Re: [ESPResSo-users] Weird results from P3M interaction?

[Rudolf Weeber]

Hi Clemens,
> I get some weird (unphysical?) results from my simulation. Therefore I
> have a couple of questions:
> 
> 
> 1) I have a system with one large charged dendrimer and counter-ions.
> Additionally, there are charged salt ions. All particles interact via
> LJ-interaction and Coulomb interaction (P3M). I attached some snapshots
> of the resulting system at the end. In the snapshot the large dendrimer
> is at the center of the particles. And (this is the confusing part) the
> free ions seem to cluster with the clusters forming a regular lattice.
> This does not seem right. My first guess is that the Coulomb interaction
> and therefore the P3M method is the cause. Does anyone have an idea?
> 
> This is the output of the P3M tuning method:
> 
> P3M tune parameters: Accuracy goal = 1.00000e-04 Bjerrum Length =
> 7.00052e+00
> System: box_l = 1.27568e+03 # charged part = 3326 Sum[q_i^2] = 3.32600e+03
> mesh cao r_cut_iL     alpha_L      err          rs_err     ks_err    
> time [ms]
> 16   3   1.79754e-01 1.07208e+01 9.97082e-05 7.071e-05 7.030e-05 3.63
> 16   2   2.46081e-01 7.66386e+00 1.19662e-04 7.071e-05 9.654e-05
> accuracy not achieved
> 16   4   1.57645e-01 1.23319e+01 9.92441e-05 7.071e-05 6.964e-05 2.65
> 16   5   1.48033e-01 1.31872e+01 9.97046e-05 7.071e-05 7.029e-05 2.51
> 16   6   1.43227e-01 1.36592e+01 9.84446e-05 7.071e-05 6.849e-05 2.55
> 16   7   1.39382e-01 1.40609e+01 9.93436e-05 7.071e-05 6.978e-05 2.71
> 142  5   2.19736e-02 9.93374e+01 9.98180e-05 7.071e-05 7.045e-05 136.16
> 142  4   2.42866e-02 8.94035e+01 9.40771e-05 7.071e-05 6.205e-05 134.00
> 142  6   2.13954e-02 1.02165e+02 9.39748e-05 7.071e-05 6.190e-05 136.81
> 142  3   2.94909e-02 7.28644e+01 9.67037e-05 7.071e-05 6.597e-05 132.60
> 142  2   5.26210e-02 3.95352e+01 9.90264e-05 7.071e-05 6.933e-05 131.29
> 142  1   1.48033e-01 1.31872e+01 2.75994e-04 7.071e-05 2.668e-04
> accuracy not achieved
> 
> resulting parameters:
> 16   16   16   5   1.48033e-01 1.31872e+01 9.97046e-05 2.51
Your system is very dilute (number density below 0.002). 
Hence, the parameters chosen are a low number of mesh points and a large real 
space cut-off.
I'm not sure, why meshes between 16 and 142 are not tested. Maybe someone with 
detailed knowledge about the tuning can comment?
On a different note: The accuracy estimates in a highly inhomogeneous system 
are to be taken with a grain of salt.



> 2) When using the P3M method I sometimes get the warning "Statistics of
> tuning samples is very bad" (But not for the simulation, which I used
> for the snapshots). Is this a problem and on which parameters does this
> depend on? Box size and accuracy?
The P3M tuning times the actual force measurement (src/core/tuning.cpp). These 
could fluctuate, e.g., because of other processes running on the same system. 
If the fluctuation is too large, this may lead to a set of parameters which 
gives slower calculations.

> 3) The description of the "exclude" feature of particles says:"no
> nonbonded interactions arecalculated". This means Coulomb interaction
> for excluded particles are still calculated, correct?
The k-space part seems to be included, but looking at the code (e.g., in 
src/core/verlet.cpp:build_verlet_lsit()), my impression is that the short-range 
part (which is up to ~2.5 Bjerrum lengths in your system) is not.
Note that the short range part of p3m is implemented as a non-bonded 
interaction (sr/core/forces_inline.hpp:add_non_bonded_pair_force()).
What are the exclusions needed for? 


> 4) I have several types of ions in my solvent, which I interact via the
> same LJ-interaction, but I want them to have different LJ interactions
> later on. So I want them as different types, which leads to 10 instead
> of 3 LJ-interaction definitions. Is the computational cost for having 10
> instead of 3 defined LJ-interactions very high? Keep in mind that the
> actual number of interacting particles stays the same.
Each pair of particles is considered once, whatever the number of particle 
types. However, you'll loose some cache efficiency, as different interaction 
parameters will have to be loaded for different pairs of particles. Probably 
noticable but not huge difference.

Hope that helps
Regards, Rudolf



-- 
Dr. Rudolf Weeber
Institute for Computational Physics
Universität Stuttgart
Allmandring 3
70569 Stuttgart
Germany
Phone: +49(0)711/685-67717
Email: address@hidden
http://www.icp.uni-stuttgart.de/~icp/Rudolf_Weeber