[gmx-developers] mdp option names

[Rossen Apostolov]

Install the commit hook too:
scp -p -P 29418 *USER*@gerrit.gromacs.org:hooks/commit-msg .git/hooks/


On 11/23/11 2:52 PM, Szilárd Páll wrote:
> Just tried and this works:
> git clone ssh://USER@gerrit.gromacs.org:29418/manual.git
>
> --
> Szilárd
>
>
>
> On Wed, Nov 23, 2011 at 2:41 PM, Alexey Shvetsov
> <alexxy at omrb.pnpi.spb.ru>  wrote:
>> Szilárd Páll писал 23.11.2011 16:39:
>>> Looks good to me, could you submit it to gerrit?
>> Sure. But i didnt find gerrit project for manual
>>
>>> Thanks!
>>> --
>>> Szilárd
>>>
>>>
>>>
>>> On Wed, Nov 23, 2011 at 12:32 PM, Alexey Shvetsov
>>> <alexxy at omrb.pnpi.spb.ru>  wrote:
>>>> Here is a patch for manual
>>>> It should fix all renamed mdp option names
>>>>
>>>> Mark Abraham писал 22.11.2011 17:18:
>>>>> On 23/11/2011 1:04 AM, Alexey Shvetsov wrote:
>>>>>> Szilárd Páll писал 22.11.2011 13:58:
>>>>>>> On Tue, Nov 22, 2011 at 10:11 AM, Alexey Shvetsov
>>>>>>> <alexxy at omrb.pnpi.spb.ru>  wrote:
>>>>>>>> Szilárd Páll писал 21.11.2011 23:45:
>>>>>>>>> On Mon, Nov 21, 2011 at 9:22 PM, Alexey Shvetsov
>>>>>>>>> <alexxy at omrb.pnpi.spb.ru>  wrote:
>>>>>>>>>> Szilárd Páll писал 21.11.2011 16:24:
>>>>>>>>>>> I was about to approve the patch in gerrit, but I realized that
>>>>>>>>>>> there
>>>>>>>>>>> is one thing we might have overlooked: mdp option names should be
>>>>>>>>>>> consistent across standard output, the man pages, and manual.
>>>>>>>>>>>
>>>>>>>>>>> Questions:
>>>>>>>>>>>
>>>>>>>>>>> i) Are there more references to mdp options in the code (e.g. help
>>>>>>>>>>> header text, warning/error
>>>>>>>>>>> messages)?
>>>>>>>>>>>
>>>>>>>>>> I'm not sure about manual. If its generated automaticaly then there
>>>>>>>>>> should
>>>>>>>>> The man pages are generated from the help messages in the code, the
>>>>>>>>> manual is a separate a latex document (source located here:
>>>>>>>>> git at git.gromacs.org:manual.git).
>>>>>>>> Ok. Then man pages should be fine. I'll check manual today.
>>>>>>> That would be great! Thanks Alexey!
>>>>>> Seems like this part of manual is generated fro source. :) so it
>>>>>> shouldnt
>>>>>> be problem
>>>>> There are certainly chunks of the manual not generated from source,
>>>>> which we should check. If we have a list of names of .mdp options,
>>>>> grepping should do the trick.
>>>>>
>>>>> Mark
>>>>>
>>>>>>> -- Szilárd
>>>>>>>
>>>>>>>>> -- Szilárd
>>>>>>>>>
>>>>>>>>>> be no problem.
>>>>>>>>>> All error messages are fixed in patch. As well as output to md.log.
>>>>>>>>>> Seems
>>>>>>>>>> all other messages were fixed in patch.
>>>>>>>>>>
>>>>>>>>>>> ii) Should we file a separate task in Redmine for fixes in the
>>>>>>>>>>> manual
>>>>>>>>>>> and get the patch approves as soon as i) is clarified?
>>>>>>>>>>>
>>>>>>>>>>> Cheers,
>>>>>>>>>>> -- Szilárd
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Oct 21, 2011 at 1:04 AM, Szilárd Páll
>>>>>>>>>>> <szilard.pall at cbr.su.se>
>>>>>>>>>>> wrote:
>>>>>>>>>>>> Although in Gromacs hyphen and underscore are interchangeable, I
>>>>>>>>>>>> do
>>>>>>>>>>>> think Alexey's suggestion is good. It improves consistency and
>>>>>>>>>>>> starting the change by generating and documenting only options
>>>>>>>>>>>> with
>>>>>>>>>>>> hyphen only could enable us to maybe brake this
>>>>>>>>>>>> non-differentiation
>>>>>>>>>>>> in
>>>>>>>>>>>> later versions (say 5+ as the option parsing will be reworked)
>>>>>>>>>>>> without
>>>>>>>>>>>> causing too much trouble.
>>>>>>>>>>>>
>>>>>>>>>>>> -- Szilárd
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Oct 20, 2011 at 9:23 PM, Justin A. Lemkul
>>>>>>>>>>>> <jalemkul at vt.edu>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>> Aren't the hyphen and underscore interchangeable, such that
>>>>>>>>>>>>> either
>>>>>>>>>>>>> is
>>>>>>>>>>>>> already accepted?
>>>>>>>>>>>>>
