Example i56: 3D Cylinder Slow Wave with Unemap Export (Uses Curve from i55)

This example simulates the slow wave activity in a 3D cylinder that mimics a part of the small intestine. The cylinder wall has three layers to represent the circular muscle (CM), Interstitial Cells of Cjal (ICC) and longitudinal muscle (LM) layers. The cylinder was generated by a script written by V. Rajagopal and fixed up by T. Austin. The cylinder has eight elements into the wall, four elements around, and one element along the length of the cylinder. We also export the solution at select grid points to be later viewed in unemap. See the description of example_i55 for a image representing this domain.

The comfile run by this example is as follows:


set Num_threads 1

$Vm = 1;
$intestine = 1;

fem def para;r;$example/cylinder
fem def coor 3,1

#
# Read in cylinder geometry
#
fem def node;r;$example/cylinder reg $intestine
fem def base;r;$example/cylinder reg $intestine
fem def elem;r;$example/cylinder reg $intestine

#
# Add fibre into the CM and LM layers
#
fem def fibr;r;$example/cylinder reg $intestine 	
fem def elem;r;$example/cylinder fibre reg $intestine

#
# Apply different grid schemes to each layer
#
fem define grid;r;$example/cylinder reg $intestine
fem update grid geometry reg $intestine

#
# Group the faces to allow connection
#
fem group grid face xi3 low element 13..16 as ICC1 reg $intestine
fem group grid face xi3 low element 21..24 as ICC2 reg $intestine

#
# Create subgroups to define layer groups
#
fem group grid element 1..4 as ELEMSa reg $intestine
fem group grid element 17..20 as ELEMSb reg $intestine
fem group grid element 9..12 as ELEMSc reg $intestine
fem group grid element 25..28 as ELEMSd reg $intestine
fem group grid element 5..8 as ELEMSe reg $intestine
fem group grid element 21..24 as ELEMSf reg $intestine
fem group grid element 13..16 as ELEMSg reg $intestine
fem group grid element 29..32 as ELEMSh reg $intestine

#
# Group the different layers
#
fem group grid grid ELEMSg,ELEMSh as LM reg $intestine			
fem group grid grid ELEMSf as ICC reg $intestine
fem group grid grid ELEMSa,ELEMSb,ELEMSc,ELEMSd,ELEMSe as CM reg $intestine
fem group grid external as boundary reg $intestine

#
# Cut the connection in the xi3 direction ie. between ICC and LM
#
fem update grid conn grid ICC1 direction 3 reg $intestine		

#
# Cut the connection in the -xi3 direction ie. between ICC and CM
#
fem update grid conn grid ICC2 direction -3 reg $intestine	

#
# Define the activation in the duodenum
#
fem define equa;r;$example/cylinder reg $intestine class $Vm
fem define cell;r;$example/cylinder reg $intestine class $Vm
fem define mate;r;$example/cylinder reg $intestine class $Vm cell
fem define mate;r;$example/cylinder reg $intestine class $Vm
fem define init;r;$example/cylinder reg $intestine class $Vm
fem define solv;r;$example/cylinder reg $intestine class $Vm

fem open history;intestine write variables yqs niqlist 1 binary;

# Perform an initial solve
fem solve to 0 reg $intestine class $Vm

# Solve with a time step of 0.02s to 0.1s
$step=0.02;
$end = 5;
for $M ( 0..$end ) {

     $time=$M*$step;

     fem solve restart to $time reg $intestine class $Vm
     fem write history time $time variables yqs niqlist 1 binary;

     # Reconnect layers
     fem update grid stimulus grid ICC1,ICC2 diffusion 0.3 up_potential direction 3 reg $intestine class $Vm

     # Export the electrical activity solution after the final step
     if($M == 5) {
        fem export ele;intestine_mono_pot reg $intestine class $Vm field as intestine; 
     }

}

fem close history binary;

$SIGNALFILE="TRACE";

$COMPPTS="5597,22407,36158,45615";
fem evaluate electrodes;$SIGNALFILE history intestine from grid yqs iy 1 electrodes $COMPPTS binary;

fem def export;r;$example/signal;
fem export sign;$SIGNALFILE signal $SIGNALFILE electrodes;

quit

Files used by this example are:

Name             Modified     Size


example_i56.com  10-Jul-2006  3.1k
cylinder.cml     07-Jul-2006  8.9k
cylinder.ipbase  07-Jul-2006  7.4k
cylinder.ipcell  07-Jul-2006  3.5k
cylinder.ipelem  07-Jul-2006   16k
cylinder.ipelfb  07-Jul-2006  7.6k
cylinder.ipequa  07-Jul-2006  1.5k
cylinder.ipfibr  07-Jul-2006   10k
cylinder.ipgrid  07-Jul-2006  613 
cylinder.ipinit  07-Jul-2006  214 
cylinder.ipmatc  07-Jul-2006  723k
cylinder.ipmate  07-Jul-2006  2.6k
cylinder.ipnode  07-Jul-2006  129k
cylinder.ippara  11-Jul-2006  5.9k
cylinder.ipsolv  13-Apr-2007  2.1k
signal.ipexpo    07-Jul-2006  712

Download the entire example:

Name                      Modified     Size


examples_i_i5_i56.tar.gz  14-Apr-2007   83k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:25:31 201662
cm-debugSuccessSat Mar 5 02:30:03 2016370
mips-irix
cmSuccessSun Aug 19 05:50:32 2007572
cm-debugSuccessWed Jul 18 05:32:56 20074402
cm-debug-clear-mallocSuccessSat Aug 18 04:57:55 20074402
cm-debug-clear-malloc7SuccessMon Jul 2 05:41:24 20074404
cm64SuccessSun Aug 19 05:54:08 2007649
cm64-debugSuccessFri Jul 13 05:30:49 20074924
rs6000-aix
cmSuccessWed Mar 4 01:28:01 200960
cm-debugSuccessMon Mar 2 02:50:16 20091457
cm64SuccessWed Mar 4 01:29:11 200970
cm64-debugSuccessTue Mar 3 02:58:42 20091362
x86_64-linux
cmSuccessSun Mar 6 00:02:32 201631
cm-debugSuccessSat Mar 5 00:11:23 2016216

Testing status by file:

Html last generated: Sun Mar 6 05:51:40 2016

Input last modified: Fri Apr 13 10:43:48 2007

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