Excitation wavefront propagation from Purkinje stimulation in canine ventricular myocardium.

Example b222: Excitation wavefront propagation from Purkinje stimulation in canine ventricular myocardium.

An eikonal equation is used to model propagation of excitation in a model of the canine ventricular myocardium with 90 tri-cubic Hermite elements. The solution describes the excitation time of the tissue given the initial excitation times from the stimuli received from the Purkinje network.

The comfile run by this example is as follows:

fem define parameter;r;r23;example;

fem define coordinate;r;rc3d;example;   # 3D rectangular Cartesian coordinates
fem define node;r;heart-mr3;example;    # 130 nodes
fem define base;r;hermite3;example;     # tri-cubic hermite bases and others
fem define element;r;heart-mr3;example; # 90 tricubic-Hermite elements
fem define fibre;r;heart-mr3;example;   #fibres
fem define element;r;heart-mr3;example fibre;
fem refine xi 2 cross;                  # refine in xi 2 direction
# Remove unnecessary versions from internal nodes where fields should be
# continuous.
FEM update node continuous_internal;

# Remove the confusion of scale factors.
# (Also allows the same bases to be used for field 1.)
fem update scale unit;

# Define 2 fields used in the solution:
#   Field 1 is tri-cubic Hermite (unit scalefactors) and will be set to
#     zero where dep. var. is not C1 continuous.
#   Field 2 determines versions for dep. var.
FEM define field;r;r23;example;
FEM define element;r;r23;example field;

# Orthotropic eikonal, Petrov-Galerkin FEM
fem define equation;r;eik-ort-pet;example;

# Set up groups for the various regions of the tissue that have different
# material properties.
fem group element 1,2,9..12,19,20,91,92,101,102,109,110 as purk-rf;
fem group element 62,71,72,79,80,161,162,169,170 as purk-rs;
fem group element 33..38,41..60,131..138,141..150 as purk-lv;
fem group element 99..100 as rest-rf;
fem group element 61,69..70,151,152,159..160 as rest-rs;
fem group element 31..32,39..40,121..132,139..140 as rest-lv;
fem group node xi3=0 element purk-rf as purk-rf;
fem group node xi3=1 element purk-rs as purk-rs;
fem group node xi3=0 element purk-lv as purk-lv;
fem group node purk-lv as purkinje;
fem group node xi3=0 element rest-rf as rest-rf;
fem group node xi3=1 element rest-rs as rest-rs;
fem group node xi3=0 element rest-lv as rest-lv;
fem group node purk-rf,purk-rs,rest-rf,rest-rs,rest-lv as endo;
fem group node 1..256 as all;
fem def material;r;myocardium-penet;example;
fem def initial;r;myocardium-purkinje-r23;example;

#fem update field from solution to 2
fem update field eikonal;               #calculate continuity field 1

# Precalculate guass point invariants
fem update gauss eikonal timing;

fem def solve;r;gmres;example;

if( 0 )
  { # skip gradual reduction in diffusion to save some time
    fem solve iterate 1 increment 0.02;
    fem solve iterate 1 increment 0.05;
    fem solve iterate 1 increment 0.07;
    fem solve iterate 1 increment 0.1;
    fem solve iterate 1 increment 0.15;
    fem solve iterate 1 increment 0.2;
    fem solve iterate 1 increment 0.25;
    fem solve iterate 1 increment 0.3;
    fem solve iterate 1 increment 0.35;
    fem solve iterate 1 increment 0.4;
    fem solve iterate 1 increment 0.45;
  }

# Twice the physiological level of diffusion is required to keep the solution
# stable.

# Read in precalculated solution
fem def initial;r;myocardium-purkinje-r23-a.5;example;
# Check that this is still the solution
fem solve iterate 2 increment 0.5;

if( $TESTING )
  {
    fem def initial;w;myocardium-purkinje-r23-a.5
  }

# Output results for cmgui
fem export node;heart as heart
fem export elem;heart as heart
fem export elements;purkinje field as heart
fem export nodes;penet-a.5 field as heart

Files used by this example are:

Name                                Modified     Size

example_b222.com                    20-Dec-2005  3.2k
eik-ort-pet.ipequa                  05-Dec-2003  1.0k
gmres.ipsolv                        16-Aug-2010  2.7k
gmres.ipsolv.old                    13-Apr-2007  2.5k
heart-mr3.ipelem                    05-Dec-2003   91k
heart-mr3.ipelfb                    05-Dec-2003   46k
heart-mr3.ipfibr                    05-Dec-2003   71k
heart-mr3.ipnode                    05-Dec-2003  345k
hermite3.ipbase                     05-Dec-2003   11k
myocardium-penet.ipmate             05-Dec-2003  2.3k
myocardium-purkinje-r23-a.5.ipinit  05-Dec-2003  243k
myocardium-purkinje-r23.ipinit      05-Dec-2003   59k
r23.ipelfd                          05-Dec-2003   56k
r23.ipfiel                          05-Dec-2003  332k
r23.ippara                          05-Dec-2003  5.8k
rc3d.ipcoor                         05-Dec-2003  728 
viewsol.com                         21-Dec-2005  1.2k

Download the entire example:

Name                           Modified     Size

examples_b_b2_b22_b222.tar.gz  17-Aug-2010  152k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:04:04 2016	4
cm-debug	Success	Sat Mar 5 00:24:22 2016	12
mips-irix
cm	Success	Sun Aug 19 02:24:33 2007	54
cm-debug	Success	Wed Aug 15 02:36:01 2007	157
cm-debug-clear-malloc	Success	Sat Aug 18 02:55:29 2007	175
cm-debug-clear-malloc7	Success	Mon Aug 20 02:52:42 2007	171
cm64	Success	Sun Aug 19 02:24:49 2007	54
cm64-debug	Success	Tue Aug 21 02:39:12 2007	160
cm64-debug-clear-malloc	Success	Thu Apr 1 11:23:53 2004	73
rs6000-aix
cm	Success	Wed Mar 4 01:11:37 2009	5
cm-debug	Success	Mon Mar 2 01:17:33 2009	43
cm64	Success	Wed Mar 4 01:11:39 2009	5
cm64-debug	Success	Tue Mar 3 01:22:52 2009	43
x86_64-linux
cm	Success	Sun Mar 6 00:01:11 2016	2
cm-debug	Success	Sat Mar 5 00:02:08 2016	7

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.

myocardium-purkinje-r23-a.5.ipinit

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 05:51:15 2016

Input last modified: Mon Aug 16 11:26:28 2010

CMISS Help / Examples / b / b2 / b22 / b222