Four muscle fibres in a cylinder

Example d11: Four muscle fibres in a cylinder

This example uses a mesh that contains four muscle fibres in a cylindrical domain. Each of the fibres is activated at a different time and a dipole source is created for each fibre. These sources are then used to calculate potentials on the surface of the cylinder.

The comfile run by this example is as follows:

if( !$example ) {
  $example = ".";
}

# Set up two problem regions, one for the cylinder
# and one for the fibres
$tissue = 1;
$muscle = 2;

# Set up two problem classes - laplace for the cylinder
# and activation for the fibres 
$laplace = 1;
$active = 2;
 
# Read in the geometry of the two regions
fem de para;r;$example/test
fem define coordinates;r;$example/eccentric_dipole
fem define regi;r;$example/eccentric_dipole
fem define node;r;$example/eccentric_dipole reg $tissue
fem define node;r;$example/fibres reg $muscle
fem define bases;r;$example/eccentric_dipole
fem define elem;r;$example/eccentric_dipole reg $tissue
fem define elem;r;$example/fibres reg $muscle

# Group the cylinder nodes to allow boundary conditions
# to be easily set
fem group node 1 as top reg $tissue      
fem group node 2..13,15..58 as middle reg $tissue  
fem group node 14 as bottom reg $tissue  

# Generate a finite difference grid over the fibres
fem define grid;r;$example/fibres reg $muscle
fem update grid geometry reg $muscle
fem update grid metric reg $muscle

# Define the laplace problem in the cylinder
fem define equation;r;$example/eccentric_dipole reg $tissue class $laplace lock 
fem define material;r;$example/eccentric_dipole reg $tissue class $laplace
fem define initial;r;$example/eccentric_dipole reg $tissue class $laplace
fem define solve;r;$example/eccentric_dipole reg $tissue class $laplace

# Define the activation problem in the fibres
fem define equation;r;$example/fibres reg $muscle class $active
fem define material;r;$example/fibres reg $muscle class $active
fem define cell;r;$example/fibres reg $muscle class $active
fem update grid material reg $muscle class $active
fem define initial;r;$example/fibres reg $muscle class $active
fem define solve;r;$example/fibres reg $muscle class $active

# Perform an initial solve
fem solve reg $tissue class $laplace
fem solve to 0 reg $muscle class $active

# Loop over time
foreach $step ( 0..30 ) {
  $time = $step/2
  # Solve the grid problem
  fem solve restart to $time reg $muscle class $active
  # Calculate the dipole sources
  fem define sour;c grid 
  # Apply the sources to the laplace problem
  fem update sour reg $tissue class $laplace
  # Solve the laplace problem
  fem solve reg $tissue class $laplace
#  Uncomment to output the solution fields over time
#    fem export elem;time$time reg $muscle class $active field as test2
#    fem export node;bemt$time reg $tissue class $laplace field as test
}

#fem export node;exfiles/test as test
#fem export elem;exfiles/test as test
#fem export elem;exfiles/bemt reg $tissue class $laplace field as test 
#fem export node;exfiles/test2 as test2 reg 2
#fem export elem;exfiles/test2 as test2 reg 2

Additional testing commands:

fem export elem;time15 reg $muscle class $active field as test2
fem export node;bemt15 reg $tissue class $laplace field as test

Files used by this example are:

Name                     Modified     Size

example_d11.com          13-Nov-2001  2.7k
animate.com              13-Nov-2001  111 
draw.com                 13-Nov-2001  1.8k
eccentric_dipole.ipbase  13-Nov-2001  8.4k
eccentric_dipole.ipcoor  13-Nov-2001  570 
eccentric_dipole.ipelem  13-Nov-2001   26k
eccentric_dipole.ipequa  26-May-2003  1.4k
eccentric_dipole.ipinit  13-Nov-2001  618 
eccentric_dipole.ipmate  13-Nov-2001   54 
eccentric_dipole.ipnode  13-Nov-2001   51k
eccentric_dipole.ipregi  13-Nov-2001   93 
eccentric_dipole.ipsolv  13-Apr-2007  1.2k
fibres.ipcell            13-Nov-2001  1.7k
fibres.ipelem            12-Feb-2004  1.3k
fibres.ipequa            26-May-2003  1.5k
fibres.ipgrid            06-Mar-2003  475 
fibres.ipinit            13-Nov-2001  1.1k
fibres.ipmate            13-Nov-2001  1.8k
fibres.ipnode            12-Feb-2004  7.4k
fibres.ipsolv            13-Nov-2001  889 
test.ippara              14-Mar-2003  5.9k
test_output.com          13-Nov-2001  128

Download the entire example:

Name                      Modified     Size

examples_d_d1_d11.tar.gz  14-Apr-2007   15k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:02:32 2016	1
cm-debug	Success	Sat Mar 5 00:04:44 2016	2
mips-irix
cm	Success	Sun Aug 19 01:41:59 2007	10
cm-debug	Success	Wed Aug 15 01:38:27 2007	31
cm-debug-clear-malloc	Success	Sat Aug 18 01:47:25 2007	40
cm-debug-clear-malloc7	Success	Mon Aug 20 01:45:04 2007	39
cm64	Success	Sun Aug 19 01:40:54 2007	11
cm64-debug	Success	Tue Aug 21 01:37:30 2007	33
cm64-debug-clear-malloc	Success	Thu Apr 1 11:52:29 2004	14
rs6000-aix
cm	Success	Wed Mar 4 01:08:17 2009	1
cm-debug	Success	Mon Mar 2 01:08:57 2009	6
cm64	Success	Wed Mar 4 01:08:17 2009	2
cm64-debug	Success	Tue Mar 3 01:14:16 2009	7
x86_64-linux
cm	Success	Sun Mar 6 00:01:06 2016	0
cm-debug	Success	Sat Mar 5 00:01:44 2016	1

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.
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.

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.
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
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.

bemt15.exnode

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.
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
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.

time15.exelem

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.
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
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 05:51:24 2016

Input last modified: Fri Apr 13 10:40:48 2007

CMISS Help / Examples / d / d1 / d11