[gmx-developers] options file handling in master

[Alexey Shvetsov]

David van der Spoel писал 08-11-2013 23:34:
> On 2013-11-08 18:41, Alexey Shvetsov wrote:
>> Hi!
>> 
>> David are you going to implement sfactors as xml file like it was done
>> in sassena?
> I have done it using xml indeed. Do you have a link for this 
> implementation?
> 
> Anyway my collaborators have made a new polynomial representation of
> the structure factors (paper submitted). Of course you can download
> the implementation from gerrit. In fact the analysis tool does not
> work completely yet, since everything is in the new code base.
> 
> We have looked at g_sans as well and we noticed the similarities with
> g_sans (and there is even g_saxs). It would be good to collaborate to
> merge these tools as far as possible.

I'm also think that some machinery should be merged (at least params 
read, and may be some parts of g(r) computation). C++ implentation isnt 
ready yet. I also going rework g_nse to new framework (we measured some 
exp nse data, and get good agreement with model).

> 
> @Teemu: Ok I will add the xml file format. Hopefully we can move more
> stuff to XML soon.
> 
>> 
>> PS I wanna submit reimplementation of g_sans using new api after you
>> WAXS stuff will be merged
>> 
>> David van der Spoel писал 08-11-2013 17:47:
>>> Hi,
>>> 
>>> I'm trying to implement new analysis tools using Teemu's framework.
>>> For some reason this only supports a subset of all gromacs files, and
>>> uses new enumerated types to distinguish them. E.g.:
>>> 
>>> options->addOption(FileNameOption("sfac").filetype(eftGenericData)
>>>                    .inputFile().required()
>>>                    .store(&fnSfactor_).defaultBasename("sfactor")
>>>                    .description("Structure factors"));
>>> 
>>> I would like this file to have the .xml extension, however in
>>> options/filenameoption.cpp we only have:
>>> 
>>> FileTypeRegistry::FileTypeRegistry()
>>> {
>>>     filetypes_.resize(eftOptionFileType_NR);
>>>     registerType(eftTopology,    efTPS);
>>>     registerType(eftTrajectory,  efTRX);
>>>     registerType(eftPDB,         efPDB);
>>>     registerType(eftIndex,       efNDX);
>>>     registerType(eftPlot,        efXVG);
>>>     registerType(eftGenericData, efDAT);
>>> }
>>> 
>>> note that the eftXXX are different from efXXX in fileio/filenm.h.
>>> 
>>> Main question therefore is:
>>> Why would we not allow all the old field types?
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> 
> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 
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