3D Cube

Example b151: 3D Cube

This example reads in a 3-d cube with spatially varying cellular material parameters and exports the parameters as element based fields. The parameters can be viewed using the view.com command file.

The comfile run by this example is as follows:

#Read in a 3d cube with spatially varying cellular material parameters and 
#export the parameters as a node based field.

#Set up problem size
fem define para;r;cube;example

#Define geometry of the problem
fem define coor;r;cube;example
fem define node;r;cube;example
fem define base;r;cube;example
fem define elem;r;cube;example
fem define fibr;d
fem define elem;r;cube;example fibre
fem define grid;r;cube;example
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;lr;example

#Define material properties for the problem

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

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

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

#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

#Export the cellular material parameters as a element based field
fem export element;grid as parameters field cell

Additional testing commands:

#not really anything to do, but need it for the testing!

Files used by this example are:

Name                    Modified     Size

example_b151.com        10-Apr-2000  1.4k
3dcube.exelem           10-Apr-2000  4.4k
3dcube.exnode           10-Apr-2000  1.3k
cell_parameters.exelem  10-Apr-2000  3.7M
cube.ipbase             10-Apr-2000  2.4k
cube.ipcell             10-Apr-2000  643 
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  580 
cube.ipgrid             06-Mar-2003  600 
cube.ipinit             10-Apr-2000  213 
cube.ipmate             10-Apr-2000  1.7k
cube.ipmate_cell_old    10-Apr-2000  2.4k
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
cubemate                10-Apr-2000  2.4k
grid.exelem             10-Apr-2000   11k
lr.ipcell               29-Jan-2003  7.9k
lr.ipequa               26-May-2003  1.4k
potential.exelem        10-Apr-2000  422k
spiral.exelem           10-Apr-2000   51k
spiral.exnode           10-Apr-2000   14k
test.ipsolv             03-Oct-2001  1.3k
test.ipsolv.old         10-Apr-2000  1.3k
test_output.com         10-Apr-2000   58 
variants.ipmatc         29-Jan-2003  1.4k
view.com                20-Nov-2001  1.8k

Download the entire example:

Name                           Modified     Size

examples_b_b1_b15_b151.tar.gz  14-Apr-2007   73k

Testing status by version:

	Status	Tested	Real time (s)
i686-linux
cm	Success	Sun Mar 6 00:02:09 2016	0
cm-debug	Success	Sat Mar 5 00:04:14 2016	1
mips-irix
cm	Success	Sun Aug 19 01:30:10 2007	4
cm-debug	Success	Wed Aug 15 01:26:19 2007	10
cm-debug-clear-malloc	Failure	Tue Aug 21 01:55:06 2007	17
	last break	Tue Apr 17 04:00:00 2007	16
	last success	Sat Feb 18 01:30:00 2006	17
cm-debug-clear-malloc7	Failure	Tue Aug 21 01:54:46 2007	17
	last break	Tue Apr 17 04:23:00 2007	16
	last success	Mon Feb 20 01:24:00 2006	16
cm64	Success	Sun Aug 19 01:30:15 2007	4
cm64-debug	Success	Tue Aug 21 01:25:42 2007	11
cm64-debug-clear-malloc	Success	Thu Apr 1 11:09:54 2004	6
rs6000-aix
cm	Success	Wed Mar 4 01:07:34 2009	1
cm-debug	Success	Mon Mar 2 01:07:41 2009	2
cm64	Success	Wed Mar 4 01:07:34 2009	1
cm64-debug	Success	Tue Mar 3 01:13:02 2009	3
x86_64-linux
cm	Success	Sun Mar 6 00:01:04 2016	0
cm-debug	Success	Sat Mar 5 00:01:35 2016	0

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:	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.

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.

grid.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.
Failure	cm-debug-clear-malloc:	ndiff test: significant differences with generic answer.
Failure	cm-debug-clear-malloc7:	ndiff test: 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 05:51:05 2016

Input last modified: Fri Apr 13 10:37:34 2007

CMISS Help / Examples / b / b1 / b15 / b151