[gmx-developers] mdp option names

[Alexey Shvetsov]

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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>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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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
>>>>>> -- 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
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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