[gmx-developers] mdp option names

[Szilárd Páll]

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
>>>>>>>>>>>>
>>>>>>>>>>>> ========================================
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>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -- 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
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>>>>>>>>>
>>>>>>>
>>>>>>> -- 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
>>> --
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>>>
>
> --
> 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
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