Example b35: Coupled 2D electro-mechanics: SAC models for Peter Kohl

A 6x5 element mesh with 42 nodes & 2009 grid pts is subjected to a plane wave along the LH edge. Element 3 represents an infarct with SACs. The wave spreads around the infarct and by stretching the infarct causes the SAC to initiate a new wave. Note that the key parameters are:

SAC conductance is -20
Threshold for SAC now set to lambda=1.1
Time constant scaling is 7 in infarct, 7 elsewhere
Time constant during repolaristation is 0.066ms
No Ca release in infarct
No 'fem update grid metric deformed'
In mech.ipacti To=10kPa and Ca_max=1 
Time step dt=0.002ms 


The comfile run by this example is as follows:

#Example_b35 6*5 coupled electromechanics 
#- case setup for Peter Kohl to test stretch-activated channel causing reentry. 
#
# Set up problem type definitions
$MECHANICS = 1
$ELECTRICS = 2
 
# Set up the geometry 4x4 elem 32*32mm bilinear basis
fem define para;r;emech;example 

fem define node;r;emech-6x5;example 
fem define base;r;emech;example 
fem define elem;r;emech-6x5;example 
fem define fibr;r;emech-0;example       #fibre angles =0
fem define elem;r;emech-6x5;example  fibre
fem define window;r;emech;example

# Set up the mechanics
fem define equa;r;mech;example class $MECHANICS lock
fem define mate;r;mech1;example #elem 3 has 10x lower k11  
fem group nodes 1,8,15,22,29,36  as LH_bdy_nodes
fem group nodes 7,14,21,28,35,42 as RH_bdy_nodes
fem group node external as bdy_nodes
fem define init;r;mech;example 
fem define solv;r;mech;example 
fem define acti;r;mech;example 

# Set up the electrical activation
fem define grid;r;elec-9x9;example class $ELECTRICS
fem update grid geometry
fem update grid metric
fem group grid external as boundary
fem group grid element 3 as infarct
fem define equa;r;elec-vcd;example class $ELECTRICS
fem define mate;r;elec-vcd7;example class $ELECTRICS
fem define cell;r;elec-vcd7;example class $ELECTRICS
fem update grid material class $ELECTRICS
fem group grid xi1=0 oneoff as lhs_line
fem define init;r;elec-lhs_line;example class $ELECTRICS
fem define solv;r;elec;example class $ELECTRICS
fem solve class $ELECTRICS to 0

# Solve the coupled equations (for this test example the hundreds loop is omitted)
for $time ( 0..1 ) 
{
  fem solve class $ELECTRICS restart to $time

  #fem update gauss calcium from_class ELECTRICS
  fem update gauss calcium from_class $ELECTRICS infarct 3 #zero Ca in elem 3
  #fem list activ full
  fem solve class $MECHANICS incr 0. iter 99
  #fem list strain elem 3 extrem
  fem update grid geom deformed class $ELECTRICS from_class $MECHANICS
  #fem update grid metric deformed class ELECTRICS from_class MECHANICS
  fem update grid material class $ELECTRICS
  fem update grid strain class $ELECTRICS
  #fem list grid class ELECTRICS yq grid infarct 
  fem draw field grid 1 class $ELECTRICS zmin=-100 zmax=100 noscale
  fem draw lines deformed rgb=white
  fem draw fibre deformed rgb=black
  refresh graphics
  #fem gxprint;step//HUN//TEN//UNIT;example portable_pix_map height=220 width=220
}

Additional testing commands:

fem list grid yq index v grid 1..100 class 2

Files used by this example are:

Name                           Modified     Size

example_b35.com 23-Feb-2006 2.3k convertframes.sh 10-Apr-2000 581 elec-9x9.ipgrid 06-Mar-2003 3.0k elec-lhs_line.ipinit 20-Nov-2001 491 elec-lhs_line_explicit.ipinit 10-Apr-2000 376 elec-vcd.ipequa 26-May-2003 1.5k elec-vcd7.ipcell 20-Nov-2001 6.9k elec-vcd7.ipmate 10-Apr-2000 211k elec-vcd7.ipmate_cell_old 10-Apr-2000 218k elec-vcd_explicit.ipequa 26-May-2003 1.5k elec.ipsolv 13-Apr-2007 2.1k elec.ipsolv.old 10-Apr-2000 1.6k elec_explicit.ipsolv 10-Apr-2000 573 em1.com 20-Nov-2001 3.4k emech-0.ipfibr 30-Jan-2001 3.5k emech-6x5.ipelem 10-Apr-2000 8.0k emech-6x5.ipelfb 10-Apr-2000 4.1k emech-6x5.ipnode 10-Apr-2000 5.5k emech.ipbase 10-Apr-2000 1.1k emech.ippara 21-Feb-2003 5.9k emech.ipwind 10-Apr-2000 212 grid.f 10-Apr-2000 5.4k mech.ipacti 03-Mar-2004 726 mech.ipequa 02-May-2004 1.8k mech.ipinit 12-Dec-2002 1.1k mech.ipsolv 16-Aug-2010 2.3k mech.ipsolv.old 13-Apr-2007 2.1k mech1.ipmate 12-Dec-2002 6.6k newreadme.txt 10-Apr-2000 3.0k outfile.movie 10-Apr-2000 7.3M peter.com 12-Jul-2002 3.2k peter_kohl.com 12-Jul-2002 3.2k quadbasis.ipbase 10-Apr-2000 1.2k readme.txt 10-Apr-2000 1.6k run.com 12-Jul-2002 3.4k setup.com 20-Nov-2001 1.6k step.com 10-Apr-2000 547 test.iod 10-Apr-2000 449k test.rgb 10-Apr-2000 197k test_output.com 19-Apr-2001 45 vcd.data 10-Apr-2000 52k vcd.f 10-Apr-2000 3.2k vcdi.data 10-Apr-2000 79k

Download the entire example:

Name                      Modified     Size

examples_b_b3_b35.tar.gz 17-Aug-2010 415k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:02:30 20160
cm-debugSuccessSat Mar 5 00:04:54 20162
mips-irix
cmSuccessSun Aug 19 01:38:14 20079
cm-debugSuccessWed Aug 15 01:34:02 200726
cm-debug-clear-mallocSuccessSat Aug 18 01:41:27 200731
cm-debug-clear-malloc7SuccessMon Aug 20 01:40:32 200729
cm64SuccessSun Aug 19 01:37:21 200710
cm64-debugSuccessTue Aug 21 01:33:37 200725
cm64-debug-clear-mallocSuccessThu Apr 1 11:25:14 200412
rs6000-aix
cmSuccessWed Mar 4 01:08:15 20091
cm-debugSuccessMon Mar 2 01:08:34 20096
cm64SuccessWed Mar 4 01:07:50 20091
cm64-debugSuccessTue Mar 3 01:13:56 20096
x86_64-linux
cmSuccessSun Mar 6 00:01:06 20161
cm-debugSuccessSat Mar 5 00:01:37 20161

Testing status by file:


Html last generated: Sun Mar 6 05:51:16 2016

Input last modified: Mon Aug 16 11:26:30 2010


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