reaction-diffusion

[Paul Van Liedekerke]

Hi

(New here)

I am exploring the possibilities to couple deal to our software which models the growth of biological cells. Therefore we would need to solve a reaction-diffusion equation (of chemicals) with the cells as (point) sources.
The cells are generally closely packed.
 
We would like Deal to solve these equations and return the solution to our software. However, I have no clear view on the capabilities or the efficiency of deal in this regard..; so could anyone give feedback whether this is a valuable solution ?

Many thanks for any input !

Paul

[Armin Ghajar Jazi]

Hi Paul,

I am not familiar with with particular physics you are talking about, however I have managed to use Dealii in our FluidSolver code. My code deals with partitioned fluid structure interaction. What I am doing essentially is solving the structural part in Dealii (based on step44 tutorial) and the fluid part in our code.

The first difficulty is of course compiling the two together, which is highly dependent on the compiling routine you are using(if it is with cmake , gnu autochain tools etc.). The new version of Dealii uses cmake where as previous versions were autochain based. After that, getting Dealii functionality in your code is just the matter of including appropriate Header files into your code.

The second part is to decide if both programs live on the same mpi-communicator. In my program Dealii lives on another communicator than my code, and I simply send the information via MPI calls back and forth, this of course necessitates a coupling environment which holds both communicators.

I would be glad to help you on this if you need assistance in any part I am familiar with!

cheers,

Armin

Paul

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[Paul Van Liedekerke]

Hi Armin

Thanks for your feedback, yet I am not that far  :-) ..I am currently going through the steps of Deal.II. I think a difficulty will be the coupling of discrete concentration sources (cells) with the continuum environment in FEM. If you have any knowledge on this issue, I ll be glad to hear it !

Cheers

Paul

2013/8/8 Armin Ghajar Jazi <arm...@gmail.com>

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[Wolfgang Bangerth]

> Thanks for your feedback, yet I am not that far :-) ..I am currently going
> through the steps of Deal.II. I think a difficulty will be the coupling of
> discrete concentration sources (cells) with the continuum environment in FEM.
> If you have any knowledge on this issue, I ll be glad to hear it !

If these are point sources, then you'll want to know about
VectorTools::create_point_source_vector().

Best
W.


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Wolfgang Bangerth email: bang...@math.tamu.edu
www: http://www.math.tamu.edu/~bangerth/