Example b212g: Using Grid-based FEM with BoxMG as the elliptic solver on a Three-Element Domain

There are a few things to note about BoxMG. First, it can only be used for domains that can be mapped to a square in 2D or a cube in 3D. It was brought into CMISS for solving large scale cardiac tissue problems as it is ideally suited for such domains. We often say that such domains are logically rectangular. Second, there are many options when using BoxMG but I have hidden most of them from the unexperienced user. The most important option to be aware of is the relaxation (or smoothing) method. If the problem is highly anisotropric, either from conductivities or a stretched mesh, then you must use line relaxation in 2D and plane relaxation in 3D. Finally, it should be noted that no benefit will be gained until the number of unknowns begins approaching 500,000. For less than 250,000 unknowns it will probably be faster to use either LU or CG with ILU. These are not hard and fast rules but something to keep in mind.

References:

Solving the cardiac bidomain equations for discontinuous conductivities, IEEE Trans. Biomedical Engineering, 53, 7, pp. 1265-1272, 2006

Fast elliptic solvers for cardiac bioelectric modeling on structured meshes, submitted to Computers in Biology and Medicine in 2007

The comfile run by this example is as follows:

#Example b211t
# ------------
fem define para;r;box;example
fem define coor;r;box;example

fem define node;r;box;example
fem define base;r;box;example
fem define elem;r;box;example

fem define fibr;d
fem define elem;r;box;example fibre

fem define grid;r;box;example
fem update grid geometry
fem define equa;r;box;example class 1,2
fem group grid xi1=low as stimulus
fem group grid xi1=high as dirichlet

fem define mate;r;box;example class 1,2
fem define cell;r;box;example class 1,2
fem define init;r;box;example class 1,2
fem define solv;r;pcg;example class 1
fem define solv;r;pbmg;example class 2

fem solve to 1.0 class 1,2

Additional testing commands:

#Testing example b212f
fem li grid yq index v class 1

Files used by this example are:

Name               Modified     Size

example_b212g.com  24-Apr-2007  631 
box.exelem         23-Apr-2007  3.9k
box.exnode         23-Apr-2007  896 
box.ipbase         23-Apr-2007  1.1k
box.ipcell         23-Apr-2007  1.7k
box.ipcoor         23-Apr-2007  858 
box.ipelem         23-Apr-2007  839 
box.ipelfb         23-Apr-2007  494 
box.ipequa         23-Apr-2007  1.4k
box.ipfibr         23-Apr-2007  828 
box.ipgrid         23-Apr-2007  541 
box.ipinit         23-Apr-2007  905 
box.ipmate         23-Apr-2007  1.7k
box.ipnode         23-Apr-2007  2.1k
box.ippara         23-Apr-2007  5.9k
domain.exelem      23-Apr-2007  2.5k
domain.exnode      23-Apr-2007  1.9k
pbmg.ipsolv        23-Apr-2007  2.5k
pcg.ipsolv         23-Apr-2007  2.2k
test_output.com    23-Apr-2007   54 

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b212_b212g.tar.gz  28-Apr-2007   10k

Testing status by version:

Testing status by file:

• cmiss_test.log
  

  i686-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  mips-irix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc7:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  rs6000-aix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  x86_64-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.

  
  
• cmiss_test.out
  

  i686-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  mips-irix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  rs6000-aix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  x86_64-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.

  
  

Html last generated: Sun Mar 6 05:51:12 2016

Input last modified: Fri Apr 27 08:50:19 2007