Example b143: SPM calcium dynamics model

This example uses the SPM calcium dynamics model. Currently the SPM model is implemented on its own, but will eventually be coupled to the HMT mechanics model.

The comfile run by this example is as follows:

# Example b143 - SPM calcium dynamics

$SIGNALS = "1..7";

fem def para;r;n98_hmt;example

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

fem def equa;r;hmt_spm;example

# Define the cellular material parameters
fem def cell;r;hmt_spm;example
fem def mate;r;n98_hmt;example cell
fem def mate;r;n98_hmt;example
fem update grid material

fem def time;r;step;example     # use these to open the L-type calcium channel ????
fem def init;r;n98_hmt;example  # use these to open the L-type calcium channel ????

# Define an explict, adaptive Adams-Moulton integration
fem def solv;r;n98_hmt;example

# Initialise the solve
fem solve to 0

# Create the history file to store the signals we want to export
fem open history;test write variables yqs niqslist $SIGNALS binary

# Loop through time
for $time (0..2)
	print "Time = $time\n";

  # Solve for the current time
  fem solve restart to $time

  # Write the signals to the history file
  fem write history time $time variables yqs binary

#  Close the history file
fem close history binary

# Generate a UnEMAP signal file
fem evaluate electrode;test history test from grid yqs iy $SIGNALS binary
		fem define export;r;hmt_spm;example
fem export signal;test electrode signal test names cell

Files used by this example are:

Name                Modified     Size

example_b143.com 05-Mar-2001 1.3k hmt_spm.ipcell 25-Sep-2000 3.4k hmt_spm.ipequa 26-May-2003 1.2k hmt_spm.ipexpo 18-Sep-2000 657 n98_hmt.ipcell 18-Sep-2000 11k n98_hmt.ipequa 26-May-2003 1.2k n98_hmt.ipexpo 18-Sep-2000 657 n98_hmt.ipinit 18-Sep-2000 214 n98_hmt.ipmatc 29-Jan-2003 379 n98_hmt.ipmate 18-Sep-2000 1.8k n98_hmt.ippara 12-Nov-2002 5.9k n98_hmt.ipsolv 21-Jan-2003 1.3k n98_hmt.ipsolv.old 25-Sep-2000 1.3k step.iptime 30-Jul-2001 1.0k

Download the entire example:

Name                           Modified     Size

examples_b_b1_b14_b143.tar.gz 19-Aug-2006 10k

Testing status by version:

StatusTestedReal time (s)
cmSuccessSun Mar 6 00:02:09 20161
cm-debugSuccessSat Mar 5 00:04:13 20161
cmSuccessSun Aug 19 01:25:32 20073
cm-debugSuccessWed Aug 15 01:22:04 20076
cm-debug-clear-mallocSuccessSat Aug 18 01:24:06 200710
cm-debug-clear-malloc7SuccessMon Aug 20 01:23:46 200710
cm64SuccessSun Aug 19 01:27:51 20073
cm64-debugSuccessTue Aug 21 01:21:32 20075
cm64-debug-clear-mallocSuccessThu Apr 1 11:09:42 20042
cmSuccessWed Mar 4 01:07:33 20091
cm-debugSuccessMon Mar 2 01:06:25 20091
cm64SuccessWed Mar 4 01:07:33 20091
cm64-debugSuccessTue Mar 3 01:11:46 20091
cmSuccessSun Mar 6 00:01:04 20160
cm-debugSuccessSat Mar 5 00:01:35 20160

Testing status by file:

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

Input last modified: Mon May 26 18:04:59 2003

CMISS Help / Examples / b / b1 / b14 / b143