Example b33: Coupled bidomain-mechanics example

Example b33 - coupled bidomain electromechanics. This example solves the bidomain equations on a 2d domain which is coupled to a mechanical deformation from the release of intracellular calcium. The VanCapelle Durer ionic current model is used. The mesh is 4*4 elements with 9*9 grid points per element. An analytic solution is used to get the extracellular boundary conditions. Solution is by sparse LU factorisation.

The comfile run by this example is as follows:

#Example_b33 4*4 small coupled bidomain-electromechanics with solution. 
#
# Set up problem type definitions
$MECHANICS = 1
$ELECTRICS = 2
$EXTRACELL = 3
 
# Set up the geometry 4x4 elem 32*32mm bilinear basis
fem define para;r;emech;example

fem define node;r;emech-4x4;example
fem define base;r;emech;example
fem define elem;r;emech-4x4;example
fem define fibr;r;emech-0;example
fem define elem;r;emech-4x4;example fibre
fem define window;c

# Set up the mechanics
fem define equa;r;mech;example class $MECHANICS lock
fem define mate;r;mech;example
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 define equa;r;elec-vcd;example class $ELECTRICS,$EXTRACELL
fem define mate;r;elec-vcd;example class $ELECTRICS
fem define cell;r;elec-vcd;example class $ELECTRICS
fem update grid material class $ELECTRICS,$EXTRACELL
fem group grid xi1=0 oneoff as lhs_line
fem define init;r;elec-lhs_line;example class $ELECTRICS,$EXTRACELL
fem define solv;r;elec;example class $ELECTRICS
fem define solv;r;elec2;example class $EXTRACELL
fem solve class $ELECTRICS,$EXTRACELL to 0

# Solve the coupled equations
for $time ( 0..19 ) 
{
  fem solve class $ELECTRICS,$EXTRACELL restart to $time
  fem update gauss calcium from_class $ELECTRICS
  fem solve class $MECHANICS incr 0. iter 99
  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 $ELECTRICS,$EXTRACELL
  fem draw field grid 1 class $ELECTRICS zmin=-120 zmax=20 noscale
  fem draw lines deformed rgb=white
  fem draw fibre deformed rgb=black
  refresh graphics
}

Additional testing commands:

fem list grid geometry grid 1..50
fem list grid yq index v grid 1..50 class 2
fem list grid yq index v grid 1..50 class 3

Files used by this example are:

Name                      Modified     Size

example_b33.com           21-Feb-2003  1.8k
elec-9x9.ipgrid           06-Mar-2003  1.8k
elec-lhs_line.ipinit      20-Nov-2001  836 
elec-vcd.ipcell           20-Nov-2001  2.3k
elec-vcd.ipequa           26-May-2003  1.4k
elec-vcd.ipmate           10-Apr-2000  1.7k
elec-vcd.ipmate_cell_old  10-Apr-2000  4.0k
elec.ipsolv               13-Apr-2007  1.8k
elec.ipsolv.old           12-Jun-2001  1.4k
elec2.ipsolv              13-Apr-2007  1.8k
elec2.ipsolv.old          12-Jun-2001  1.4k
emech-0.ipfibr            30-Jan-2001  2.0k
emech-4x4.ipelem          10-Apr-2000  4.3k
emech-4x4.ipelfb          10-Apr-2000  2.3k
emech-4x4.ipnode          10-Apr-2000  4.2k
emech.ipbase              10-Apr-2000  1.1k
emech.ippara              21-Feb-2003  5.9k
mech.ipacti               03-Mar-2004  735 
mech.ipequa               02-May-2004  1.8k
mech.ipinit               12-Dec-2002  995 
mech.ipmate               12-Dec-2002  6.4k
mech.ipsolv               16-Aug-2010  2.7k
mech.ipsolv.old           13-Apr-2007  2.5k
quadbasis.ipbase          10-Apr-2000  1.2k
test_output.com           19-Apr-2001  122 

Download the entire example:

Name                      Modified     Size

examples_b_b3_b33.tar.gz  17-Aug-2010   13k

Testing status by version:

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.

  
  
• cmiss_test.out
  

  i686-linux
  Failure	cm:	ndiff test: significant differences with generic answer.
  Failure	cm-debug:	ndiff test: 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
  Failure	cm:	ndiff test: significant differences with generic answer.
  Failure	cm-debug:	ndiff test: significant differences with generic answer.

  
  

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

Input last modified: Mon Aug 16 11:26:29 2010