Implicit 1D/2D coupled branch/tissue

Example b211j: Implicit 1D/2D coupled branch/tissue

This example solves the monodomain equation using the cubic ionic current model implicitly. There are three 1d elements coupled to one 2d element. Activation spreads down the 1d elements and into the 2d host mesh.

The comfile run by this example is as follows:

#--------------
#Assign regions
#--------------

# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: ASSIGN variable MESH2D 1
$MESH2D = 1


# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: ASSIGN variable TREE1D 2
$TREE1D = 2

 
fem define para;r;branch;example

 
#--------------------------------------------
#Define two regions, one for the tree and one
#  for the host mesh.
#--------------------------------------------
fem define regi;r;branch;example
 
#---------------------------------------------
#Define a 1d basis for the tree and a 2d basis
#  for the host mesh.
#---------------------------------------------
fem define base;r;branch;example
 
#-------------------------------------
#Define the host mesh in region MESH2D
#-------------------------------------
fem define node;r;square;example reg $MESH2D
fem define elem;r;square;example reg $MESH2D
fem define fibr;d reg $MESH2D
fem define elem;r;square;example fibre reg $MESH2D
 
#-------------------------------------
#Define the host mesh in region MESH2D
#-------------------------------------
fem define node;r;branch;example reg $TREE1D
fem define elem;r;branch;example reg $TREE1D
 
#-----------------------------------------------
#Set up a finite difference grid in both regions
#-----------------------------------------------
fem define grid;r;1and2d;example reg $MESH2D,$TREE1D
fem update grid geometry reg $MESH2D,$TREE1D
fem update grid metric reg $MESH2D,$TREE1D
fem group grid external as boundary1 reg $MESH2D
fem group grid external as boundary2 reg $TREE1D
 
#-----------------------------------
#Set up equations in the two regions
#-----------------------------------
fem define equa;r;square;example reg $MESH2D,$TREE1D
 
#----------------------------------------------
#Define material parameters for the two regions
#----------------------------------------------
fem define mate;r;square;example reg $MESH2D
fem define cell;r;square;example reg $MESH2D
fem define mate;r;branch;example reg $TREE1D
fem define cell;r;branch;example reg $TREE1D
fem update grid material reg $MESH2D
fem update grid material reg $TREE1D
 
#--------------------------------------
#Define initial and boundary conditions
#--------------------------------------
fem define init;r;square;example reg $MESH2D
fem define init;r;branch;example reg $TREE1D
 
#-------------------------------
#Define coupling between regions
#-------------------------------
fem define coup;c tree_region $TREE1D tissue_region $MESH2D
 
#--------------------------
#Define solution parameters
#--------------------------
fem define solv;r;square;example reg $MESH2D,$TREE1D

fem export node;tissue as tissue reg $MESH2D
fem export elem;tissue as tissue reg $MESH2D
fem export node;tree as tree reg $TREE1D
fem export elem;tree as tree reg $TREE1D
 
#-----
#Solve
#-----
fem solve to 0 reg $MESH2D,$TREE1D
fem define wind;c
 

# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: DO UNIT=0..9
for $UNIT ( 0..9 ) 
{


# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: DO DEC=0,5
for $DEC ( 0,5 ) 
{


# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: fem solve restart to $UNIT//.//$DEC reg $MESH2D,$TREE1D
fem solve restart to "${UNIT}.$DEC" reg $MESH2D,$TREE1D

fem update grid solution
fem draw grid values zmin=-120 zmax=20 noscale reg $MESH2D
fem draw field grid 1 zmin=-120 zmax=20 noscale reg $TREE1D
refresh graphics

# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: fem export elem;tissue_//$UNIT//$DEC field reg $MESH2D as tissue
fem export elem;tissue_${UNIT}$DEC field reg $MESH2D as tissue


# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: fem export elem;tree_//$UNIT//$DEC field reg $TREE1D as tree
fem export elem;tree_${UNIT}$DEC field reg $TREE1D as tree


# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: ENDDO
}



# Command updated by fixcom.sh on Wed Aug 23 17:49:58 NZT 2000
# Old command: ENDDO
}



#See draw.com for viewing in cmgui

Additional testing commands:

fem list grid yq index v

Files used by this example are:

Name                    Modified     Size

example_b211j.com       20-Nov-2001  4.0k
1and2d.irgrid           11-Mar-2003  875 
branch.ipbase           10-Apr-2000  1.9k
branch.ipcell           10-Apr-2000  1.7k
branch.ipelem           10-Apr-2000  833 
branch.ipinit           10-Apr-2000  483 
branch.ipmate           10-Apr-2000  1.7k
branch.ipmate_cell_old  10-Apr-2000  3.5k
branch.ipnode           10-Apr-2000  852 
branch.ippara           12-Nov-2002  5.9k
branch.ipregi           10-Apr-2000   93 
draw.com                20-Nov-2001  2.2k
square.ipcell           10-Apr-2000  1.7k
square.ipelem           10-Apr-2000  336 
square.ipelfb           10-Apr-2000  225 
square.ipinit           10-Apr-2000  289 
square.ipmate           10-Apr-2000  1.7k
square.ipmate_cell_old  10-Apr-2000  3.5k
square.ipnode           10-Apr-2000  801 
square.irequa           26-May-2003  2.9k
square.irsolv           13-Apr-2007  2.8k
square.irsolv.old       10-Apr-2000  2.4k
test_output.com         23-Apr-2001   25

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b211_b211j.tar.gz  14-Apr-2007   10k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:02:15 2016	1
cm-debug	Success	Sat Mar 5 00:04:16 2016	1
mips-irix
cm	Success	Sun Aug 19 01:35:41 2007	8
cm-debug	Success	Wed Aug 15 01:35:31 2007	22
cm-debug-clear-malloc	Success	Sat Aug 18 01:41:53 2007	32
cm-debug-clear-malloc7	Success	Mon Aug 20 01:38:15 2007	30
cm64	Success	Sun Aug 19 01:36:35 2007	8
cm64-debug	Success	Tue Aug 21 01:31:26 2007	22
cm64-debug-clear-malloc	Success	Thu Apr 1 11:14:00 2004	11
rs6000-aix
cm	Success	Wed Mar 4 01:08:11 2009	2
cm-debug	Success	Mon Mar 2 01:08:04 2009	4
cm64	Success	Wed Mar 4 01:08:11 2009	2
cm64-debug	Success	Tue Mar 3 01:13:15 2009	5
x86_64-linux
cm	Success	Sun Mar 6 00:01:05 2016	1
cm-debug	Success	Sat Mar 5 00:01:35 2016	1

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
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 05:51:08 2016

Input last modified: Fri Apr 13 10:38:02 2007

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