[gmx-developers] mdp option names

Wed Nov 23 15:30:49 CET 2011

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
>>>>>>>>> or send it to gmx-developers-request at gromacs.org [23].
>>>>>
>>>>> --
>>>>> 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
>>> gmx-developers at gromacs.org [34]
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers [35]
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-developers-request at gromacs.org [36].
>
>
> 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