History for Cm New User Notes

changed:
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**Note: Paths apply to the Bioengineering Institute file system.**

Home Directory for CMISS code:

  * /hpc/cmiss    

    - Main repository for lots of stuff related to CMISS, in particular, 
      you'll find cmgui and cm in this directory.

Important Sub-directories:

  * /hpc/cmiss/cm/source  

    - Contains all fortran files and include files that together constitutes
      back-end part of CMISS (called cm).

  * /hpc/cmiss/examples   

    - Contains the examples which are best seen online.

Environment Variables:

    To set up your environment to work with CMISS at the Bioengineering Institute there are three environment variables that should be configured so that CMISS executes correctly.

    * CMISS_ROOT /hpc/cmiss

    * CMISS_EXAMPLES $CMISS_ROOT/examples

    * PATH Include the $CMISS_ROOT/bin/ directory for your operating system and the general one.

    A script to do just this is available here:

    for tcsh or csh add sourcing of /hpc/cmiss/bin/user.csh into your .cshrc in your home directory,

    for ksh or bash add sourcing of /hpc/cmiss/bin/user.sh into your .profile in your home directory. 

CMISS Website:

   http://www.cmiss.org

CMISS Examples Website:

   http://cmiss.bioeng.auckland.ac.nz/development/examples/

A Strategy for Getting Started:

  * From CMISS website, go to [frontpage] for all of your beginner questions.  (Very Useful!)
  
  * On this web page click on [editingcmsource]
    in order to download all or part of cm.  To get your hands dirty, follow
    directions under _Initial Setup_ and _Local cm_.  Go no further
    than _Debugging_ for now.

       * Must be added to cmiss group before you can download the
         code. To check, type 'groups' in linux terminal.

       * Replace the command  

            'cvs checkout cm/Makefile cm/make cm/source/fe11.f cm/source/fe20.f'

            with

            'cvs checkout cm/Makefile cm/make cm/source/fe11 cm/source/fe20'

            or the split up command appropriately.

  * Once you have the code you can type 'gmake' in the cm/
    directory and this will create an executable.  The executable
    will be located in bin/i686-linux/ as cm-debug.

  * Now you are ready to run some examples so got to "CMISS Examples":http://cmiss.bioeng.auckland.ac.nz/development/examples

  * Make sure your environment is set for CMISS_EXAMPLES by typing
    'echo $CMISS_EXAMPLES' in your terminal.  If not set, then in linux type
    'setenv CMISS_EXAMPLES /product/cmiss/examples'.

  * Then go _Defining a finite element of boundary element mesh->
    Creating simple 2D meshes->Defining a simple 2D FEM mesh_
    and look at this example.  

  * Run this example inside of 'cm/bin/i686-linux' by issuing the
    command './cm-debug -example 111'.  Note that all examples are
    run in the same fashion by typing './cm-debug -example xxxx'.

  * Go through the long list of examples in the same way as described
    above. 

General Beginner's Advice:

  * Go to "cm Lookup Frontend":http://cmiss.bioeng.auckland.ac.nz/cgi-bin/cmiss-lookup.cgi and search
    for *solve* and see what you get.  Note that there exists a
    button to view the routines.  You can also use this if you are 
    unsure of any parameters or variables.  

  * One of the key input files is the parameter file.  To see an
    example, from the 'CMISS Examples' website go 'Cardiac
    Electro-mechanics modeling-> Coupled electromechanics->
    Coupled bidomain-mechanics example' and look at the 
    emech.ippara file that is linked to at the bottom.  Understanding
    these parameter is essential to run 3D problems.  

    Note: You can search for these parameters with 'cm source 
    viewer' found on the [frontpage] webpage.

  * To define a parameter file for a problem, you run 'cm' and then
    type 'fem define para;p;ex-file' and then fill in the appropriate
    numbers.  

  * It appears that creating a parameter file is a bit of voodoo plus experience.
    There is currently no way to run setup, however there exists the use of 
    'minimal' which I have yet to understand.

  * To see an example (with some comments) of an ippara file for a Bidomain 
    problem go to "Bidomain Example":https://www.bioeng.auckland.ac.nz/cms/CMISSFolder/bidomain.ipgrid/file_view .

Advice on Creating/Understanding Dot-Com Files:

  * A 'dot-ippara' file is not necessary for small simple problems.

  * There are two ways to define the finite element mesh depending
    on whether the mesh is relatively structured or not.  (This all
    takes place after defining your 'dot-ippara' file.)  If you want
    a structured mesh then you must set 'dot-ipbase' and 'dot-ipmesh'.
    However, if you desire a less structured mesh, then you must set
    in sequence a 'dot-ipnode', 'dot-ipbase', and 'dot-ipelem'.