[gmx-developers] mdp option names

[Szilárd Páll]

Great, thanks!
--
Szilárd



On Wed, Nov 23, 2011 at 3:30 PM, Alexey Shvetsov
<alexxy at omrb.pnpi.spb.ru> wrote:
> Rossen Apostolov писал 23.11.2011 16:53:
>>
>> Install the commit hook too:
>>
>> scp -p -P 29418 USER at gerrit.gromacs.org:hooks/commit-msg .git/hooks/
>
> I already did it =) and submited patch to gerrit =D
>>
>>  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 [37]
>>>
>>> --
>>> Szilárd
>>>
>>> On Wed, Nov 23, 2011 at 2:41 PM, Alexey Shvetsov
>>> [38] 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
>>>>> [30] 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
>>>>>>>>> [3] wrote:
>>>>>>>>>
>>>>>>>>>> Szilárd Páll писал 21.11.2011 23:45:
>>>>>>>>>>
>>>>>>>>>>> On Mon, Nov 21, 2011 at 9:22 PM, Alexey Shvetsov
>>>>>>>>>>> [1] 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 [2]).
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>>>> [11]
>>>>>>>>>>>>> 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
>>>>>>>>>>>>>> [10]
>>>>>>>>>>>>>> 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 [4]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> -- ========================================
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [6]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ========================================
>>>>>>>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>>>>>>>> gmx-developers at gromacs.org [7]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [8]
>>>>>>>>>>>>>>> Please don't post (un)subscribe requests to
>>>>>>>>>>>>>>> the list. Use the
>>>>>>>>>>>>>>> www
>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>> or send it to
>>>>>>>>>>>>>>> gmx-developers-request at gromacs.org [9].
>>>>>>>>>>>>
>>>>>>>>>>>> -- 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 [12]
>>>>>>>>>>>> mailto:alexxy at gentoo.org [13]
>>>>>>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru [14]
>>>>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>>>>> gmx-developers at gromacs.org [15]
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>>>>
>>>>>>>>>>>> [16]
>>>>>>>>>>>> Please don't post (un)subscribe requests to the
>>>>>>>>>>>> list. Use the www
>>>>>>>>>>>> interface
>>>>>>>>>>>> or send it to gmx-developers-request at gromacs.org
>>>>>>>>>>>> [17].
>>>>>>>>>>
>>>>>>>>>> -- 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 [18]
>>>>>>>>>> mailto:alexxy at gentoo.org [19]
>>>>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru [20]
>>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>>> gmx-developers at gromacs.org [21]
>>>>>>>>>>
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>>
>>>>>>>>>> [22]
>>>>>>>>>> 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 [24]
>>>>>> mailto:alexxy at gentoo.org [25]
>>>>>> mailto:alexxy at omrb.pnpi.spb.ru [26]
>>>>>> --
>>>>>> gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org [27]
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers [28]
>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-developers-request at gromacs.org
>>>>>> [29].
>>>>
>>>> --
>>>> 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 [31]
>>>> mailto:alexxy at gentoo.org [32]
>>>> mailto:alexxy at omrb.pnpi.spb.ru [33]
>>>> --
>>>> gmx-developers mailing list
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>>
>>
>> Links:
>> ------
>> [1] mailto:alexxy at omrb.pnpi.spb.ru
>> [2] mailto:git at git.gromacs.org:manual.git
>> [3] mailto:alexxy at omrb.pnpi.spb.ru
>> [4] https://gerrit.gromacs.org/229
>> [5] https://gerrit.gromacs.org/229
>> [6] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> [7] mailto:gmx-developers at gromacs.org
>> [8] http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> [9] mailto:gmx-developers-request at gromacs.org
>> [10] mailto:jalemkul at vt.edu
>> [11] mailto:szilard.pall at cbr.su.se
>> [12] mailto:alexxyum at gmail.com
>> [13] mailto:alexxy at gentoo.org
>> [14] mailto:alexxy at omrb.pnpi.spb.ru
>> [15] mailto:gmx-developers at gromacs.org
>> [16] http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> [17] mailto:gmx-developers-request at gromacs.org
>> [18] mailto:alexxyum at gmail.com
>> [19] mailto:alexxy at gentoo.org
>> [20] mailto:alexxy at omrb.pnpi.spb.ru
>> [21] mailto:gmx-developers at gromacs.org
>> [22] http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> [23] mailto:gmx-developers-request at gromacs.org
>> [24] mailto:alexxyum at gmail.com
>> [25] mailto:alexxy at gentoo.org
>> [26] mailto:alexxy at omrb.pnpi.spb.ru
>> [27] mailto:gmx-developers at gromacs.org
>> [28] http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> [29] mailto:gmx-developers-request at gromacs.org
>> [30] mailto:alexxy at omrb.pnpi.spb.ru
>> [31] mailto:alexxyum at gmail.com
>> [32] mailto:alexxy at gentoo.org
>> [33] mailto:alexxy at omrb.pnpi.spb.ru
>> [34] mailto:gmx-developers at gromacs.org
>> [35] http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> [36] mailto:gmx-developers-request at gromacs.org
>> [37]
>> http://omrb.pnpi.spb.ru/ssh://USER@gerrit.gromacs.org:29418/manual.git
>> [38] mailto:alexxy at omrb.pnpi.spb.ru
>
> --
> 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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