> wrote:
> >> Hello cclib developers,
> >>  I've recently started to use cclib with the reaction mechanism
> >> generation software that I work on (http://rmg.sourceforge.net). I
> >> figured I would pass along some of the modifications I have made to
> >> cclib (see the attached .gitpatch file; these assume v1.0 as the
> >> starting point) in case they could be
> >> of benefit to you or other users.
> >> The modifications include:
> >> 1. Fixed (or at least partially fixed) a bug encountered when
> >> parsing triplet
> >> oxygen atom results from Gaussian03. Originally, this case (see attached
> >> QVGXLLKOCUKJST-UHFFFAOYAJmult3Fixed.out) failed during parsing of
> >> orbital symmetry and assignment of HOMOS due to the fact that there were
> >> no alpha virtual orbitals.
> >> 2. Implemented parsing of certain quantities from MOPAC2009 results.
> >> 3. Parsed a few additional quantities from Gaussian output, like
> >> molecular mass,
> >> rotational symmetry number, and rotational constants.
> >> I have tested my changes mostly, if not exclusively, with PM3
> >> calculations from
> >> Gaussian03 and MOPAC2009, but testall.py with the modified code
> >> seems to give
> >> the same results for Gaussian03 as it did before my modifications (91
> >> tests pass and 3 tests are skipped).
> >>
> >> If you think any of these changes are useful, please feel free to
> >> include them
> >> (or something based on them) in the next cclib release (and feel
> >> free to remove
> >> any of my superfluous comments). Also, if you have any questions about
> >> the changes, please let me know.
> >>
> >> Thanks very much for your work on cclib and for making it open-source,
> >> Greg Magoon

-- 
written by Karol Langner
Wed Apr  7 12:25:50 CEST 2010