Example b232: Simple Explicit 3D Cubic Ionic Activation (monodomain) using Grid-based FE

The collocation grid connectivity information in region 1 is determined from cleavage plane information in region 2.

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 b232
# ------------

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

# cleavage planes must be plane (flat)
fem define node;r;cleavage;example reg 2 #nodes for cleavage plane elements
fem define elem;r;cleavage;example reg 2 #elements defining cleavage cuts

fem define fibr;d                   #default fibre angle
fem define elem;r;cube;example fibre
fem define grid;r;cube;example              #grid density
fem update grid geometry
fem group grid xi1=low as stimulus
fem update grid connectivity      #make grid pts adjacent to cleavage be bdry pts

if($TESTING) {
  fem list grid;connectivity connectivity
}
fem group grid external as boundary

fem define equa;r;cube;example              #cubic monodomain
fem define mate;r;cube;example

fem list grid group

# set num_threads 32

fem define cell;r;cube;example

fem define init;r;cube;example
fem define solv;r;cube;example

# cmgui output
fem export node;3dcube as cube reg 1
fem export elem;3dcube grid_numbers as cube reg 1
fem export node;cleavage as cleavage reg 2
fem export elem;cleavage as cleavage reg 2

fem solve to 0
fem export elem;"gridfield_000" field

# loop through time from 0 to 5 msec
foreach $count ( '001'..'050' ) {
 my $time = $count / 10;
 fem solve restart to "$time"
 print "time: $time\n";
 fem export elem;"gridfield_$count" field
}

#See draw.com to view results

Files used by this example are:

Name              Modified     Size

example_b232.com  03-May-2003  1.7k
cleavage.ipelem   18-Sep-2000  406 
cleavage.ipnode   03-May-2003  1.1k
cube.ipbase       22-Aug-2000  2.4k
cube.ipcell       22-Aug-2000  1.8k
cube.ipcoor       22-Aug-2000  570 
cube.ipelem       22-Aug-2000  404 
cube.ipelfb       22-Aug-2000  233 
cube.ipequa       26-May-2003  1.4k
cube.ipgrid       06-Mar-2003  603 
cube.ipinit       18-Sep-2000  567 
cube.ipmate       18-Sep-2000  1.8k
cube.ipnode       18-Sep-2000  1.7k
cube.ippara       12-Nov-2002  5.9k
cube.ipregi       22-Aug-2000   93 
cube.ipsolv       13-Apr-2007  1.8k
cube.ipsolv.old   18-Sep-2000  1.5k
draw.com          03-May-2003  3.3k
region1.ipcoor    22-Aug-2000  572 
region2.ipcoor    22-Aug-2000  572 

Download the entire example:

Name                           Modified     Size

examples_b_b2_b23_b232.tar.gz  14-Apr-2007   16k

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.
  Success	cm64-debug-clear-malloc:	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.

  
  
• connectivity.opgrid
  

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

  
  
• gridfield_030.exelem
  

  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.
  Success	cm64-debug-clear-malloc:	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 05:51:16 2016

Input last modified: Fri Apr 13 10:40:17 2007