[gmx-developers] Structure of the 5.0 source code

[Mark Abraham]

On Thu, May 29, 2014 at 8:10 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

>
> 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.
>

Though there is http://jenkins.gromacs.org/job/Doxygen_Gerrit_5_0/javadoc/
as a temporary measure.

Mark

> 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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
> >>>
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> >>>
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> >>>
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> or send a mail to gmx-developers-request at gromacs.org.
> >>
> >> --
> >> Gromacs Developers mailing list
> >>
> >> * Please search the archive at
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> posting!
> >>
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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-developers
> or 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-developers
> or 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-developers
> or send a mail to gmx-developers-request at gromacs.org.
>
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