Isovolumic contraction of LV mesh in RC coordinates

Example 5f1: Isovolumic contraction of LV mesh in RC coordinates

An ellipsoidal shaped mesh in rectangular Cartesian coordinates is inflated and then coupled with a isovolumic cavity region during the isovolumic contraction phase where an active stress component is added to the fiber direction.

The example is made for testing the coupling of the wall and cavity regions and thus the result from the inflation is read in and the simulation is started from after the inflation phase.

Created by Espen Remme November 2003.

The comfile run by this example is as follows:

#Example 5f1

# You may want to use the optimized multiprocessor version of cmiss
# for this example.
#set num_threads 3

$INFLATION = 0;
$IVC = 1;

# Regions
$WALL = 1;
$CAVITY = 2;
$iterations = 15;

fem def param;r;full_big;example
fem define coor;r;rcCoord;example reg $WALL
fem define base;r;basisfuncs;example

fem define nodes;r;rc3;example reg $WALL
fem define elements;r;rc;example reg $WALL


fem define fibre;r;simple;example reg $WALL
fem define element;r;simple;example fibre reg $WALL

$name = "heartOriginal"
$file = $name
fem export nodes;$file as $name offset 0000
fem export elements;$file as $name offset_elem 0000

# Material groups
fem group nodes 1,18 as apexNodes
fem group nodes 2..5,19..22 as subApexNodes
fem group nodes 6..17,23..34 as normalNodes
fem group nodes 14..17,31..34 as baseNodes
# Boundary Condition groups
fem group nodes 1,18 as fixedApexNodes
fem group nodes 14..17,31..34 as fixedBaseNodes
fem group nodes 14,16 as y_axisNodes
fem group nodes 15,17 as z_axisNodes
 # Residual strains groups
fem group nodes 6..13 as nodes095
fem group nodes 1..5,14..22,31..34 as nodes100
fem group nodes 23..30 as nodes105

fem define equation;r;equation;example reg $WALL lock
fem define material;r;inhomo_nodes;example reg $WALL
fem define acti;r;calcium000;example reg $WALL

if($INFLATION)
{
  fem define initial;r;x_Base_node_restricted;example reg $WALL
  fem define solve;r;solve;example reg $WALL
  fem solve increment 0.0 iter 10 # due to residual strains
  fem solve increment 1 iter 20
  fem define initial;w;wall_inflated reg $WALL
} else #All ready solved the inflation phase
{
  fem define initial;r;wall_inflated;example reg $WALL
  fem define solve;r;solve;example reg $WALL
  fem evaluate residuals wrt geom_params
}

$name = "heartInflated"
$file = $name
fem export nodes;$file field as $name offset 1000
fem export elements;$file field as $name offset_elem 1000


if($IVC)
{
  fem define region;r;regions;example
  fem define coord;r;cavityCoord;example region $CAVITY
  fem define node;r;cavity;example region $CAVITY
  fem define element;r;cavity;example region $CAVITY

  # Set up equations, material properties and initial conditions
  # for cavity region
  fem define equation;r;equationRegions;example region $WALL,$CAVITY lock
  fem define material;r;materialCavityIVC;example region $CAVITY
  fem define initial;r;initCavity;example region $CAVITY
  #
  # Define cavity-to-wall coupling and solution procedure information
  fem define coupling;r;coupled;example
  fem define solve;r;solveRegion;example coupled region $WALL,$CAVITY
  #
  # Transfer wall deformation from the inflation problem to 
  # geometric dependent variables for the cavity region
  fem update solution coupled source_region $WALL
  fem update solution cavity_reference average 104 in 1 node 14..17 region $CAVITY

  fem evaluate residuals wrt geom_params coupled
  fem list element total region $CAVITY
  fem list element deformed total region $CAVITY
  #fem evaluate reactions coupled

  fem define active;r;calcium010;example
  fem solve coupled increment 0.0 iter $iterations error 1.0e-3
  fem define active;r;calcium014;example
  fem solve coupled increment 0.0 iter $iterations error 1.0e-3
  fem define active;r;calcium018;example
  fem solve coupled increment 0.0 iter $iterations error 1.0e-3

  $name = "heartIVC"
  $file = $name
  fem export nodes;$file field as $name offset 2000
  fem export elements;$file field as $name offset_elem 2000

  fem define initial;w;wall_endIVC region $WALL
  fem define initial;w;coupled_endIVC region $WALL,$CAVITY
  
