[gmx-developers] Structure of the 5.0 source code

[Mark Abraham]

On May 29, 2014 12:55 AM, "Jorge de Antonio" <j.de.antonio at grs-sim.de>
wrote:
>
> Hi,
>
> Thanks again for your help. Also I see that the structure in the gromacs
4.5 and 5.0 has changed. I had some extra c files in the kernel directory
in src in the old version. Those functions defined were called in the md.c.
Now I came up with the question… where should I put these extra files in
(5.0 version)? My first attempt was to paste them (with the corresponding
changes) into src/programs/mdrun/.

Yes, that should work fine.

> I would appreciate if someone can help about how the files and
directories are set in the source code. I haven’t found anything in the
documentation.

It's hard to say, because 90 percent of it depends on 90 percent of it, and
all changing. Stuff will continue to move around while we continue to
re-create some modularity. src/programs/mdrun,
src/gromacs/{gmxlib,mdlib,gmxana,gmxpreprocess,legacyheaders} are all
buckets of semi-random stuff historically located in similarly named
directories. Many of those locations will disappear eventually. Other
directories have some more modularity, but the quality of that expression
will vary a lot. There is Doxygen available for much of the newly written
code, which describes some of the organisation, but I have not yet written
the code to deploy it automatically to the web.

Mark

> Thanks again for your time.
> Best,
>
> Jorge
>
>
> On 22 May 2014, at 15:18, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>> Hi,
>>
>> Clues for this might be found by examining the git history for that
file. Get the GROMACS git repository and use something like
>>
>> git log -- src/gromacs/gmxana/gmx_chi.c src/tools/gmx_chi.c
>>
>> to see the history for whatever that file was called at the time. This
should give you some metadata about the change.
>>
>> Mark
>>
>> On May 21, 2014 12:40 PM, "Jorge de Antonio" <j.de.antonio at grs-sim.de>
wrote:
>>>
>>> Dear developers,
>>>
>>> I’ve noticed that there is a substancial change in the gmx_chi.c file
(located in /src/gromacs/gmxana) when comparing to the 4.5.1. The thing is
I must modify the variable int naa (in the histogramming function) but that
variable doesn’t exist anymore in the new version. I guess is somehow
related with the gmx_residue_type_t rt. I would appreciate some help in
getting a better understanding of this function. Thanks a lot.
>>>
>>> Cheers,
>>> Jorge
>>> --
>>> Gromacs Developers mailing list
>>>
>>> * Please search the archive at
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>>>
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gmx-developers-request at gromacs.org.
>>
>> --
>> Gromacs Developers mailing list
>>
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>>
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>
>
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> Thanks again. Also I see that the structure in the gromacs 4.5 and 5.
>
>
> On 22 May 2014, at 15:18, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>> Hi,
>>
>> Clues for this might be found by examining the git history for that
file. Get the GROMACS git repository and use something like
>>
>> git log -- src/gromacs/gmxana/gmx_chi.c src/tools/gmx_chi.c
>>
>> to see the history for whatever that file was called at the time. This
should give you some metadata about the change.
>>
>> Mark
>>
>> On May 21, 2014 12:40 PM, "Jorge de Antonio" <j.de.antonio at grs-sim.de>
wrote:
>>>
>>> Dear developers,
>>>
>>> I’ve noticed that there is a substancial change in the gmx_chi.c file
(located in /src/gromacs/gmxana) when comparing to the 4.5.1. The thing is
I must modify the variable int naa (in the histogramming function) but that
variable doesn’t exist anymore in the new version. I guess is somehow
related with the gmx_residue_type_t rt. I would appreciate some help in
getting a better understanding of this function. Thanks a lot.
>>>
>>> Cheers,
>>> Jorge
>>> --
>>> Gromacs Developers mailing list
>>>
>>> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developersor send a mail to
gmx-developers-request at gromacs.org.
>>
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developersor send a mail to
gmx-developers-request at gromacs.org.
>
>
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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gmx-developers-request at gromacs.org.
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