[gmx-developers] Future developments

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 24 17:26:45 CET 2009

Mark Abraham wrote:
> David van der Spoel wrote:
>> Erik Lindahl wrote:
>>> Hi,
>>> On Feb 24, 2009, at 1:35 PM, David van der Spoel wrote:
>>>> Hi,
>>>> yesterday I put a question on the developer list on where to put a 
>>>> new mini-library for statistics. Right now it is used only from the 
>>>> analysis tools but it might also be used from other parts of the 
>>>> code. Hence I suggested placement in gmxlib, or even directly in 
>>>> src. If no one object I will do this later today.
>>>> More in general, we should decide on the future structure of the 
>>>> source tree, do we want a src directory with dozens of 
>>>> subdirectories, or should it be hierarchical. Do we move to one 
>>>> library or do we keep four different ones?
>>> Long-term I'd say we want one library, but with proper namespaces :-)
>> What does that mean in C?
> Nothing good :-)
> You can simulate it by requiring prefixes to function and/or variable 
> names, so kernel__mdrunner(), but you need some convention to keep clear 
> what bit is the namespace name and what is the function name.
> You can also declare a struct full of pointers to functions which are 
> only defined statically, so that you'd have to call kernel.mdrunner(). 
> The kernel function arrays are essentially doing this already :-) The 
> approach comes with the upside of being partially object-oriented.

Either of these have the problem that it is not obvious what kernel 
means :(. Very bad name indeed, I apologize. The nonbonded kernels are 
in src/gmxlib/nonbonded and grompp.c and mdrun.c etc. are in src/kernel.

I've put up draft coding standards at the wiki, with an example of an 
abstract data type. Please edit as you see fit.


By the way, domdec.c does not follow the indentation rules strictly :).
> Mark
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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