} else
{
  fem define active;r;calcium018;example
  fem define initial;r;wall_endIVC;example region $WALL
  fem define solve;r;solve;example reg $WALL
  fem eval resid wrt geom reg $WALL
  #fem solve increment 0.0 iter 20 error 1.0e-1
} # if $IVC

Files used by this example are:

Name                           Modified     Size

example_5f1.com                05-Nov-2003  3.7k
basisfuncs.ipbase              05-Nov-2003   16k
calcium000.ipacti              03-Mar-2004  757 
calcium010.ipacti              03-Mar-2004  760 
calcium014.ipacti              03-Mar-2004  760 
calcium018.ipacti              03-Mar-2004  760 
cavity.ipelem                  05-Nov-2003   13k
cavity.ipnode                  05-Nov-2003   43k
cavityCoord.ipcoor             05-Nov-2003  678 
coupled.ipcoup                 05-Nov-2003  437 
createCavityNodes.pl           05-Nov-2003   10k
draw.com                       05-Nov-2003  1.1k
equation.ipequa                02-May-2004  2.1k
equationRegions.irequa         02-May-2004  3.8k
full_big.ippara                05-Nov-2003  5.8k
inhomo_nodes.ipmate            05-Nov-2003   17k
initCavity.ipinit              05-Nov-2003   12k
materialCavityIVC.ipmate       05-Nov-2003  390 
rc.ipelem                      05-Nov-2003   15k
rc3.ipnode                     05-Nov-2003   75k
rcCoord.ipcoor                 05-Nov-2003  678 
regions.ipregi                 05-Nov-2003   93 
simple.ipelfb                  05-Nov-2003  4.3k
simple.ipfibr                  05-Nov-2003  6.2k
solve.ipsolv                   16-Aug-2010  2.2k
solve.ipsolv.old               13-Apr-2007  2.1k
solveRegion.irsolv             16-Aug-2010  2.6k
solveRegion.irsolv.old         13-Apr-2007  2.4k
wall_endIVC.ipinit             05-Nov-2003  191k
wall_inflated.ipinit           05-Nov-2003  194k
x_Base_node_restricted.ipinit  05-Nov-2003  9.8k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Failure	Sun Mar 6 01:27:33 2016	82
	last break	Tue Feb 24 03:55:00 2015	80
	last success	Sun Apr 17 01:23:00 2011	183
cm-debug	Failure	Sun Mar 6 02:26:58 2016	429
	last break	Tue Feb 3 12:38:00 2015	436
	last success	Sat Apr 16 04:09:00 2011	616
mips-irix
cm	Success	Sun Aug 19 06:09:53 2007	666
cm-debug	Success	Wed Jun 27 06:00:33 2007	3454
cm-debug-clear-malloc	Success	Fri Jul 13 05:13:58 2007	3768
cm-debug-clear-malloc7	Failure	Fri Aug 10 04:52:13 2007	3483
	last break	Fri Aug 10 03:54:00 2007	3483
cm64	Success	Sun Aug 19 04:33:07 2007	705
cm64-debug	Success	Fri Aug 3 05:45:16 2007	3906
cm64-debug-clear-malloc	Success	Fri May 20 11:31:42 2005	1553
rs6000-aix
cm	Success	Wed Mar 4 01:31:17 2009	82
cm-debug	Success	Mon Mar 2 02:45:03 2009	1242
cm64	Success	Wed Mar 4 01:31:30 2009	87
cm64-debug	Success	Tue Mar 3 02:54:51 2009	1183
x86_64-linux
cm	Failure	Sun Mar 6 00:05:33 2016	43
	last break	Tue Aug 12 00:03:00 2014	54
	last success	Sun Apr 17 00:34:00 2011	53
cm-debug	Failure	Sun Mar 6 00:11:34 2016	197
	last break	Tue Aug 12 00:03:00 2014	258
	last success	Sat Apr 16 00:47:00 2011	244

Testing status by file:

signal

mips-irix

SIGKILL cm-debug-clear-malloc7: exit due to SIGKILL signal.

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.

coupled_endIVC.irinit

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.
Missing	cm-debug-clear-malloc7:	output file not generated for ndiff; 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 05:50:28 2016

Input last modified: Mon Aug 16 11:19:15 2010

CMISS Help / Examples / 5 / 5f / 5f1

mips-irix
SIGKILL	cm-debug-clear-malloc7:	exit due to SIGKILL signal.