Re: [cclib-devel] Modifications to cclib 1.0

[Gregory M. <gm...@MI...>]

On a related note:
Would there be any license-related issues if we were to include the modified
cclib code with our RMG distribution (cf.
http://github.com/GreenGroup/RMG-Java/ and 
http://rmg.sourceforge.net/)? RMG is
distributed under the MIT/X11 License 
(http://rmg.sourceforge.net/license.html),
and, as I understand, cclib is available under the LGPL license.

Thanks in advance,
Greg

Quoting Gregory Magoon <gm...@mi...>:

> Hi Noel,
> Thanks for the quick response. In answer to your questions:
>
> 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
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>>
>
>
>