Re: [cclib-devel] Modifications to cclib 1.0

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

Hi Adam,
Thanks for clarifying this and pointing me to version 2.1 of the LGPL. I was
originally looking at LGPL v3, which isn't as clear to me as LGPL 2.1 (despite
the fact that it is shorter). I've included the following notice in our 
license
documentation
(http://github.com/GreenGroup/RMG-Java/blob/6a4a5130af709f20433c71c2c16ad21c53ce2ddd/web/source/license.txt):

"The contents of source/cclib/ are modified portions of cclib 1.0
(http://cclib.sourceforge.net) and form a software library available under the
terms of the LGPL:
[LGPL 2.1 license text]"

I've also included a notice at the top of the files I've modified, as 
described
in Section 2 of LGPL 2.1.

Thanks again for your feedback,
Greg

Quoting Adam Tenderholt <ate...@gm...>:

> My understanding is that you can distribute any program (proprietary
> or open source) with a LGPL'd library. However, if you make
> modifications to that library, you must make those changes available
> under the LGPL and make note of which files were changed. As I recall,
> you already submitted patches of your changes to us which might
> satisfy the requirement to make those changes available.
>
> Also, if you have an "About dialog" that mentions the copyright and
> license of RMG, you need to include appropriate copyright/license
> information for cclib and I believe include a copy of the LGPL.
>
> There are probably a couple of other points in the text of the LGPL
> (http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html) that you need
> to consider, but it's a pretty intense document so I don't know the
> finer details. Perhaps give it a skim to see if there is anything that
> jumps out at you.
>
> Adam
>
>
> On Thu, Apr 29, 2010 at 8:22 AM, Gregory Magoon <gm...@mi...> wrote:
>> 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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>>>>
>>>
>>>
>>>
>>
>>
>>
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