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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= Getting started =
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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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*Step 1: '''Install Virtual Box'''
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Information about the individual models are given in the next section.
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If you don't have a virtualization utility already installed on your system,
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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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go to the [https://www.virtualbox.org Oracle VirtualBox website]
 
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to download a binary package suitable for your host operating system.
 
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Follow the [https://www.virtualbox.org/manual/ch01.html#intro-installing documentation]  
 
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to install the software components and to start the VirtualBox Manager.
 
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<!--
 
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In the VirtualBox Manager, check that a "Host only Network" vboxnet0 is present and properly configured with an active DHCP server
 
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(under Windows: VirtualBox > File > Settings > Network ; under OSX VirtualBox > Preferences > Network)
 
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From a terminal on the host, check the network connectivity with the VM by a "ssh vm@amzyan.local"; enter the same "vm" password.
 
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-->
 
  
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*Step 2: '''Download the Virtual Machine ONELAB_VM'''
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== ONELAB models ==
  
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[http://sites.uclouvain.be/immc/mema/alain/ubuntuPLOS-i386-latest.ova Virtual Machine]
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[[Cryotherapy|Cryotherapy]] : Thermal analysis of the cryogenic treatment of warts
  
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[http://sites.uclouvain.be/immc/mema/alain/ubuntuPLOSi386-latest.ova.sha1 SHA1 checksum]
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[[Beam3D|Beam3D]] : Didactical model of a 3D cantilever elastic beam
  
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*Step 3: In the VirtualBox Manager, import the downloaded OVA file
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[[Laser|Laser]] : Thermal analysis of laser skin stimulation
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by following the [https://www.virtualbox.org/manual/ch01.html#ovf instructions]
 
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A new VM entry - named ONELAB_VM appears in the left panel.
 
  
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*Step 4:
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[[Patch|Drug patch]] : Analysis of drug diffusion from a patch into the skin
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Start the VM by double clicking its entry in the VirtualBox Manager.
 
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Enter "plos" for login and "plos" again for password (without quotes)
 
  
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*Step 5: Open the browser of the Virtual Machine, reload this page and continue continue the installation from within the Virtual Machine.
 
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<!-- Do not delete
 
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[[ONELAB metamodels with Elmer]]
 
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[[Fluid Dynamics]]
 
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First take a look at this [[Tutorial|tutorial]] to see how ONELAB can be installed.
 
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-->
 
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== LASER ==
 
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Download and inflate the archive
 
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http://onelab.info/files/elmerfem/lab_peau.zip
 
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in a work directory.
 
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Then run <code>gmsh</code> and click File-> Open-> lab_peau.ol 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.
 
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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 - remote solvers ==
 
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Download and inflate the archive
 
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http://onelab.info/files/elmerfem/cryo.zip
 
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in a work directory.
 
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Then run <code>gmsh</code> and click File-> Open-> cryo.ol from the menu.
 
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The physical background is the cryogenic treatment of warts by application of a cryogenic fluid.
 
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The idea is to maximize the destruction of wart tissue cells while minimizing damages 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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<!--
 
This metamodel illustrates the possibility of running clients on a '''remote host'''.
 
This metamodel illustrates the possibility of running clients on a '''remote host'''.
 
Remote solving uses <code>ssh</code> and <code>rsync</code>, and is thus available on Linux and Mac-OS systems only.
 
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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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  
 
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  
 
as explained here: http://linuxproblem.org/art_9.html
 
as explained here: http://linuxproblem.org/art_9.html
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-->

Latest revision as of 12:57, 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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