Example b212b: 2D bidomain point using Beeler Reuter (defib with electroporation) model

This example uses the defibrillation Beeler Reuter model to solve for transmembrane potential in the smallest 2D bidomain possible (3 by 3 gridpoints). The action potential can be viewed using UNEMAP. This exmaple includes electroporation and scales the action potential duration by a factor of 8.

The comfile run by this example is as follows:

# Set up for bidomain.
$VM = 1
$PHI_E = 2

# Define parameter set
fem def para;r;test;example

# Define geometry
fem def base;r;spiral;example
fem def node;r;point;example
fem def elem;r;check_eg;example

# Define grid and useful grid groups.
fem def grid;r;point;example
fem update grid geometry 
fem update grid metric 
fem group grid external as boundary

# Define bidomain equations and material properties.
#  Turn on electroporation and scale the APD
fem def equa;r;spiral_bi;example class $VM,$PHI_E

fem def mate;r;check_eg;example class $VM,$PHI_E
fem def cell;r;spiral;example class $VM,$PHI_E
fem update grid material;example class $VM,$PHI_E

# Define initial and boundary conditions.
fem def init;r;point_bi;example class $VM,$PHI_E
fem def solve;r;spiral;example class $VM
fem def solve;r;spiral;example class $PHI_E

# Define window and solve to 0.
fem define window;c
fem solve to 0 class $VM,$PHI_E
fem draw field grid 1 zmin=-110 zmax=80 class $VM

# Open a binary history file to store the membrane potential
fem open history;test write variables yq niqlist 1 class $VM

# Loop through time

for $HUN ( 0..0 ) 
{
  for $TEN ( 0..9 ) 
  {
    for $UNIT ( 0..9 ) 
    {
      fem solve restart to "${HUN}${TEN}$UNIT" class $VM,$PHI_E
      fem draw field grid 1 zmin=-110 zmax=80 class $VM
      refresh graphics

      fem write history time "${HUN}${TEN}$UNIT" variables yq
    }
  }
}

# Close the history file, calculate the signal file
# from the history file, define export properties and export.
fem close history class $VM
fem evaluate electrode;test history test from grid yq
fem define export;r;point;example
fem convert signal infile test outfile test
fem export signal;test electrode signal test

Additional testing commands:

fem list signal signal test binary
fem list grid yq index v class 1
fem list grid yq index v class 2

Files used by this example are:

Name               Modified     Size

example_b212b.com  13-Dec-2002  1.7k
check_eg.ipelem    02-Oct-2002  341 
check_eg.ipmate    10-Apr-2000  1.7k
point.ipexpo       10-Apr-2000  657 
point.ipgrid       06-Mar-2003  535 
point.ipnode       02-Oct-2002  825 
point_bi.ipinit    10-Apr-2000  1.3k
spiral.ipbase      10-Apr-2000  1.1k
spiral.ipcell      10-Apr-2000  2.0k
spiral.ipsolv      13-Apr-2007  1.8k
spiral.ipsolv.old  10-Apr-2000  1.4k
spiral_bi.ipequa   26-May-2003  1.6k
test.binhis        10-Apr-2000  4.2k
test.ippara        12-Nov-2002  5.9k
test_output.com    23-Apr-2001  101 

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b212_b212b.tar.gz  14-Apr-2007   13k

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.

  
  
• 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.
  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.

  
  
• test.iphist
  

  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.

  
  
• test.ipsign
  

  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 05:51:11 2016

Input last modified: Fri Apr 13 10:38:46 2007