3D Explicit LR2

Example b211m: 3D Explicit LR2

Explict Luo-Rudy phase 2 over a small, one element, cube. If the geometry and fields are exported, they can be viewed using the cmiss_input/cmiss_input/movie.com command file. The signal file can be viewed using UnEMAP.

The comfile run by this example is as follows:

# Example b211m - Explict Luo-Rudy phase 2 over a small, one element,
# cube. If the geometry and fields are exported, they can be viewed 
# using the draw.com command file. The signal file can be viewed using 
# UnEMAP.

# 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 .= $chopped;
}
#Set up problem size
fem define para;r;$example/cube;

#Define geometry of the problem
fem define coor;r;$example/cube;
fem define node;r;$example/cube;
fem define base;r;$example/cube;
fem define elem;r;$example/cube;
fem define fibr;d;
fem define elem;r;$example/cube fibre;
fem define grid;r;$example/cube;
fem update grid geometry;
fem update grid metric;
#  Some useful groups
fem group grid external as boundary;
fem group grid grid 92,93,101 as stimulus_site;

#Define equation to solve
#  Define monodomain with LR2 kinetics
fem define equa;r;$example/lr;

#Define material properties for the problem

#  Define cellular material properties
fem define cell;r;$example/lr;
#    Define cell variants and spatially varying material parameters
fem define mate;r;$example/cube cell;
#  Define continuum material parameters
fem define mate;r;$example/cube;
fem update grid material;

#Define continuum initial conditions
#  Set no-flux boundary condition
fem define init;r;$example/cube;

#Define the explicit solve, using the adams integrator
fem define solv;r;$example/test;

#The geometry can be exported to CMGUI via these commands
fem export node;3dcube as cube;              #Export node geometry
fem export elem;3dcube as cube;              #Export element geometry

#Can export the cellular material parameters with the command:
fem export element;parameters as cube field cell;

#Solve the problem

#  Initialise the solve
fem solve to 0;

#  Open a binary history file to store the membrane potential (YQ(1))
fem open history;cube write variables yq niqlist 1 binary;

# Loop through time (solve for 3ms)
for $HUN ( 0..0 ) {
    for $TEN ( 0..0 ) {
        for $UNIT ( 0..5 ) {
            # Solve for the current time
            fem solve restart to "${HUN}${TEN}$UNIT";
            # Write the membrane potential to the history file
            fem write history time "${HUN}${TEN}$UNIT" variables yq binary;
            # Export the field to CMGUI
            fem export elem;gridfield_1${HUN}${TEN}$UNIT field as cube;
        }
    }
}

# Close the history file
fem close history binary;
# Calculate the binary signal file from the history file
fem evaluate electrode;cube history cube from grid binary;
# Define UnEmap export properties
fem define export;r;$example/cube;
# Export the binary signal file to UnEmap
fem export signal;cube electrode signal cube;

Files used by this example are:

Name               Modified     Size

example_b211m.com  23-Jan-2003  2.8k
cube.ipbase        10-Apr-2000  2.4k
cube.ipcoor        10-Apr-2000  570 
cube.ipelem        10-Apr-2000  404 
cube.ipelfb        10-Apr-2000  233 
cube.ipequa        26-May-2003  1.4k
cube.ipexpo        10-Apr-2000  660 
cube.ipgrid        06-Mar-2003  600 
cube.ipinit        10-Apr-2000  213 
cube.ipmatc        30-Jan-2003  727 
cube.ipmate        10-Apr-2000  1.7k
cube.ipnode        10-Apr-2000  1.8k
cube.ippara        12-Nov-2002  5.9k
cube.ipsolv        13-Apr-2007  1.8k
cube.ipsolv.old    10-Apr-2000  1.4k
draw.com           03-Oct-2000  3.5k
lr.ipcell          20-Nov-2001  4.5k
lr.ipequa          26-May-2003  1.4k
movie.com          10-Apr-2000  445 
test.ipsolv        23-Jan-2003  1.3k

Download the entire example:

Name                                 Modified     Size

examples_b_b2_b21_b211_b211m.tar.gz  14-Apr-2007   45k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:07:28 2016	7
cm-debug	Success	Sat Mar 5 00:31:14 2016	20
mips-irix
cm	Success	Sun Aug 19 02:22:02 2007	50
cm-debug	Success	Wed Aug 15 02:46:19 2007	190
cm-debug-clear-malloc	Success	Sat Aug 18 03:05:56 2007	210
cm-debug-clear-malloc7	Success	Mon Aug 20 03:05:21 2007	206
cm64	Success	Sun Aug 19 02:22:55 2007	53
cm64-debug	Success	Tue Aug 21 02:56:52 2007	199
cm64-debug-clear-malloc	Success	Thu Apr 1 11:16:26 2004	86
rs6000-aix
cm	Success	Wed Mar 4 01:12:25 2009	7
cm-debug	Success	Mon Mar 2 01:25:28 2009	61
cm64	Success	Wed Mar 4 01:13:01 2009	6
cm64-debug	Success	Tue Mar 3 01:28:46 2009	68
x86_64-linux
cm	Success	Sun Mar 6 00:01:18 2016	5
cm-debug	Success	Sat Mar 5 00:03:15 2016	13

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.

3dcube.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.

3dcube.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.

cube.binsig

i686-linux
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
mips-irix
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
Success	cm-debug-clear-malloc:	diff test: no differences with generic answer.
Success	cm-debug-clear-malloc7:	diff test: no differences with generic answer.
Success	cm64:	diff test: no differences with generic answer.
Success	cm64-debug:	diff test: no differences with generic answer.
Success	cm64-debug-clear-malloc:	diff test: no differences with generic answer.
rs6000-aix
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
Success	cm64:	diff test: no differences with generic answer.
Success	cm64-debug:	diff test: no differences with generic answer.
x86_64-linux
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.

cube.signal

i686-linux
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
mips-irix
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
Success	cm-debug-clear-malloc:	diff test: no differences with generic answer.
Success	cm-debug-clear-malloc7:	diff test: no differences with generic answer.
Success	cm64:	diff test: no differences with generic answer.
Success	cm64-debug:	diff test: no differences with generic answer.
Success	cm64-debug-clear-malloc:	diff test: no differences with generic answer.
rs6000-aix
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.
Success	cm64:	diff test: no differences with generic answer.
Success	cm64-debug:	diff test: no differences with generic answer.
x86_64-linux
Success	cm:	diff test: no differences with generic answer.
Success	cm-debug:	diff test: no differences with generic answer.

gridfield_1000.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.

gridfield_1001.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.

gridfield_1002.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.

gridfield_1003.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.

gridfield_1004.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.

gridfield_1005.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.

parameters.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 05:51:09 2016

Input last modified: Fri Apr 13 10:38:06 2007

CMISS Help / Examples / b / b2 / b21 / b211 / b211m