Difference between revisions of "Elmer"

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= Introduction =
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== Getting started ==
  
 
[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 first need to install the generic ONELAB virtual machine on your system  
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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  
 
by following [[ONELAB virtual machine|these instructions]].
 
by following [[ONELAB virtual machine|these instructions]].
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When done, you can log in into the virtual machine (username: "olvm", passwd: olvm)
 
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and proceed with the installation of the Elmer software, and the download of benchmark ONELAB models.
 
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The instructions to do so are given in the next section.
 
  
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= Installation =
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The ONELAB Virtual machine is distributed with Gmsh and Elmer preinstalled.
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When done with the installation, log in (username: olvm, passwd: olvm)
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and proceed by downloading benchmark ONELAB models. You have to be online.
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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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* 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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The Virtual machine is configured so that Gmsh and Elmer can be installed straightforwardly  by issuing simple commands in a terminal.
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Information about the individual models are given in the next section.
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Proceed as follows.
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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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;Step 1: Download installation scripts
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== ONELAB models ==
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:Open a terminal by clicking on the "terminal" icon in the launcher panel and issue the command
 
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:<code>install_scripts.sh</code>
 
  
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[[Cryotherapy|Cryotherapy]] : Thermal analysis of the cryogenic treatment of warts
  
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Then, the command
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[[Beam3D|Beam3D]] : Didactical model of a 3D cantilever elastic beam
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:<code>install_gmsh.sh</code>
 
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will download the nightly-build of Gmsh from http://geuz.org/gmsh, install it, and place a Gmsh icon on the Desktop.
 
  
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When done, issue the command
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[[Laser|Laser]] : Thermal analysis of laser skin stimulation
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:<code>install_elmer.sh</code>
 
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which will download the source code of Elmer and compile it on the virtual machine. This may take several minutes.
 
  
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Now, you have a woking installation of Gmsh and Elmer on the virtual machine. A number of Elmer model examples can be downloaded by issuing the command
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[[Patch|Drug patch]] : Analysis of drug diffusion from a patch into the skin
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:<code>getElmerModels.sh</code>
 
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After all, you have a directory "ELMERMODELS" in your home directory with a number of Elmer models, which are now presented with more details.
 
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= ONELAB models =
 
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[[Cryotherapy|Cryotherapy]]
 
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== CRYO  ==
 
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[[File:CryoEngineering.png|CryoEngineering.png|300px|thumb|right|Cryo-engineering metamodel]]
 
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Launch Gmsh and open <code>ELMERMODELS/CRYO/cryo.py</code> from the "File" menu.
 
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The physical background is the cryogenic treatment of warts by application of a cryogenic fluid. The idea is to maximize the destruction of wart tissue cells while minimizing damages to healthy skin tissue. A damage function depending on temperature distribution and exposure time is built to represent this trade-off. The purpose of the modeling is to determine the application time that minimizes the damage function.
 
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Geometrical and modeling parameters can be interactively modified in the ONELAB window. By clicking on the "Run" button, the thermal solver of Elmer is invoked. After execution, a plot of the damage function vs. time is displayed, and the computed optimum application time <code>tmin</code> is highlighted in the ONELAB window.
 
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== BEAM ==
 
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This model is the didactical analysis of a clamped beam (static 3D elasticity). The dimensions of the beam and the material parameter can be modified interactively in the ONELAB window, as well as a number of modeling parameters. Diagrams of the internal moments can be generated by checking the box <code>Compute MT diagrams</code>.
 
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Launch Gmsh and open <code>ELMERMODELS/BEAM/beam.py</code> from the "File" menu.
 
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== PATCH ==
 
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[[File:Patch.png|Patch.png|300px|thumb|left|Drug patch metamodel]]
 
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This metamodel is toolkit for drug patch conception.
 
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The user can determine the geometry of the patch and initial drug concentrations.
 
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A number of drugs are pre-tabulated with their diffusivities.
 
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Elmer solves a convection-diffusion equation and post processing tools display the rate at which drug is transmitted to the skin.
 
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== LASER ==
 
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Download and inflate the archive [http://onelab.info/files/elmerfem/LASER.zip LASER.zip] in a work directory. Right-click on the icon <code>laser.ol</code> and open the file with <code>gmsh</code>. Alternatively, start <code>gmsh</code> and click <code>File > Open > laser.ol</code> from the menu.
 
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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. For a correct interpretation of the experimental data, an accurate knowledge of the temperature distribution in time and across the skin is needed. The metamodel allows selecting various laser types (Gaussian, flat-top) and various stimulus characteristics (imposed flux or controlled temperature). Each simulation generates a graphical result file <code>plot.pdf</code> that is directly interpretable by clinicians.
 
  
  

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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