Example cellml/cubic: Cubic polynomial model.

This example solves the cubic polynomial model defined by a CellML version of the model. It is a simple model of activation and has no recovery.

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/cubic;

# 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/cubic;

# Define the CellML model to use and map the parameters to CMISS and
# specify initial/boundary conditions for the cell model.
fem define cell;r;$example/cubic;

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

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

# Define an explicit Adams integrator.
fem define solve;r;$example/cubic;

# Initialise the solve.
fem solve to 0;

# Create a history file to store output variables of interest.
fem open history;cubic write variables yqs niqslist 1..3 binary;

# Loop through time integrating the cellular model.
$Tend = 150;
$dt = 1.0;
for ($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;cubic history cubic from grid yqs iy 1..3 binary;

# Define an export of the CMISS signals to UnEMAP signals..
fem define export;r;$example/cubic;
# ..and export the signals to a UnEMAP signal file.
fem export signal;cubic electrodes signal cubic names cell;

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

Files used by this example are:

Name          Modified     Size

cubic.com 05-Apr-2003 2.0k cubic.binsig 05-Apr-2003 7.1k cubic.cml 04-Oct-2003 11k cubic.ipcell 11-Jun-2003 2.7k cubic.ipequa 26-May-2003 1.5k cubic.ipexpo 05-Apr-2003 657 cubic.ipinit 05-Apr-2003 214 cubic.ipmatc 05-Apr-2003 356 cubic.ipmate 05-Apr-2003 3.2k cubic.ippara 05-Apr-2003 5.9k cubic.ipsolv 05-Apr-2003 907

Download the entire example:

Name                          Modified     Size

examples_cellml_cubic.tar.gz 19-Aug-2006 9.7k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:02:31 20160
cm-debugSuccessSat Mar 5 00:04:26 20161
mips-irix
cmSuccessSun Aug 19 01:38:33 200711
cm-debugSuccessWed Aug 15 01:32:08 200715
cm-debug-clear-mallocSuccessSat Aug 18 01:36:38 200723
cm-debug-clear-malloc7SuccessMon Aug 20 01:35:31 200723
cm64SuccessSun Aug 19 01:41:07 200711
cm64-debugSuccessTue Aug 21 01:28:54 200715
cm64-debug-clear-mallocSuccessThu Apr 1 11:43:31 20047
rs6000-aix
cmSuccessWed Mar 4 01:07:52 20092
cm-debugSuccessMon Mar 2 01:07:34 20092
cm64SuccessWed Mar 4 01:08:45 20091
cm64-debugSuccessTue Mar 3 01:12:19 20093
x86_64-linux
cmSuccessSun Mar 6 00:01:06 20160
cm-debugSuccessSat Mar 5 00:01:37 20161

Testing status by file:


Html last generated: Sun Mar 6 05:51:20 2016

Input last modified: Sat Oct 4 14:37:28 2003


CMISS Help / Examples / cellml / cubic