Fenton and Karma

Example cellml/fenton_karma_1998: Fenton and Karma - 1998

This example solves the Fenton & Karma 1998 simplified ventricular myocyte model, defined by a CellML version of the model.

Fenton & Karma provide a three current simplification of the original BR and LR I models, as well as a modified BR and a guniea-pig LV epicardial model. All four of these versions are given in this example as separate parameter sets (IPCELL files) for the same set of equations in the single CellML file.

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

The comfile run by this example is as follows:

# 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;
}

# We want to run the same model for multiple different parameter sets, so
# set up a function to do the solve and call it for each parameter set
sub runModel {
    $model = shift;

    fem define cell;r;"$example/$model";
    fem define material;d cell;
    fem define material;d;
    fem update grid material;
    fem define initial;d;
    fem define solve;r;$example/lsoda;
    fem solve to 0;
    fem open history;$model write variables yqs niqslist 1..13 binary;
    $Tend = 1500;
    $dt = 1.0;
    for ($time=0;$time<$Tend;$time+=$dt) {
        fem solve restart to $time;
        fem write history time $time variables yqs binary;
    }
    fem close history binary;
    fem evaluate electrode;$model history $model from grid yqs iy 1..13 binary;
    fem define export;r;$example/fenton_karma_model_1998;
    fem export signal;$model electrodes signal $model names cell;
}

fem define parameters;r;$example/cellml;
fem define node;d;
fem define bas;d;
fem define elem;d;
fem define grid;d;
fem update grid geometry;
fem update grid metric;
fem define equation;r;$example/cellml;

@models = ("FK_BR","FK_mod_BR","FK_mod_LR_I","FK_GP");
foreach $model (@models) {
    &runModel($model);
}

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

Files used by this example are:

Name                            Modified     Size

fenton_karma_1998.com           14-Nov-2003  1.6k
FK_BR.binsig                    14-Nov-2003  127k
FK_BR.ipcell                    14-Nov-2003  5.6k
FK_GP.binsig                    14-Nov-2003  127k
FK_GP.ipcell                    14-Nov-2003  5.6k
FK_mod_BR.binsig                14-Nov-2003  127k
FK_mod_BR.ipcell                14-Nov-2003  5.7k
FK_mod_LR_I.binsig              14-Nov-2003  127k
FK_mod_LR_I.ipcell              14-Nov-2003  5.6k
cellml.ipequa                   08-Nov-2003  1.5k
cellml.ippara                   08-Nov-2003  5.9k
fenton_karma_model_1998.cml     14-Nov-2003   33k
fenton_karma_model_1998.ipexpo  14-Nov-2003  658 
lsoda.ipsolv                    08-Nov-2003  1.2k

Download the entire example:

Name                                      Modified     Size

examples_cellml_fenton_karma_1998.tar.gz  19-Aug-2006  179k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:09:39 2016	13
cm-debug	Success	Sat Mar 5 00:33:24 2016	22
mips-irix
cm	Success	Sun Aug 19 05:43:17 2007	265
cm-debug	Success	Wed Aug 15 05:56:19 2007	480
cm-debug-clear-malloc	Success	Sat Aug 11 03:43:31 2007	511
cm-debug-clear-malloc7	Success	Mon Aug 20 05:54:06 2007	493
cm64	Success	Sun Aug 19 05:58:39 2007	267
cm64-debug	Success	Tue Aug 21 03:59:08 2007	476
cm64-debug-clear-malloc	Success	Thu Apr 1 11:48:19 2004	224
rs6000-aix
cm	Success	Wed Mar 4 01:21:32 2009	30
cm-debug	Success	Mon Mar 2 01:26:44 2009	76
cm64	Success	Wed Mar 4 01:24:11 2009	43
cm64-debug	Success	Tue Mar 3 01:36:43 2009	82
x86_64-linux
cm	Success	Sun Mar 6 00:01:46 2016	8
cm-debug	Success	Sat Mar 5 00:03:39 2016	12

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.

FK_BR.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.

FK_GP.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.

FK_mod_BR.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.

FK_mod_LR_I.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 05:51:20 2016

Input last modified: Fri Nov 14 20:16:26 2003

CMISS Help / Examples / cellml / fenton_karma_1998