[gmx-developers] mdp option names

[Alexey Shvetsov]

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

> --
> 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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-- 
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