Difference between revisions of "Elmer"

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== Getting started ==
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[http://www.csc.fi/english/pages/elmer Elmer] is an open source (GPL) computational tool for multi-physics problems.  
 
[http://www.csc.fi/english/pages/elmer Elmer] is an open source (GPL) computational tool for multi-physics problems.  
 
It is developed by CSC in collaboration with Finnish universities, research laboratories and industry.
 
It is developed by CSC in collaboration with Finnish universities, research laboratories and industry.
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To test ONELAB models working with Elmer, you shall need a working installation of the code.
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The easiest way to do so, is to install the [[ONELAB virtual machine|ONELAB virtual machine]] on your system
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by following [[ONELAB virtual machine|these instructions]].
  
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<!-- Do not delete
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The ONELAB Virtual machine is distributed with Gmsh and Elmer preinstalled.
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[[ONELAB metamodels with Elmer]]
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When done with the installation, log in (username: olvm, passwd: olvm)
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[[Fluid Dynamics]]
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and proceed by downloading benchmark ONELAB models. You have to be online.
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-->
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* Open a terminal from the left menu bar.
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* Issue the command <code>getElmerModels.sh -test</code> at the prompt. The model examples listed in the next section are then downloaded in the directory <code>ELMERMODELS</code>.  Always execute this command in a new terminal. This command overwrite an eventual already existing <code>ELMERMODELS</code> directory. Valuable data in the latter directory should therefore be copied elsewhere before executing the command.  
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Two complete metamodels using Elmer are available on the read-only svn distribution of gmsh, which can be downloaded from http://www.geuz.org/gmsh.  
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* The option <code>-test</code> asks for an automatic check on the downloaded models, which are solved immediately after being downloaded. The result the check is given in the file <code>ELMERMODELS/report.txt</code>.
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You also need a working recent (nightly-build) version of gmsh to be executable on your system.
 
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First take a look at this [[Tutorial|tutorial]] to see how ONELAB can be installed.
 
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== LASER ==
 
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The metamodel "LASER" is launched as follows:
 
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<code>
 
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# cd <nowiki>$</nowiki>GMSH_DIR/projects/onelab/METAMODELS/LASER (the variable ''GMSH_DIR'' refers to the home directory of your Gmsh installation)
 
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# gmsh lab_peau.geo -s
 
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</code>
 
  
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The shell variable ''GMSH_DIR'' refers to the home directory of your Gmsh installation, see [[Tutorial]].
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Information about the individual models are given in the next section.
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The "-s" option amounts to click on "Tool/Onelab" in the Gmsh menu.  
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For beginners, a detailed tutorial that leading through the successive steps of a first session with the ONELAB-laser model is available [http://onelab.info/files/laser/laser_tuto.pdf here].
  
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The physical background of this model is the laser stimulation of skin in order to measure the density of [[http://en.wikipedia.org/wiki/Nociceptionreceptors|nociceptive]] receptors.
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== ONELAB models ==
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For a correct interpretation of the experimental data, an accurate nowledge of the temperature distribution in time and across the skin is needed.
 
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The metamodel allows selecting various models of stimulation (imposed flux, imposed temperature and controlled temperature)
 
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and various laser types (Gaussian or flat-top).
 
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Each simulation generates a Matlab or Gnuplot graphical output that is directly interpretable by clinicians.
 
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Check in the "lab_peau.ol" file how the switch between Matlab and Gnuplot is done,
 
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and modify the file if necessary according to your system settings.
 
  
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== CRYO ==
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[[Cryotherapy|Cryotherapy]] : Thermal analysis of the cryogenic treatment of warts
  
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The cryo-engineering metamodel "CRYO" is launched as follows:
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[[Beam3D|Beam3D]] : Didactical model of a 3D cantilever elastic beam
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<code>
 
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# cd <nowiki>$</nowiki>GMSH_DIR/projects/onelab/METAMODELS/CRYO
 
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# gmsh cryo.geo -s
 
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</code>
 
  
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The shell variable ''GMSH_DIR'' refers to the home directory of your Gmsh installation, see [[Tutorial]].
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[[Laser|Laser]] : Thermal analysis of laser skin stimulation
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The "-s" option amounts to click on "Tool/Onelab" in the Gmsh menu.
 
