Re: [ESPResSo-devel] adress sample and code base

[Pierre de Buyl]

Hi Olaf,

On Thu, Nov 21, 2013 at 04:17:31PM +0100, Olaf Lenz wrote:
> The ADResS implementation in ESPResSo is merely a proof-of-concept
> implementation. It does *not* give any performance advantage over a full
> simulation in high resolution, and it contains only the most basic ADResS
> functionality. If you want to use ADResS, you should probably go for
> ESPResso++.

Thanks for your quick reply!

> Have a look at
> 
> http://lists.nongnu.org/archive/html/espressomd-users/2013-11/msg00007.html
> 
> Otherwise, here you'll finde ES++
>   http://www.espresso-pp.de/
> 
> We were already thinking whether we remove it from the ESPResSo code
> entirely.

I was aware of espressopp but could not get myself to navigate through the
entangled boost C++ code. I had read the message you link to above (the person
asking the question is in the same project as I am) but it sounded a lot less
dramatic than yours :-)

Your version makes it quite clear that I should have my project depend on
espresso adress.

Cheers,

Pierre

> 
> Olaf
> 
> 
> 2013/11/21 Pierre de Buyl <address@hidden>
> 
> > Dear Espresso developers,
> >
> > I am interested in AdResS simulations (ideally of polymeric systems) and
> > have
> > started to check the sample that comes with espresso.
> >
> > The sample script is broken and I have started to put a missing piece back
> > into
> > the system, the computation of the number of particles in ex,cg and hy
> > (exact/all atom, coarse grained and hybrid) in the system. To achieve
> > that, I
> > have:
> > 1. Added a global variable "int adress_regime[3]" to store the result.
> > 2. Added a tcl routine "tclcommand_nregime".
> >
> > The global may have been local instead but having a global means that one
> > could
> > compute adress_regime within the force or integration loop instead (saving
> > an
> > iteration).
> >
> > I mimicked the routine "energy_kinetic" to write "nregime". To get the
> > "status"
> > of a particle, I compare its weigth w to 0, 1 and 0<w<1 after having found
> > that
> > in other parts of the code.
> >
> > By the way, I tried to find a previous implementation of the routine via
> > github,
> > google and "git grep n_regime $(git rev-list --all)" with no success.
> >
> > If anyone knowledgeable with Espresso/AdResS would be willing to have a
> > look and
> > comment on https://github.com/pdebuyl/espresso_work/commits/add_nregimeI'd 
> > be
> > happy, if appropriate, to file a PR.
> >
> > The branch add_nregime works with the scripts attached, Adress_t.tcl and
> > auxiliary.tcl. These are not clean enough to commit, however.
> >
> > Regards,
> >
> > Pierre
> >
> > PS: a short intro is due on the list, I guess. I am a physicist working
> > (currently) at the dept of chemistry, KU Leuven. I have experience in
> > writing
> > simulation code but polymer modeling is a recent topic. I have already
> > discussed
> > with some developers of Espresso about http://nongnu.org/h5md/
> >
> 
> 
> 
> -- 
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
> Phone: +49-711-685-63607

-- 
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Pierre de Buyl
KU Leuven - Polymer Chemistry and Materials
T +32 16 327355
W http://homepages.ulb.ac.be/~pdebuyl/
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