[gmx-developers] mdp option names

[Szilárd Páll]

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).

--
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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