Torso and one ventricle fixed point iterations

Example b2141: Torso and one ventricle fixed point iterations

This example demonstrates how to couple a single ventricle and a single torso region through a multiple surface fixed point iteration

The comfile run by this example is as follows:

#Example b2141
#
# This example demonstrates how to couple a single ventricle
#  and a single torso region through a multiple surface fixed
#  point iteration
#

# Problem classes
$CAVITY=1 
$VENTCL=2 
$BEMHRT=3 
$GRIDHT=4 

# Problem regions
$TLPL=1 
$BLPL=2
$TMEM=3 
$EXTC=4 

# Iteration variables
$NUM_ITERS=0 
$MAX_ITERS=50 
$FINISHED=0
$POTE_TOL=0.1 
$FLUX_TOL=0.1 
$POTE1=1.0
$FLUX1=1.0
$POTE2=1.0
$FLUX2=1.0
$ALPHA1=0.0 
$ALPHA2=0.7 

# Define problem geometry
fem define para;r;torsoslice;example
fem define regi;r;torsoslice;example
fem define node;r;cavity3;example reg $CAVITY
fem define node;r;ventcl3;example reg $VENTCL
fem define node;r;bemhrt3;example reg $BEMHRT
fem define node;r;gridht;example  reg $GRIDHT
fem define base;r;linear;example
fem define elem;r;cavity3;example reg $CAVITY
fem define elem;r;ventcl3;example reg $VENTCL
fem define elem;r;bemhrt3;example reg $BEMHRT
fem define elem;r;gridht;example  reg $GRIDHT

# Define finite difference grid
fem define grid;r;gridht;example reg $GRIDHT
fem update grid geom reg $GRIDHT
fem update grid metric reg $GRIDHT
fem group grid xi2=0 as endocardium reg $GRIDHT
fem group grid xi2=1 as epicardium reg $GRIDHT
fem group grid external as boundary reg $GRIDHT
fem group grid line 1 xidirn 2 as stimulus reg $GRIDHT

# Create node to grid mapping
fem update node grid grid_reg $GRIDHT bem_reg $BEMHRT
fem update node geomet from grid reg $BEMHRT

# Define equations
fem define equa;r;cavity;example reg $CAVITY class $TLPL lock
fem define equa;r;ventcl;example reg $VENTCL class $BLPL lock
fem define equa;r;gridht;example reg $GRIDHT class $TMEM,$EXTC lock

# Define material parameters
fem define mate;r;cavity;example reg $CAVITY class $TLPL
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

# Define initial conditions
fem define init;r;cavity;example reg $CAVITY class $TLPL
fem define init;r;ventcl;example reg $VENTCL class $BLPL
fem define init;r;gridht;example reg $GRIDHT class $TMEM,$EXTC

# Define grid to boundary element coupling
fem up elem region $GRIDHT,$VENTCL,$CAVITY class $EXTC,$BLPL,$TLPL grids boundary

# Define solution parameters
fem define solv;r;gridht;example reg $GRIDHT class $TMEM
fem define solv;r;gridht;example reg $GRIDHT class $EXTC
fem define solv;r;cavity;example reg $CAVITY class $TLPL
fem define solv;r;ventcl;example reg $VENTCL class $BLPL

# Solve the passive torso problems
fem solve reg $CAVITY class $TLPL
fem solve reg $VENTCL class $BLPL

# Solve the bidomain problem
fem solve activ coupled to 0 reg $GRIDHT,$CAVITY,$VENTCL class $TMEM,$EXTC,$TLPL,$BLPL

for $TEN ( 0..0 ) {
  for $UNIT (0..0) {
    for $DECI ( 0..9 ) {
      for $HUND ( 0..9 ) {

        # Solve a bidomain time step
        fem solve activ coupled transmembrane restart to "$TEN$UNIT".'.'."$DECI$HUND" reg $GRIDHT class $TMEM,$EXTC noupdate
        $NUM_ITERS = 0
        $FINISHED = 0

