[gmx-developers] mdp option names

[Szilárd Páll]

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!
--
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
>>> --
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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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