Navier-Stokes flow including external pressure field derived from soft-tissue mechanics solution

Example 9823b: Navier-Stokes flow including external pressure field derived from soft-tissue mechanics solution

This example demonstrates the second stage of coupling lung mechanical deformation to pulmonary blood flow. After determining the deformed geometry of the arterial model within the lung volume we then want to calculate the distribution of flow within the arterial network. To do this we incorporate the pressure values, as calculated via the soft-tissue mechanics model ( see mechanics examples) into the flow solution as an external pressure field acting on the blood vessels. The reduced Navier-Stokes equations are solved using a Lax-Wendroff numerical technique ( see flow examples) to yield the pressure, velocity and flow solutions within the arterial model.

Created by Kelly Burrowes, 01/2007.

The above figures represent the pressure (kPa) and velocity (mm/s) distributions, repsectively, within the simple arterial geometry.

To create an image in order to visualise the results of the simulation, use CMGUI with the file draw.com.

The comfile run by this example is as follows:

# Example 9823b

# 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 define param;r;$example/flow;                      #Define array bounds
fem define coord;r;$example/flow;                      #Define co-ordinate system for problem
fem define base;r;$example/flow;                       #Define 1D linear basis function for model

fem define node;r;$example/small_arteries;             #Read in nodes and elements representing
fem define element;r;$example/small_arteries;          #the arterial vessel geometry

fem define field;r;$example/radius;                    #Define the radius field for the blood vessels
fem define element;d;$exampe/radius field;             #Sets up element field variables

fem define;add field;d;$example/all field_variables 2; #Adds an addition 2 fields to contain the
                                                       #pressure and velocity solutions
fem define element;d;$example/all field;

fem define;add field;r;$example/external_pressure;     #Defines external pleural pressure field
fem define elem;d;$example/external_pressure field;

fem define grid;r;$example/flow coronary;
# Defines grid points with coronary option to discretise the spatial computational domain. 
fem update grid geometry;
fem define equation;r;$example/flow;                   #Defines equations                          
fem define material;r;$example/flow;                   #Reads in physical & mechanical properties
fem update material field material 4 no_field 1;
fem update material field material 13 no_field 4;      #Updates external pressure field for grid
#####  NB: CMISS code currently assumes external pressure field is material parameter #13  #####
fem define time;r;$example/step;        
fem define initial;r;$example/flow;                    #Defines initial conditions
fem define solve;r;$example/flow;                      #Defines solution parameters

$time_initial=0.00;                                    #Sets the initial time
$time_final=5;                                         #Sets the final time
$time_step=0.0008;                                     #Sets the time step time
$write_out_period=1;                                   #Sets the results write out period

fem export points;$time_initial grid as vessel offset 0;   
fem export grid;vessel as vessel offset_node 0 elastic_tube; 

# Results output loop

for ($time=$time_initial;$time<$time_final;$time=$time+$write_out_period)
{
fem solve restart to $write_out_period delta_t $time_step;
fem export points;$time+$write_out_period grid as vessel offset 0
}

Additional testing commands:

fem list nodes

Files used by this example are:

Name                      Modified     Size

example_9823b.com         19-Jan-2007  2.8k
0.exnode                  19-Jan-2007   10k
1.exnode                  19-Jan-2007   10k
2.exnode                  19-Jan-2007   10k
3.exnode                  19-Jan-2007   10k
4.exnode                  19-Jan-2007   10k
5.exnode                  19-Jan-2007   10k
draw.com                  19-Jan-2007  2.0k
external_pressure.ipfiel  19-Jan-2007  1.5k
field.com                 19-Jan-2007  614 
flow.ipbase               19-Jan-2007  893 
flow.ipcoor               19-Jan-2007  572 
flow.ipequa               19-Jan-2007  1.3k
flow.ipgrid               19-Jan-2007  216 
flow.ipinit               19-Jan-2007  908 
flow.ipmate               19-Jan-2007  6.7k
flow.ippara               19-Jan-2007  5.9k
flow.ipsolv               19-Jan-2007  759 
radius.ipfiel             19-Jan-2007  2.2k
small_arteries.ipelem     19-Jan-2007  2.5k
small_arteries.ipnode     19-Jan-2007  2.2k
step.iptime               19-Jan-2007  1.5k
test.com                  19-Jan-2007  2.6k
test_output.com           19-Jan-2007   15 
transit.out               19-Jan-2007  506 
vessel.exelem             19-Jan-2007   13k

Download the entire example:

Name                                 Modified     Size

examples_9_98_982_9823_9823b.tar.gz  20-Jan-2007   93k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:03:24 2016	2
cm-debug	Failure	Sun Mar 6 00:05:13 2016	1
	last break	Fri Jun 5 00:14:00 2015	0
	last success	Thu Jun 4 00:13:00 2015	6
mips-irix
cm	Success	Sun Aug 19 01:46:32 2007	14
cm-debug	Success	Wed Aug 15 01:54:40 2007	67
cm-debug-clear-malloc	Success	Sat Aug 18 02:06:59 2007	71
cm-debug-clear-malloc7	Success	Mon Aug 20 02:00:43 2007	79
cm64	Success	Sun Aug 19 01:46:55 2007	15
cm64-debug	Success	Tue Aug 21 01:53:16 2007	68
rs6000-aix
cm	Success	Wed Mar 4 01:09:08 2009	3
cm-debug	Success	Mon Mar 2 01:12:59 2009	17
cm64	Success	Wed Mar 4 01:09:09 2009	3
cm64-debug	Success	Tue Mar 3 01:17:02 2009	16
x86_64-linux
cm	Success	Sun Mar 6 00:02:05 2016	16
cm-debug	Failure	Sun Mar 6 00:01:25 2016	0
	last break	Fri Jun 5 00:04:00 2015	0
	last success	Thu Jun 4 00:04:00 2015	25

Testing status by file:

signal

i686-linux

SIGABRT cm-debug: exit due to SIGABRT signal.

x86_64-linux

SIGABRT cm-debug: exit due to SIGABRT 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.
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.
Missing	cm-debug:	output file not generated for ndiff; 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.
Missing	cm-debug:	output file not generated for ndiff; generic answer.

Html last generated: Sun Mar 6 05:50:36 2016

Input last modified: Fri Jan 19 15:15:15 2007

CMISS Help / Examples / 9 / 98 / 982 / 9823 / 9823b

i686-linux
SIGABRT	cm-debug:	exit due to SIGABRT signal.
x86_64-linux
SIGABRT	cm-debug:	exit due to SIGABRT signal.