f



2D/3D reaction-diffusion solver in matlab

Hiya,

For my phd thesis, I wrote a custom unstructured finite element (tri /
tet) 2D/3D reaction-diffusion solver in matlab.  It uses an adams-
bashforth / trapezoidal predictor-corrector time integrator with a
customised GMRES linear solver (which itself uses matlab's '\'
operator), with adaptive time-stepping based on the Gresho and Sani
depiction in their CFD books.  Hence, this thing handles multiple
space and time scales - which I needed for the computational cell
biology modeling I performed.  Note, there's no Newton solver in
it...yet?

Anyway, I'm curious if anyone in the matlab community would find this
tool useful?  I'm considering releasing this into the wild (via
sourceforge or mathwokds I'm not sure yet), but that entails writing
documentation and probably making it comprehensible to other human
beings (oh boy!  :).  Any feedback from you folks I would greatly
appreciate...

thanks!

shawn
0
shawn2479 (9)
3/22/2012 12:06:25 AM
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"Shawn" wrote in message <bebd6580-2df2-4b61-92af-b857a00ed5db@s9g2000pba.googlegroups.com>...
eling I performed.  Note, there's no Newton solver in
> it...yet?
> 
> Anyway, I'm curious if anyone in the matlab community would find this
> tool useful? 

IMO any good quality is useful.

Bruno
0
b.luong5955 (6401)
3/22/2012 7:24:13 AM
On Mar 22, 8:24=A0pm, "Bruno Luong" <b.lu...@fogale.findmycountry>
wrote:
> "Shawn" wrote in message <bebd6580-2df2-4b61-92af-b857a00ed...@s9g2000pba=
..googlegroups.com>...
>
> eling I performed. =A0Note, there's no Newton solver in
>
> > it...yet?
>
> > Anyway, I'm curious if anyone in the matlab community would find this
> > tool useful?
>
> IMO any good quality is useful.
>
> Bruno

Well, it got me a phd.  :)

Originally I intended to write it in C++ for speed, but ran out of
time.  So I optimised the heck out of it in matlab with vector
operations and it's speed is comparable to codes in C I used while I
was at Sandia Labs.

Hm - I suppose I'll look into writing documentation...

thanks!

shawn
0
shawn2479 (9)
3/25/2012 11:43:13 PM
I would be interested in this, especially since it is optimized with vector operations. Thanks,

Trey
0
6/21/2013 2:27:07 PM
Hi Shawn,

I'm interested!
I'm PhD working on reaction/diffusion system and this tool would save me lot of time!
Did you release it?
Where? With which name?

Thanks!

Yannick
0
Yannick
5/7/2015 1:01:01 AM
On Thursday, March 22, 2012 at 12:06:25 AM UTC, shawn wrote:
> Hiya,
> 
> For my phd thesis, I wrote a custom unstructured finite element (tri /
> tet) 2D/3D reaction-diffusion solver in matlab.  It uses an adams-
> bashforth / trapezoidal predictor-corrector time integrator with a
> customised GMRES linear solver (which itself uses matlab's '\'
> operator), with adaptive time-stepping based on the Gresho and Sani
> depiction in their CFD books.  Hence, this thing handles multiple
> space and time scales - which I needed for the computational cell
> biology modeling I performed.  Note, there's no Newton solver in
> it...yet?
> 
> Anyway, I'm curious if anyone in the matlab community would find this
> tool useful?  I'm considering releasing this into the wild (via
> sourceforge or mathwokds I'm not sure yet), but that entails writing
> documentation and probably making it comprehensible to other human
> beings (oh boy!  :).  Any feedback from you folks I would greatly
> appreciate...
> 
> thanks!
> 
> shawn

Hi Shawn.
My Phd research is also about implementation of reaction diffusion systems in 2d and 3d.
So yes it will be definitely helpful.
Wakil,
0
wakilsarfaraz
11/19/2015 10:00:04 AM
Reply:

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Web resources about - 2D/3D reaction-diffusion solver in matlab - comp.soft-sys.matlab

Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation
The Turing, or reaction-diffusion (RD), model is one of the best-known theoretical models used to explain self-regulated pattern formation in ...

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