[gmx-developers] mdp option names

[Alexey Shvetsov]

Here is a patch for manual
It should fix all renamed mdp option names

Mark Abraham писал 22.11.2011 17:18:
> 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
>>>>>>>>>
>>>>>>>>> ========================================
>>>>>>>>> -- gmx-developers mailing list
>>>>>>>>> gmx-developers at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>>>>>>> www
>>>>>>>>> interface
>>>>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> -- 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
>>>>>> -- gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>>>> www
>>>>>> interface
>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>>
>>>>
>>>> -- 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
>>>> -- gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface
>>>> or send it to gmx-developers-request at gromacs.org.
>>>>
>>

-- 
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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