Example 9832: Creating a full pulmonary blood flow circuit

This example demonstrates how to create a full pulmonary circuit model and how to solve blood flow equations within it. It reads in an arterial mesh and demonstrates how to create a matching venous mesh with arteries and veins connected at the terminal level by a capillary sheet. It then solves a static blood flow problem with each extra-capillary vessel treated as an elastic tube and each capillary connection treated as a lumped parameter sheet of capillaries.

Created by Alys Clark, 02/2011.

Arteries (cylinders)

Capillary sheets (spheres)

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


The comfile run by this example is as follows:

# Example 962
# Evaluate airway flows using compliance-resistance model.

# 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;
}
#=================================
#Vessel element fields
$num_elem_fields=5;
$flow=2;
$resistance=3;
$elem_rad=4; 
$velocity=5; 
$lpm_field=1;
#-------
#Vessel node fields
$num_node_fields=3; #number of node fields
$radius=1;
$pressure=2;
$unstressed_radius=3;

#=================================
## Set up problem
fem de param;r;blood_flow;
fem de coor 3,1;
fem de base;r;blood_flow;

#=================================
## Read in nodes and elements to form arterial geometry
fem de node;r;test_vessels as arteries;
fem de elem;r;test_vessels 1d as arteries;
fem update scale_factor normalise;

##create a mesh from the existing nodes and elements, add a nodal field
##for the vessel radius and create an element field
##which tells cmiss when to use the lumped parameter model (lpm_field)
##(we assign the field value 0 in the arteries and cmiss makes it 1 in 
##capillaries and 2 in the veins)

fem de mesh;c airway field efield lpm_field 1 value 0;
fem evaluate ordering; #evaluate Strahler order of arteries

##append the mesh with another (veins) that matches the original and is
## joined by capillaries at terminal vessels 
 
fem de mesh;c matching terminal_mesh efield; 

#=================================
##Define inlet and outlet vessels as boundary conditions
fem group node 1 as inlet_node;
fem group elem 1 as inlet_elem;
fem group node 19 as terminal_nodes;
fem group elem 18 as terminal;#


##Group elements for diameter calculations (and eventual output)
fem group elem 1..17 as artery;
fem group elem 18..34 as vein;
fem group elem 35..43 as capillary;
fem group elem all as vessels;

#=================================
##set up radii (unstrained)
fem update mesh geometry element 1 radius_field $radius constant 1.0;
fem update mesh geometry element artery radius_field $radius Rd_strahler ratio_diameter 1.5;
fem update mesh geometry element 18 radius_field $radius constant 1.0;
fem update mesh geometry start_elem 18 element vein radius_field $radius Rd_strahler ratio_diameter 1.5;

#=================================
##Set up default node and element fields
fem de;add field;d field_variable $num_node_fields;#
fem de;add field;d elements field_variables $num_elem_fields flow_field $flow resistance_field $resistance radius $elem_rad velocity $velocity;
fem update field $elem_rad elements from radius;
fem define element;d;full_mesh field;
#=================================

##Set up equation & material parameters
$scale_turbulence=0.0; #This removes any turbulence scaling and reduces to Poiseuille flow equations
fem de equ;r;blood_flow compliance vessel SCALE_TURBULENCE $scale_turbulence; 
fem de mate;r;blood_flow;

#=================================
##Set initial conditions: PRESSURE BCS#
$gravfactor=1.0;  #(mm^3/s)
$inlet_flow=1;#Inlet /outlet flow
$exit_pressure=500; #Outlet pressure (venous) (Pa)
$ptrans=4.25;  
fem de init;c lung elem inlet_elem fixed flow transpulmonary $ptrans; #define inlet flow and Ppl
fem update init elem inlet_elem constant $inlet_flow; #set fixed inlet flow as above
fem de;add init;c lung node terminal_nodes fixed pressure Palv 0;
fem update init node terminal_nodes constant $exit_pressure gravity $gravfactor position supine inlet_ref_node 1;  #set LAP

fem de values;r;blood_flow;

#=================================
##Solve
fem de solve;r;blood_flow;
fem solve from 0 to 1 delta_t 1.0;

#=================================
#Update fields
fem update field $elem_rad elements from radius;
fem update field $flow elements from solution to 2;
fem update field $velocity elements velocity; #must update after updating flow
fem update field from solution to $pressure;


#=================================
##Export some results
fem de field;w;element_fields elements;
fem export node;vessels as vessels;
fem export elem;arteries as arteries elem artery;
fem export elem;vein as vein elem vein;
fem export elem;capillaries as capillaries elem capillary;
fem export properties;flow as solution field index $flow name flow;
fem export properties;flow_cap as solution field index $flow name flow elem capillary;

fem quit;


Files used by this example are:

Name                   Modified     Size

example_9832.com 17-Feb-2011 4.3k arteries.exelem 17-Feb-2011 4.1k blood_flow.ipbase 17-Feb-2011 1.1k blood_flow.ipequa 17-Feb-2011 1.9k blood_flow.ipmate 17-Feb-2011 476 blood_flow.ippara 17-Feb-2011 5.7k blood_flow.ipsolv 17-Feb-2011 1.8k blood_flow.ipvalu 10-Mar-2011 1.7k capillaries.exelem 17-Feb-2011 3.0k ctlung.snhist 17-Feb-2011 13 draw.com 17-Feb-2011 497 element_fields.ipfiel 10-Mar-2011 14k flow.exelem 17-Feb-2011 3.5k flow_cap.exelem 17-Feb-2011 897 fort.12 17-Feb-2011 1.1k micro_flow_ladder.out 10-Mar-2011 16k micro_flow_unit.out 10-Mar-2011 1.3k test_vessels.ipelem 17-Feb-2011 5.3k test_vessels.ipnode 17-Feb-2011 6.8k vein.exelem 17-Feb-2011 4.1k vessels.exelem 17-Feb-2011 43k vessels.exnode 10-Mar-2011 12k

Download the entire example:

Name                           Modified     Size

examples_9_98_983_9832.tar.gz 11-Mar-2011 80k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmFailureSun Mar 6 00:05:14 20160
last breakSun Feb 20 01:46:00 20111
cm-debugFailureSun Mar 6 00:05:14 20160
last breakSat Feb 19 01:36:00 20111
x86_64-linux
cmFailureSun Mar 6 00:01:25 20160
last breakSun Feb 20 01:10:00 20112
cm-debugFailureSun Mar 6 00:01:25 20160
last breakSat Feb 19 01:08:00 20110

Testing status by file:


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

Input last modified: Thu Mar 10 09:49:20 2011


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