        # Find a converged solution
        while( !$FINISHED && $NUM_ITERS<=$MAX_ITERS ) {
          $NUM_ITERS++ 

          fem solve activ coupled extra rest reg $GRIDHT,$CAVITY,$VENTCL cl $TMEM,$EXTC,$TLPL,$BLPL noupdate static alpha $ALPHA1
          fem update init from grid region $CAVITY,$BEMHRT,$GRIDHT class $EXTC,$TLPL,$EXTC alpha $ALPHA2
          fem update init from grid region $VENTCL,$BEMHRT,$GRIDHT class $EXTC,$BLPL,$EXTC alpha $ALPHA2
          fem solve reg $CAVITY class $TLPL
          fem solve reg $VENTCL class $BLPL
          fem check conv grid_reg $BEMHRT grid_cl $EXTC bem_reg $CAVITY bem_cl $TLPL grid_update_cl $EXTC return POTE1 FLUX1
          fem check conv grid_reg $BEMHRT grid_cl $EXTC bem_reg $VENTCL bem_cl $BLPL grid_update_cl $EXTC return POTE2 FLUX2

          $FINISHED = (abs($POTE1)<=$POTE_TOL && abs($FLUX1)<=$FLUX_TOL && abs($POTE2)<=$POTE_TOL && abs($FLUX2)<=$FLUX_TOL)
          print("Iteration $NUM_ITERS\n");
          }

        # Update the transmembrane potential field
        fem solve activ coupled trans rest reg $GRIDHT,$CAVITY,$VENTCL class $TMEM,$EXTC,$TLPL,$BLPL update static alpha $ALPHA1

        if($NUM_ITERS<$MAX_ITERS) {
          print("Solution converged in $NUM_ITERS iterations\n");
        }
        else {
          print("Solution did not converge in $MAX_ITERS iterations\n");
          print("Outside potential $POTE1 Outside flux $FLUX1\n");
        }
      }
    }
  }
}

Additional testing commands:

#Testing example b2141
fem list node sol reg 1 cl 1
fem list node sol reg 2 cl 2

Files used by this example are:

Name               Modified     Size

example_b2141.com  06-Jun-2001  4.4k
bemhrt3.ipelem     06-Jun-2001   32k
bemhrt3.ipnode     06-Jun-2001   38k
cavity.ipequa      26-May-2003  1.2k
cavity.ipinit      06-Jun-2001  2.2k
cavity.ipmate      06-Jun-2001  606 
cavity.ipsolv      13-Apr-2007  1.5k
cavity3.ipelem     06-Jun-2001   32k
cavity3.ipnode     06-Jun-2001   38k
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  541 
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  1.9k
gridht.ipsolv.old  06-Jun-2001  1.4k
linear.ipbase      06-Jun-2001  2.2k
test_output.com    06-Jun-2001   82 
torsoslice.ipbase  06-Jun-2001  2.5k
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  1.2k
ventcl.ipmate      06-Jun-2001  606 
ventcl.ipsolv      13-Apr-2007  1.2k
ventcl3.ipelem     06-Jun-2001   16k
ventcl3.ipnode     06-Jun-2001   19k

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b214_b2141.tar.gz  14-Apr-2007   30k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:04:53 2016	5
cm-debug	Success	Sat Mar 5 00:24:27 2016	13
mips-irix
cm	Success	Sun Aug 19 03:08:52 2007	101
cm-debug	Success	Wed Aug 15 02:59:00 2007	240
cm-debug-clear-malloc	Success	Sat Aug 18 03:14:55 2007	245
cm-debug-clear-malloc7	Success	Mon Aug 20 03:13:37 2007	244
cm64	Success	Sun Aug 19 03:13:46 2007	106
cm64-debug	Success	Tue Aug 21 03:46:32 2007	265
cm64-debug-clear-malloc	Success	Thu Apr 1 11:21:52 2004	119
rs6000-aix
cm	Success	Wed Mar 4 01:12:02 2009	5
cm-debug	Success	Mon Mar 2 01:20:14 2009	42
cm64	Success	Wed Mar 4 01:11:31 2009	6
cm64-debug	Success	Tue Mar 3 01:25:00 2009	40
x86_64-linux
cm	Success	Sun Mar 6 00:01:14 2016	3
cm-debug	Success	Sat Mar 5 00:02:18 2016	8

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 05:51:13 2016

Input last modified: Fri Apr 13 10:39:20 2007

CMISS Help / Examples / b / b2 / b21 / b214 / b2141