  
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The physical background is the cryogenic treatment of warts by application of a cryogenic fluid.
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[[Patch|Drug patch]] : Analysis of drug diffusion from a patch into the skin
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The idea is to maximize the destruction of wart tissue cells while minimizing damages done to healthy skin tissue.
 
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An damage function depending on temperature distribution and time is built to represent this trade-off and the purpose of the modeling
 
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is to determine the application time that minimizes this damage function.
 
  
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Various geometrical and modeling parameters can be interactively modified in the ONELAB window.
 
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After execution, a plot of the damage function displayed and the optimum application time <code>tmoin</code> is uploaded to the ONELAB window.
 
  
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[[File:CryoEngineering.png|CryoEngineering.png|300px|thumb|right|Cryo-engineering metamodel]]
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<!--
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This metamodel illustrates the possibility of running clients on a '''remote host'''.
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Remote solving uses <code>ssh</code> and <code>rsync</code>, and is thus available on Linux and Mac-OS systems only.
  
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This metamodel illustrates also the possibility of running a client on a remote host.
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After selecting the option ''remote'' of the parameter ''host'' and clicking on ''Check'', empty boxes will appear
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After selecting the option "remote" of the parameter "host" and clicking on "Check", empty boxes will appear
 
 
to be filled in with information about a remote host (''user@remote''), a remote working directory,
 
to be filled in with information about a remote host (''user@remote''), a remote working directory,
 
and a remote bin directory where the executable of the remote client can be found.  
 
and a remote bin directory where the executable of the remote client can be found.  
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Alternatively, if entered directly in the file <code>cryo.ol</code> in the definition of the variables ''HOST'', ''REMDIR'' and ''ELMERDIR'', they will be available for all ONELAB sessions.
 
Alternatively, if entered directly in the file <code>cryo.ol</code> in the definition of the variables ''HOST'', ''REMDIR'' and ''ELMERDIR'', they will be available for all ONELAB sessions.
 
As long as ''HOST'' and ''REMDIR'' are empty, the client is solved on the local machine, whatever the value of the flag ''host''.
 
As long as ''HOST'' and ''REMDIR'' are empty, the client is solved on the local machine, whatever the value of the flag ''host''.
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In order to automize the task, an automatic login from host A  to host B is needed so as to avoid entering constantly the password
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as explained here: http://linuxproblem.org/art_9.html
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-->

Latest revision as of 11:57, 23 January 2015

Getting started

Elmer is an open source (GPL) computational tool for multi-physics problems. It is developed by CSC in collaboration with Finnish universities, research laboratories and industry. To test ONELAB models working with Elmer, you shall need a working installation of the code. The easiest way to do so, is to install the ONELAB virtual machine on your system by following these instructions.

The ONELAB Virtual machine is distributed with Gmsh and Elmer preinstalled. When done with the installation, log in (username: olvm, passwd: olvm) and proceed by downloading benchmark ONELAB models. You have to be online.

  • Open a terminal from the left menu bar.
  • Issue the command getElmerModels.sh -test at the prompt. The model examples listed in the next section are then downloaded in the directory ELMERMODELS. Always execute this command in a new terminal. This command overwrite an eventual already existing ELMERMODELS directory. Valuable data in the latter directory should therefore be copied elsewhere before executing the command.
  • The option -test asks for an automatic check on the downloaded models, which are solved immediately after being downloaded. The result the check is given in the file ELMERMODELS/report.txt.

Information about the individual models are given in the next section. For beginners, a detailed tutorial that leading through the successive steps of a first session with the ONELAB-laser model is available here.

ONELAB models

Cryotherapy : Thermal analysis of the cryogenic treatment of warts

Beam3D : Didactical model of a 3D cantilever elastic beam

Laser : Thermal analysis of laser skin stimulation

Drug patch : Analysis of drug diffusion from a patch into the skin


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