[gmx-developers] c++ in master

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 23 11:20:43 CET 2013

On 2013-01-22 15:37, Berk Hess wrote:
> On 01/22/2013 03:08 PM, David van der Spoel wrote:
>> On 2013-01-22 14:26, Berk Hess wrote:
>>> Hi,
>>> We should (re)start the discussion on 5.0, and especially C++, soon.
>>> It is currently not clear if we would want everything to be C++, or have
>>> some core functionality in C only.
>>> But what it clear is that we want to get rid of these massive collective
>>> data structures that get passed around
>>> everywhere and forcerec is a good example of that.
>>> The nbnxn "module", for example. uses it's own data structure, which at
>>> the moment hangs in forcerec,
>>> but should probably be moved out.
>> But that would give an extra argument to pass around. Encapsulating
>> these modules in a C++ class is more neat, but boils down to the same
>> "container" object.
> At a high level they should be encapsulated.
> But at a lower level we shouldn't be passing all the shit in forcerec to
> every function in mdlib (and more).
>> Should we organize a physical meeting in Stockholm some time soon?
> That's probably a good idea.]
Feb 5 or 12 would suit me, but I'm open to suggestions.

> But we should make sure the whole community has a say in these important
> decisions.

Absolutely, so community speak up!

However it is probably easier to generate a draft and then invite people 
to comment this. That can go in 2-3 iterations if the people most 
skilled in C++ contribute.

> Cheers,
> Berk
>>> Cheers,
>>> Berk
>>> On 01/22/2013 02:19 PM, David van der Spoel wrote:
>>>> Hi,
>>>> we've developed some code for refinement based the master branch. This
>>>> is being written in C++, following the GMX coding requirements as good
>>>> as we comprehend them:
>>>> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Allowed_C%2b%2b_Features
>>>> What we would like to do is add our new class to the forcerec
>>>> structure, such that it gets initiated and passed along with
>>>> everything else. However having a class definition in forcerec.h
>>>> necessitates that all files including forcerec.h are compiled by the
>>>> C++ compiler (which is hard to do with cmake).
>>>> Rather than renaming *.c to *.cpp I built a C-wrapper around the C++
>>>> object, which defeats the purpose of C++ programming in a sense, but
>>>> allows including the features we want with least disturbance.
>>>> So the question we need to start thinking about is:
>>>> When are we going to move .c to .cpp files?
>>>> Maybe this is not needed for functions that do not call any other
>>>> gromacs functions (e.g. the kernels) but I guess it will be for
>>>> virtually everything else.

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

More information about the gromacs.org_gmx-developers mailing list