Example b231: Explicit 3D Cubic Ionic Activation (monodomain)


This example solves the Cubic Ionic Activation model, using the monodomain equations in a rectangular cardiac tissue sample. The model combines the cleavage plane information shown in the sample.

The collocation grid connectivity information in region 1 is determined from cleavage plane information in region 2. This example also uses DTAR, (Dynamic Tracking of Acitve Region) to reduce computation. The images below show the tissue sample, and the FEM model of this sample.

Tissue Sample Fem Model of Sample

The output from this problem can be viewed using draw.com which loops through wave.com to read in the grid field information.



The comfile run by this example is as follows:

# Example b231
# ------------
# WARNING - this example will not run as an example
#           it is for reference only.  

fem define para;r;cube;example

fem define regi;r;cube;example              #two regions
fem define coor;r;region1;example reg 1     #rect.cartesian
fem define coor;r;region2;example reg 2     #rect.cartesian

fem define base;r;cube;example              #define linear basis functions
fem define node;r;cube;example              #define nodes for tissue sample
fem define elem;r;cube;example              #define elemnets for tissue sample

fem define node;r;cleavage;example reg 2    #cleavage plane nodes (3009)
fem define elem;r;cleavage;example reg 2    #cleavage plane elements (1442)

fem define fibr;d                   #default fibre angle
fem define elem;r;cube;example fibre
fem define grid;r;cube;example              #grid density = 70*16*16
fem update grid geometry
fem update grid metric level 1

# Define grid connectivity information in tissue 
# element,(region 1) from cleavage information in region 2
fem update grid connectivity      
fem group grid external as boundary

fem define equa;r;cube;example              #cubic monodomain
fem define mate;r;cube;example
fem define cell;r;cube;example
fem update grid material

fem group grid grid 5252,5253,6372,6373,7492,7493,8612,8613,9732,9733,10852,10853 as gp0
fem group grid grid 11972,11973,13092,13093,5182,5183,6302,6303,7422,7423,8542,8543 as gp1
fem group grid grid 9662,9663,10782,10783,11902,11903,13022,13023,5112,5113,6232,6233 as gp2
fem group grid grid 7352,7353,8472,8473,9592,9593,10712,10713,11832,11833,12952,12953 as gp3
fem group grid grid 5042,5043,6162,6163,7282,7283,8402,8403,9522,9523,10642,10643 as gp4
fem group grid grid 11762,11763,12882,12883,4972,4973,6092,6093,7212,7213,8332,8333 as gp5
fem group grid grid 9452,9453,10572,10573,11692,11693,12812,12813,4902,4903,6022,6023 as gp6
fem group grid grid 7142,7143,8262,8263,9382,9383,10502,10503,11622,11623,12742,12743 as gp7
fem group grid grid 4832,4833,5952,5953,7072,7073,8192,8193,9312,9313,10432,10433 as gp8
fem group grid grid 11552,11553,12672,12673,4762,4763,5882,5883,7002,7003,8122,8123 as gp9
fem group grid grid 9242,9243,10362,10363,11482,11483,12602,12603 as gp10

# group these grid points as stimulus site for initial activation
fem group grid grid gp0,gp1,gp2,gp3,gp4,gp5,gp6,gp7,gp8,gp9,gp10 as stimulus_site #70*16*16

set num_threads 32

fem define init;r;cube;example    #current=0.5(mA/mm^3)  duration=1(ms)
fem define solv;r;cube;example    #Use DTAR (Dynamic Tracking of Active Region)
fem solve to 0

#cmgui output
fem export node;3dcube as cube reg 1
fem export elem;3dcube as cube reg 1

# loop through time from 0 to PN.M msec (19.9msec)

# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command: DO P=0..1
for $P ( 0..1 ) 
{


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command: DO N=0..9
for $N ( 0..9 ) 
{


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command:   DO M=0..9
for $M ( 0..9 ) 
{


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command:     fem solve restart to PN//.M 
fem solve restart to "PN.M"


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command:     fem export elem;gridfield_1//$P//$N//M field
fem export elem;gridfield_1${P}${N}M field


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command:   ENDDO
}


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command: ENDDO
}


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command: ENDDO
}


# Command updated by fixcom.sh on Wed Aug 23 17:50:12 NZT 2000
# Old command: deassign M
 




#See draw.com to view results

Files used by this example are:

Name                  Modified     Size

example_b231.com 12-Jul-2001 3.7k 3dcube.exelem 10-Apr-2000 7.2k 3dcube.exnode 10-Apr-2000 1.3k cleavage.exelem 10-Apr-2000 315k cleavage.exnode 10-Apr-2000 160k cleavage.ipelem 10-Apr-2000 464k cleavage.ipnode 10-Apr-2000 557k cube.ipbase 10-Apr-2000 2.4k cube.ipcell 10-Apr-2000 1.7k cube.ipcoor 10-Apr-2000 570 cube.ipelem 10-Apr-2000 404 cube.ipelfb 10-Apr-2000 233 cube.ipequa 26-May-2003 1.4k cube.ipgrid 06-Mar-2003 612 cube.ipinit 10-Apr-2000 528 cube.ipmate 10-Apr-2000 1.7k cube.ipmate_cell_old 10-Apr-2000 3.5k cube.ipnode 10-Apr-2000 2.2k cube.ippara 04-Jan-2006 5.8k cube.ipregi 10-Apr-2000 93 cube.ipsolv 13-Apr-2007 2.2k cube.ipsolv.old 10-Apr-2000 1.6k draw.com 12-Jul-2001 2.4k region1.ipcoor 10-Apr-2000 572 region2.ipcoor 10-Apr-2000 572 wave.com 10-Apr-2000 758

Download the entire example:

Name                           Modified     Size

examples_b_b2_b23_b231.tar.gz 14-Apr-2007 380k

Graphical output from this problem is given here.


Html last generated: Sun Mar 6 05:51:15 2016

Input last modified: Fri Apr 13 10:40:15 2007


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