[MMTK] Coulomb Crystal with MMTK

Konrad Hinsen hinsen at cnrs-orleans.fr
Sat Jun 21 13:11:21 UTC 2008

On 18.06.2008, at 10:43, Mario Tacconi wrote:

> My question are:
> 1- may MMTK  be modified to handle time-varying external electric  
> field?
> 2- may MMTK be modified to handle a dissipative force?

Yes, of course - anything is possible, the question is just how much  
effort this represents.

> 2- If the answears to the previous question were "yes" which kind  
> of  modifications  should  be  done?
> I mean, I have  to  implement  a force field and an "ad hoc"  
> Universe sub class, that's for sure, but should I
> implement even an integrator?

The force field mechanism in MMTK is limited to conservative force  
fields, as is the Velocity-Verlet integrator, so you will have to  
implement dissipative forces in a special integrator. Implementing a  
time-dependent force field is possible but requires significantly  
more work than implementing a standard potential energy term.

Considering that your system seems unusual (by MMTK standards) but  
rather simple, perhaps the best solution is to write a special energy 
+integrator module (for example in Pyrex) and use MMTK only for I/O  
(system setup, trajectories).

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr

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