[gmx-developers] mdp option names

[Alexey Shvetsov]

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.

>
> --
> 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
>> --
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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