Example cellml/vancapelle_durrer_1980: van Capelle - Durrer 1980

This example solves the original van Capelle - Durrer activation model (1980), defined by a CellML version of the model.

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/vcd;

# 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/vcd;

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

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

# 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;vcd write variables yqs niqslist 1..4 binary;

# Loop through time integrating the cellular model.
$Tend = 1000;
$dt = 1.0;
for ($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;vcd history vcd from grid yqs iy 1..4 binary;

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

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

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

Files used by this example are:

Name                        Modified     Size

vancapelle_durrer_1980.com 25-Jun-2003 2.2k cellml.ipequa 25-Jun-2003 1.5k cellml.ipinit 25-Jun-2003 214 cellml.ipmatc 25-Jun-2003 356 cellml.ipmate 25-Jun-2003 3.2k lsoda.ipsolv 25-Jun-2003 1.2k vcd.binsig 30-Jun-2003 50k vcd.cml 25-Jun-2003 21k vcd.ipcell 30-Jun-2003 3.1k vcd.ipexpo 25-Jun-2003 657 vcd.ippara 25-Jun-2003 5.9k

Download the entire example:

Name                                           Modified     Size

examples_cellml_vancapelle_durrer_1980.tar.gz 19-Aug-2006 24k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:03:27 20163
cm-debugSuccessSat Mar 5 00:12:36 20164
mips-irix
cmSuccessSun Aug 19 02:16:11 200745
cm-debugSuccessWed Aug 15 01:57:39 200778
cm-debug-clear-mallocSuccessSat Aug 18 02:15:38 200795
cm-debug-clear-malloc7SuccessMon Aug 20 02:08:30 200789
cm64SuccessSun Aug 19 02:17:45 200745
cm64-debugSuccessTue Aug 21 02:02:04 200784
cm64-debug-clear-mallocSuccessThu Apr 1 11:52:15 200434
rs6000-aix
cmSuccessWed Mar 4 01:09:22 20092
cm-debugSuccessMon Mar 2 01:11:08 200912
cm64SuccessWed Mar 4 01:09:51 20092
cm64-debugSuccessTue Mar 3 01:15:28 200912
x86_64-linux
cmSuccessSun Mar 6 00:01:11 20161
cm-debugSuccessSat Mar 5 00:01:45 20162

Testing status by file:


Html last generated: Sun Mar 6 05:51:21 2016

Input last modified: Mon Jun 30 14:17:15 2003


CMISS Help / Examples / cellml / vancapelle_durrer_1980