One ventricle direct assembly

Example b2142: One ventricle direct assembly

This example directly couples a circular boundary element region to an annular bidomain grid region.

The comfile run by this example is as follows:

#Example b2142
#
# This example directly couples a circular boundary element
#  region to an annular bidomain grid region. 
#

# Set up problem regions
#  (1 grid and 1 bem)
$VENTCL=1 
$GRIDHT=2 

# Set up problem classes
#  (1 laplace and 2 bidomain)
$BLPL=1 
$TMEM=2 
$EXTC=3 

# Define problem geometry
fem define para;r;torsoslice;example
fem define regi;r;torsoslice;example
fem define node;r;ventcl3;example reg $VENTCL
fem define node;r;gridht;example  reg $GRIDHT
fem define base;r;linear;example
fem define elem;r;ventcl3;example reg $VENTCL
fem define elem;r;gridht;example  reg $GRIDHT

# Generate the grid mesh
fem define grid;r;gridht;example reg $GRIDHT
fem update grid geom reg $GRIDHT
fem update grid metric reg $GRIDHT
fem group grid external as boundary reg $GRIDHT
fem group grid xi2=0 as endocardium reg $GRIDHT
fem group grid line 1 xidirn 2 as stimulus reg $GRIDHT

# Calculate the mapping from grid points to
#  boundary element nodes
fem update node grid grid_reg $GRIDHT bem_reg $VENTCL

# Adjust the boundary element node positions to align
#  exactly with the boundary collocation points - this
#  should be the case - only the refine command makes
#  them a bit different when the mesh was initially created
fem update node geomet from grid reg $VENTCL

# Define the problem setup
fem define equa;r;ventcl;example reg $VENTCL class $BLPL lock
fem define equa;r;gridht;example reg $GRIDHT class $TMEM,$EXTC lock
fem define mate;r;ventcl;example reg $VENTCL class $BLPL
fem define mate;r;gridht;example reg $GRIDHT class $TMEM,$EXTC
fem define cell;r;gridht;example reg $GRIDHT class $TMEM,$EXTC
fem update grid material reg $GRIDHT class $TMEM,$EXTC
fem define init;r;ventcl;example reg $VENTCL class $BLPL
fem define init;r;gridht;example reg $GRIDHT class $TMEM,$EXTC
fem define solv;r;gridht;example reg $GRIDHT class $TMEM
fem define solv;r;gridht;example reg $GRIDHT class $EXTC
fem define solv;r;ventcl;example reg $VENTCL class $BLPL

# Solve the laplace problem
fem solve reg $VENTCL class $BLPL

# Solve the coupled bidomain problem for 10ms
fem solve activ coupled to 10 reg $GRIDHT,$VENTCL class $TMEM,$EXTC,$BLPL grid endocardium cptype 2

Additional testing commands:

#Testing example b2142
fem list node solution
fem list node flux

Files used by this example are:

Name               Modified     Size

example_b2142.com  06-Jun-2001  2.1k
gridht.ipcell      06-Jun-2001  1.7k
gridht.ipelem      06-Jun-2001  2.2k
gridht.ipequa      26-May-2003  1.4k
gridht.ipgrid      06-Mar-2003  539 
gridht.ipinit      06-Jun-2001  841 
gridht.ipmate      06-Jun-2001  1.8k
gridht.ipnode      06-Jun-2001  5.1k
gridht.ipsolv      13-Apr-2007  1.8k
gridht.ipsolv.old  06-Jun-2001  1.4k
linear.ipbase      06-Jun-2001  2.2k
test_output.com    06-Jun-2001   66 
torsoslice.ippara  12-Nov-2002  5.9k
torsoslice.ipregi  06-Jun-2001   93 
ventcl.ipequa      26-May-2003  1.2k
ventcl.ipinit      06-Jun-2001  572 
ventcl.ipmate      06-Jun-2001  606 
ventcl.ipsolv      13-Apr-2007  1.2k
ventcl3.ipelem     06-Jun-2001  8.2k
ventcl3.ipnode     06-Jun-2001  9.8k

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b214_b2142.tar.gz  14-Apr-2007   20k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:02:26 2016	1
cm-debug	Success	Sat Mar 5 00:05:00 2016	1
mips-irix
cm	Success	Sun Aug 19 01:36:36 2007	7
cm-debug	Success	Wed Aug 15 01:35:27 2007	28
cm-debug-clear-malloc	Success	Sat Aug 18 01:46:42 2007	38
cm-debug-clear-malloc7	Success	Mon Aug 20 01:44:22 2007	39
cm64	Success	Sun Aug 19 01:35:47 2007	8
cm64-debug	Success	Tue Aug 21 01:34:36 2007	28
cm64-debug-clear-malloc	Success	Thu Apr 1 11:20:30 2004	16
rs6000-aix
cm	Success	Wed Mar 4 01:08:15 2009	1
cm-debug	Success	Mon Mar 2 01:08:25 2009	5
cm64	Success	Wed Mar 4 01:07:49 2009	1
cm64-debug	Success	Tue Mar 3 01:13:27 2009	5
x86_64-linux
cm	Success	Sun Mar 6 00:01:06 2016	1
cm-debug	Success	Sat Mar 5 00:01:37 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.

extcGKK.ipmatr

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 05:51:14 2016

Input last modified: Fri Apr 13 10:39:22 2007

CMISS Help / Examples / b / b2 / b21 / b214 / b2142