HMT Cardiac Mechanics

Example b131: HMT Cardiac Mechanics

Example b131 - HMT Cardiac Mechanics Model This example solves the HMT model for a single cell. It outputs each of the state variables (Vm, Cai, Cab, lambda, To, T, z) to a UnEMAP signal file. This example also uses a time variable to set a time varying boundary condition - namely the time course of the extension ratio (lambda).

The comfile run by this example is as follows:

# Example b131 - HMT
#
# Solves the HMT model for a single cell, with a step change in
# length defined by a time varying boundary condtion set by using
# a time variable.

fem define parameters;r;hmt;example

fem define node;d
fem define base;d
fem define element;d
fem define grid;d
fem update grid geom
fem update grid metric

fem define equation;r;hmt;example

fem define cell;r;hmt;example
fem define material;r;hmt;example cell
# Need to define the material conductivities even though they are not 
# really used
fem define material;r;hmt;example
fem update grid material

# read in the time variable describing the step length change
fem define time;r;step;example

# assign the time variable to use for the time varying boundary 
# condition
fem define initial;r;step;example

fem define solve;r;hmt;example

fem solve to 0

fem open history;hmt write variables yqs niqslist 1,2,3,4,5,6,7 binary


for $time ( 0..999 ) 
{
#  Solve for the current time
fem solve restart to $time

#  Write the membrane potential to the history file
fem write history time $time variables yqs binary
}

# Close the history file
fem close history binary

# Write out signal files for all the state variables.

# First as individual signal files
for $UNIT ( 1..7 ) 
{
fem evaluate electrode;hmt_$UNIT history hmt from grid yqs iy $UNIT binary
fem define export;r;hmt;example
fem export signal;hmt_$UNIT electrode signal "hmt_$UNIT"
}

# Then with all variables in one signal file
fem evaluate electrode;hmt_all history hmt from grid yqs iy 1..7 binary
fem define export;r;hmt_all;example
fem export signal;hmt_all electrode signal hmt_all

Additional testing commands:

fem list signal signal hmt_1 binary
fem list signal signal hmt_2 binary
fem list signal signal hmt_3 binary
fem list signal signal hmt_4 binary
fem list signal signal hmt_5 binary
fem list signal signal hmt_6 binary
fem list signal signal hmt_7 binary
fem list signal signal hmt_all binary

fem list time

Files used by this example are:

Name                  Modified     Size

example_b131.com      07-Oct-2001  1.6k
hmt.ipcell            18-Jul-2002  3.5k
hmt.ipequa            26-May-2003  1.2k
hmt.ipexpo            10-Apr-2000  657 
hmt.ipmatc            29-Jan-2003  431 
hmt.ipmate            05-Mar-2001  1.8k
hmt.ippara            12-Nov-2002  5.9k
hmt.ipsolv            03-Oct-2001  900 
hmt.ipsolv.old        10-Apr-2000  854 
hmt_all.ipexpo        10-Apr-2000  657 
step.ipinit           10-Apr-2000  535 
step.iptime           30-Jul-2001  1.0k
step_version2.iptime  10-Apr-2000  728 
test_output.com       20-Apr-2001  305

Download the entire example:

Name                           Modified     Size

examples_b_b1_b13_b131.tar.gz  19-Aug-2006  125k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:03:44 2016	2
cm-debug	Success	Sat Mar 5 00:12:21 2016	3
mips-irix
cm	Success	Sun Aug 19 02:12:44 2007	41
cm-debug	Success	Wed Aug 15 01:52:19 2007	64
cm-debug-clear-malloc	Success	Sat Aug 18 02:04:20 2007	71
cm-debug-clear-malloc7	Success	Mon Aug 20 01:59:20 2007	68
cm64	Success	Sun Aug 19 02:13:00 2007	42
cm64-debug	Success	Tue Aug 21 01:52:30 2007	65
cm64-debug-clear-malloc	Success	Thu Apr 1 11:09:37 2004	29
rs6000-aix
cm	Success	Wed Mar 4 01:09:10 2009	2
cm-debug	Success	Mon Mar 2 01:09:43 2009	8
cm64	Success	Wed Mar 4 01:09:10 2009	1
cm64-debug	Success	Tue Mar 3 01:14:21 2009	7
x86_64-linux
cm	Success	Sun Mar 6 00:01:05 2016	2
cm-debug	Success	Sat Mar 5 00:01:42 2016	2

Testing status by file:

cmiss_test.log

i686-linux
Success	cm:	cmiss_test.log.retain.
Success	cm-debug:	cmiss_test.log.retain.
mips-irix
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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
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Success	cm-debug:	cmiss_test.log.retain.
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Success	cm64-debug:	cmiss_test.log.retain.
x86_64-linux
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Success	cm-debug:	cmiss_test.log.retain.

cmiss_test.out

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x86_64-linux
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hmt_1.binsig

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hmt_1.signal

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hmt_2.signal

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hmt_3.binsig

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hmt_3.signal

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hmt_4.binsig

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hmt_4.signal

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hmt_6.binsig

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hmt_6.signal

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hmt_7.binsig

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hmt_all.binsig

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hmt_all.signal

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

Input last modified: Mon May 26 18:04:06 2003

CMISS Help / Examples / b / b1 / b13 / b131