Example b212e: Implicit 2D Cubic Ionic Activation (bidomain) using Grid-based FE solving with AMG


This example uses the Grid-based Finite Element Method and AMG as an iterative solution method. It solves the Cubic Ionic Activation model, using the bidomain equations over a two dimensional slice with fibres.

After running this example, the output from this problem may be viewed by running draw.com.


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

fem define grid;r;box;example
fem update grid geometry
fem group grid external as boundary
fem group grid xi1=low as stimulus

fem define equa;r;box;example class 1,2
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 solve;r;lu-solve;example class 1
fem define solve;r;lu-solve;example class 2

# cmgui output
fem export node;box as box
fem export elem;box grid_numbers as box

fem export elem;"gridfield_000" field

# loop through time from 0 to 10 msec
foreach $count ( '001'..'020' ) 
{
 my $time = $count / 2;
 if( $count == 1 ) {
   fem solve to $time class 1,2
 } else {
   fem solve to "$time" class 1,2 restart
 }
 print "time: $time\n";
 fem export elem;"gridfield_$count" field class 1
}

#See draw.com to view results

Additional testing commands:

#Testing example b212d
fem li grid yq index v

Files used by this example are:

Name                 Modified     Size

example_b212e.com 23-Apr-2007 1.0k amg-solve.ipsolv 23-Apr-2007 2.0k box.exelem 10-Jan-2005 3.9k box.exnode 10-Jan-2005 896 box.ipbase 10-Jan-2005 1.1k box.ipcell 10-Jan-2005 1.7k box.ipcoor 10-Jan-2005 858 box.ipelem 10-Jan-2005 584 box.ipelfb 10-Jan-2005 358 box.ipequa 10-Jan-2005 1.5k box.ipfibr 10-Jan-2005 828 box.ipgrid 10-Jan-2005 537 box.ipinit 17-Jan-2005 852 box.ipmate 10-Jan-2005 1.7k box.ipnode 10-Jan-2005 1.0k box.ippara 10-Jan-2005 5.9k draw.com 10-Jan-2005 4.2k lu-solve.ipsolv 13-Apr-2007 2.1k lu-solve.ipsolv.tmp 16-Aug-2010 2.1k test_output.com 10-Jan-2005 46

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b212_b212e.tar.gz 17-Aug-2010 10k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmFailureSun Mar 6 00:06:58 20160
last breakTue Apr 24 01:23:00 20071
last successSun Apr 8 01:10:00 20071
cm-debugFailureSun Mar 6 00:06:59 20161
last breakTue Apr 24 01:23:00 20071
last successFri Apr 13 01:12:00 20072
mips-irix
cmFailureTue Aug 21 01:32:36 20075
last breakTue Apr 24 01:42:00 20075
last successThu Apr 12 01:31:00 20075
cm-debugFailureTue Aug 21 01:38:56 200710
last breakTue Apr 24 01:46:00 200710
last successWed Apr 11 01:22:00 20079
cm-debug-clear-mallocFailureTue Aug 21 01:45:46 200712
last breakTue Apr 24 01:53:00 200712
last successSat Apr 7 01:26:00 200713
cm-debug-clear-malloc7FailureTue Aug 21 01:45:26 200712
last breakTue Apr 24 01:53:00 200712
last successMon Apr 9 01:24:00 200712
cm64FailureTue Aug 21 01:40:36 20074
last breakTue Apr 24 01:46:00 20075
last successThu Apr 12 01:32:00 20074
cm64-debugFailureTue Aug 21 02:33:24 200710
last breakTue Apr 24 01:50:00 20078
last successFri Apr 13 01:24:00 200710
rs6000-aix
cmFailureWed Mar 4 01:10:29 20091
last breakTue Apr 24 02:21:00 20071
last successWed Apr 11 02:08:00 20071
cm-debugFailureWed Mar 4 01:13:40 20093
last breakThu Sep 13 02:09:00 20073
cm64FailureWed Mar 4 01:10:29 20090
last breakTue Apr 24 02:22:00 20071
last successWed Apr 11 02:08:00 20071
cm64-debugFailureWed Mar 4 01:10:40 20093
last breakThu Sep 13 02:09:00 20073
x86_64-linux
cmFailureSun Mar 6 00:01:38 20160
last breakTue Apr 24 01:19:00 20070
last successSun Apr 8 01:07:00 20071
cm-debugFailureSun Mar 6 00:01:38 20160
last breakTue Apr 24 01:19:00 20071
last successFri Apr 13 01:10:00 20071

Testing status by file:


Html last generated: Sun Mar 6 05:51:11 2016

Input last modified: Mon Aug 16 11:40:08 2010


CMISS Help / Examples / b / b2 / b21 / b212 / b212e