Example cellml/aliev_panfilov_1996: Panfilov modified FitzHugh-Nagumo

This example solves the modified FitzHugh-Nagumo activation model by Aliev and Panfilov (1996), defined by a CellML version of the model.

Their modifications to the original FHN model are designed to allow the model to better represent the action potential shape and restitution properties of cardiac tissue. The image below illustrates the restitution properties of the model, with the yellow trace the free action potential, the green for a cycle length of 700ms, and the red for a cycle length of 350ms.

NOTE: This example requires a CellML 1.0 enabled version of CMISS to run.

The comfile run by this example is as follows:

# Example showing how to use a cellml model

# If the example path is not set, default to current directory
if (! defined $example) {
    $example = "./";
}
# Drop off the trailing / in the example path
$chopped = chop $example;
if ($chopped ne "/") {
    $example .= $chopped;
}

fem define parameters;r;$example/fhn;

# default nodes, elements and grids to get a single grid point
fem define node;d;
fem define bas;d;
fem define elem;d;
fem define grid;d;
fem update grid geometry;
fem update grid metric;

# Define the a user defined CellML electrophysiological model
fem define equation;r;$example/cellml;

# Define the CellML model to use and map the parameters to CMISS and
# specify initial/boundary conditions for the cell model.
# Note: the "save temporary files" question is set to yes for testing
#       of the generated code. You might want to turn this off if you
#       are not running this as a test example.
fem define cell;r;$example/fhn_panfilov;

# Initialise the spatial properties of the model (there are none).
fem define material;r;$example/fhn cell;
fem define material;r;$example/fhn;
fem update grid material;

# Define the zero transmembrane flux boundary condition.
fem define initial;r;$example/fhn;

# Define an explicit LSODA integrator.
fem define solve;r;$example/lsoda;

# Initialise the solve.
fem solve to 0;

# Create a history file to store output variables of interest.
fem open history;fhn_panfilov write variables yqs niqslist 1..5 binary;

# Loop through time integrating the cellular model.
$Tend = 1500;
$dt = 1.0;
for ($time=0;$time<$Tend;$time+=$dt) {
    fem solve restart to $time;
    fem write history time $time variables yqs binary;
}

fem close history binary;

# Evaluate signals for the variables from the history file.
fem evaluate electrode;fhn_panfilov history fhn_panfilov from grid yqs iy 1..5 binary;

# Define an export of the CMISS signals to UnEMAP signals..
fem define export;r;$example/fhn;

# ..and export the signals to a UnEMAP signal file.
fem export signal;fhn_panfilov electrodes signal fhn_panfilov names cell;

# For testing we compare the generated CMISS signal files
if ($TESTING) {
    fem compare signal;fhn_panfilov basis both masterfile $example/fhn_panfilov comparefile fhn_panfilov binary;
}

Files used by this example are:

Name                     Modified     Size

aliev_panfilov_1996.com  21-Jun-2003  2.2k
cellml.ipequa            21-Jun-2003  1.5k
fhn.ipexpo               21-Jun-2003  657 
fhn.ipinit               21-Jun-2003  214 
fhn.ipmatc               21-Jun-2003  356 
fhn.ipmate               21-Jun-2003  3.2k
fhn.ippara               21-Jun-2003  5.9k
fhn_panfilov.binsig      17-Feb-2004   80k
fhn_panfilov.cml         17-Feb-2004   18k
fhn_panfilov.ipcell      21-Jun-2003  3.5k
lsoda.ipsolv             21-Jun-2003  1.2k

Download the entire example:

Name                                        Modified     Size

examples_cellml_aliev_panfilov_1996.tar.gz  19-Aug-2006   45k

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.

  
  
• fhn_panfilov.opcomp
  

  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 05:51:19 2016

Input last modified: Wed Feb 18 13:17:58 2004