Embedding and deforming an arterial model within a lung surface volume

Example 9823a: Embedding and deforming an arterial model within a lung surface volume

This example demonstrates the first stage of coupling lung mechanical deformation to pulmonary blood flow. The arterial model is embedded within the lung volume model. The nodal xi locations of the arterial network are calculated with respect to the lung volume model. A deformation is applied to the lung volume model which results in a consistent deformation of the embedded arterial geometry.

Created by Kelly Burrowes, 01/2007. To create an image in order to visualise the results of the simulation, use CMGUI with the file draw.com.

These figures demonstrate the lung surface and arterial mesh before and after deformation.

The comfile run by this example is as follows:

# Example 9823a

# If the example path is not set, default to current directory
if (! defined $example) {
    $example = "./";
}
# Drop off the trailing / in the example path
$chopped = chop $example;
if ($chopped ne "/") {
    $example .= $chopped;
}

fem de param;r;$example/mech-flow;                       #Define parameters
fem de coor 3,1;                                #Define coordinate system
fem de base;r;$example/all_lobe_cubic;                   #Define basis functions (1) 3D cubic hermite, 
                                                #(2) 2D cubic hermite, (3) 1D linear

fem de region;r;$example/two;                            #Defines 2 regions

fem de node;r;$example/left_fitted reg 1;                #Reads in lung volume nodes to region 1
fem de elem;r;$example/left_fitted reg 1;                #Reads in lung volume elements

fem export node;left_lung as left_lung reg 1;   #Exports lung nodes and elements
fem export elem;left_lung as left_lung reg 1;   #for viewing

fem de node;r;$example/small_arteries reg 2;             #Reads in simple arterial geometry
fem de elem;r;$example/small_arteries reg 2;             #into region 2

fem export node;arteries as arteries reg 2;     #Exports the arterial geometry
fem export elem;arteries as arteries reg 2;

fem de xi;c nodes contain of 2 in 1;            #Calculates the xi locations of the nodes of region 2 in region 1
fem de xi;w;art_nodes nodes contain reg 2;      #Writes out these xi locations to a file (art_nodes.ipxi)

fem de node;r;$example/left_scaled; #Reads in deformed nodal coordiates of host mesh

fem update mesh position of 2 in 1 undeform contain;

fem export node;arteries_2 as arteries_2 reg 1; #Exports the new arterial node and element locations
fem export node;arteries_2 as arteries_2 reg 2;

fem de node;w;left_art_deform reg 2;            #Writes the deformed nodal locations to a .ipnode file

Additional testing commands:

fem list nodes reg 2

Files used by this example are:

Name                     Modified     Size

example_9823a.com        18-Jan-2007  1.9k
all_lobe_cubic.ipbase    18-Jan-2007  4.0k
art_nodes.ipxi           18-Jan-2007  774 
arteries.exelem          18-Jan-2007  2.0k
arteries.exnode          18-Jan-2007  1.1k
arteries_2.exnode        18-Jan-2007  1.1k
cubic_1d.ipbase          18-Jan-2007  2.6k
draw.com                 18-Jan-2007  567 
left_art_deform.ipnode   18-Jan-2007  2.4k
left_fitted.ipelem       18-Jan-2007   35k
left_fitted.ipnode       18-Jan-2007  164k
left_lung.exelem         18-Jan-2007  202k
left_lung.exnode         18-Jan-2007   61k
left_lung_scaled.exelem  18-Jan-2007  202k
left_lung_scaled.exnode  18-Jan-2007   61k
left_scaled.ipelem       18-Jan-2007   35k
left_scaled.ipnode       18-Jan-2007  164k
mech-flow.ippara         18-Jan-2007  5.9k
scale_lung.com           18-Jan-2007  465 
small_arteries.ipelem    18-Jan-2007  2.5k
small_arteries.ipnode    18-Jan-2007  2.2k
test.com                 18-Jan-2007   95 
test_output.com          18-Jan-2007   21 
two.ipregi               18-Jan-2007   93

Download the entire example:

Name                                 Modified     Size

examples_9_98_982_9823_9823a.tar.gz  20-Jan-2007  255k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:02:08 2016	1
cm-debug	Success	Sat Mar 5 00:05:27 2016	3
mips-irix
cm	Success	Sun Aug 19 01:38:45 2007	10
cm-debug	Success	Wed Aug 15 01:34:12 2007	26
cm-debug-clear-malloc	Failure	Tue Aug 21 02:23:35 2007	31
	last break	Wed Jan 24 02:55:00 2007	30
cm-debug-clear-malloc7	Failure	Tue Aug 21 02:31:17 2007	30
	last break	Wed Jan 24 02:36:00 2007	29
cm64	Success	Sun Aug 19 01:39:29 2007	10
cm64-debug	Success	Tue Aug 21 01:34:40 2007	27
rs6000-aix
cm	Success	Wed Mar 4 01:08:59 2009	2
cm-debug	Success	Mon Mar 2 01:09:06 2009	8
cm64	Success	Wed Mar 4 01:08:59 2009	2
cm64-debug	Success	Tue Mar 3 01:14:50 2009	9
x86_64-linux
cm	Success	Sun Mar 6 00:01:04 2016	1
cm-debug	Success	Sat Mar 5 00:01:16 2016	2

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.
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.
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.

art_nodes.ipxi

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.
Failure	cm-debug-clear-malloc:	ndiff test: significant differences with generic answer.
Failure	cm-debug-clear-malloc7:	ndiff test: 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.
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 05:50:36 2016

Input last modified: Fri Jan 19 10:58:01 2007

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