[gmx-developers] mdp option names

[Mark Abraham]

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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>>>>>>>>
>>>>>>>
>>>>>
>>>>> -- 
>>>>> 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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>