>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>
>>>>>>>>>>>>> Alexey Shvetsov wrote:
>>>>>>>>>>>>>> Hi all!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Seems it will be good idea to have all mdp option names
>>>>>>>>>>>>>> consistent.
>>>>>>>>>>>>>> In
>>>>>>>>>>>>>> its
>>>>>>>>>>>>>> current state some of them has '-' in its names like E-t while
>>>>>>>>>>>>>> some
>>>>>>>>>>>>>> other
>>>>>>>>>>>>>> options has '_' in their names like init_step. It will be good
>>>>>>>>>>>>>> if
>>>>>>>>>>>>>> all
>>>>>>>>>>>>>> options
>>>>>>>>>>>>>> will have same naming scheme like only '_' in names or only '-'
>>>>>>>>>>>>>> in
>>>>>>>>>>>>>> its
>>>>>>>>>>>>>> names.
>>>>>>>>>>>>>> Also it will simplyfy mdp file generation and parsing  by
>>>>>>>>>>>>>> external
>>>>>>>>>>>>>> software.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I prepared two patches in gerrit
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://gerrit.gromacs.org/229<- it replaces '_' to '-' in mdp
>>>>>>>>>>>>>> option
>>>>>>>>>>>>>> names
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://gerrit.gromacs.org/229<- it changes mdp.html and
>>>>>>>>>>>>>> mdp_opt.html
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> PS currently we use such mdp file parser for gromacs grid ui in
>>>>>>>>>>>>>> nnn
>>>>>>>>>>>>>> grid
>>>>>>>>>>>>>>
>>>>>>>>>>>>> -- ========================================
>>>>>>>>>>>>>
>>>>>>>>>>>>> Justin A. Lemkul
>>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>>>>>>> MILES-IGERT Trainee
>>>>>>>>>>>>> Department of Biochemistry
>>>>>>>>>>>>> Virginia Tech
>>>>>>>>>>>>> Blacksburg, VA
>>>>>>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>>>>>>>
>>>>>>>>>>>>> ========================================
>>>>>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>>>>>> gmx-developers at gromacs.org
>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>>>>>>>>> www
>>>>>>>>>>>>> interface
>>>>>>>>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>>>>>>>>>
>>>>>>>>>> -- Best Regards,
>>>>>>>>>> Alexey 'Alexxy' Shvetsov
>>>>>>>>>> Petersburg Nuclear Physics Institute, Russia
>>>>>>>>>> Department of Molecular and Radiation Biophysics
>>>>>>>>>> Gentoo Team Ru
>>>>>>>>>> Gentoo Linux Dev
>>>>>>>>>> mailto:alexxyum at gmail.com
>>>>>>>>>> mailto:alexxy at gentoo.org
>>>>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>>> gmx-developers at gromacs.org
>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>>> interface
>>>>>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>>>>>>
>>>>>>>> -- Best Regards,
>>>>>>>> Alexey 'Alexxy' Shvetsov
>>>>>>>> Petersburg Nuclear Physics Institute, Russia
>>>>>>>> Department of Molecular and Radiation Biophysics
>>>>>>>> Gentoo Team Ru
>>>>>>>> Gentoo Linux Dev
>>>>>>>> mailto:alexxyum at gmail.com
>>>>>>>> mailto:alexxy at gentoo.org
>>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>>>>> -- gmx-developers mailing list
>>>>>>>> gmx-developers at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>> interface
>>>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>>>>
>>>> --
>>>> Best Regards,
>>>> Alexey 'Alexxy' Shvetsov
>>>> Petersburg Nuclear Physics Institute, Russia
>>>> Department of Molecular and Radiation Biophysics
>>>> Gentoo Team Ru
>>>> Gentoo Linux Dev
>>>> mailto:alexxyum at gmail.com
>>>> mailto:alexxy at gentoo.org
>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>> --
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>
>> --
>> Best Regards,
>> Alexey 'Alexxy' Shvetsov
>> Petersburg Nuclear Physics Institute, Russia
>> Department of Molecular and Radiation Biophysics
>> Gentoo Team Ru
>> Gentoo Linux Dev
>> mailto:alexxyum at gmail.com
>> mailto:alexxy at gentoo.org
>> mailto:alexxy at omrb.pnpi.spb.ru
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-developers-request at gromacs.org.
>>
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