Emmanuel Maitre - Homepage
Emmanuel Maitre - Homepage

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bombec [2011/02/08 23:59]
maitre
bombec [2011/02/09 00:04] (current)
maitre
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  {{ tt.png?​400|Tank treading motion of a 3D vesicle in shear flow. Thomas Milcent.}}  {{ tt.png?​400|Tank treading motion of a 3D vesicle in shear flow. Thomas Milcent.}}
  {{ vort.png?​250 |Vorticity plot of a 3D membrane.}}  {{ vort.png?​250 |Vorticity plot of a 3D membrane.}}
 +
 +
 +==== Generic Fluid/​Elastic structure coupling ====
 +{{ cardio.png?​200|Real geometry of a cardiomyocyte}}{{ solide3d.png?​300|Rigid sphere falling in a fluid. Claire Bost PhD Thesis.}}
 +
 +In this generic case we write elasticity in Eulerian coordinates inside the solid and fluid equations outside. We use a Level Set  function to ensure stress continuity at interface. Our application concerns the simulation of isolated cardiomyocyte contraction (see picture of a numerized cardiomycyte on the right. Experimental data from Yves Usson). For the theory behind the method we refer to an [[http://​www-ljk.imag.fr/​Publications/​Basilic/​com.lmc.publi.PUBLI_Article@1173f83c0d0_17200b4/​cmm_revised.pdf|article in M2AN]] in 2008, and a [[http://​hal.archives-ouvertes.fr/​hal-00177593/​fr/​|special issue of MCM]] on computational biology in 2009.
 +  * **cardio3d:​** is a computational code written in C which implements the method developed in the fore mentioned articles. It encompasses a coupling between the cardiomyocyte elasticity, the carrier fluid equation, and an active contraction triggered by a the propagation of a calcium wave.
 +
 +==== Coupling between a rigid solid and a fluid ====
 +This part has been mainly developed by Georges-Henri Cottet using particle methods and Claire Bost during her [[http://​tel.archives-ouvertes.fr/​tel-00341209/​fr/​|PhD Thesis]] using a finite difference computational code in 2D and 3D. We use penalization techniques to enforce the velocity field to be rigid in the solid part. In fact the solid part is first considered as fluid; then we compute a mean velocity and vorticity on the solid domain and penalize in an implicit manner (as a damping term) the fluid velocity distance to that rigid field. We prove a convergence result in [[http://​hal.archives-ouvertes.fr/​hal-00352808/​fr/​|a submitted article]] where this method is developed.
 +  * **Solide rigide:** Is a computational code developed in C by Claire Bost to implement the method studied in [[http://​hal.archives-ouvertes.fr/​hal-00352808/​fr/​|this preprint]]. ​
 +
 +===== How to build and use Bombec ? =====
 +  - The first thing to do is to get an up-to-date version of Bombec thanks to the following svn command: <​code>​svn checkout svn+ssh://​user@scm.ljkforge.imag.fr/​svnroot/​bombec</​code>​ where "​user"​ is your login in LJKForge. This will create or update the directory bombec in your current location.
 +  - Create at the same level as directory "​sources"​ a directory named "​build"​. If this directory already exists, you can delete it to start from scratch.
 +  - cd to directory "​build"​ and type (need cmake version 2.6 or newer):<​code>​cmake ../sources
 +make
 +make install</​code>​**Note:​** cmake selects automatically the C and Fortran 90 compilers. If it fails to choose the right compilers, you can force it. For instance on computer Abel to select Intel compilers you have to type:<​code>​
 +setenv FC /​opt/​intel/​intel-fc/​8.1.025/​bin/​ifort
 +setenv CC /​opt/​intel/​intel-cc/​8.1.029/​bin/​icc
 +setenv CXX /​opt/​intel/​intel-cc/​8.1.029/​bin/​icc
 +</​code>​before invoking cmake. If you first tried another compilers set, you have to start over from scratch by removing the "​build"​ directory.
 +  - cd to subdirectory corresponding to your application and launch the executable. For instance for membrane 2D:<​code>​cd membrane2D
 +./​membrane2d</​code>​
 +  - Visualize the results. Depending on the application this will require OpenDX or Paraview.
 +
 +
 +
 +
 +
 +===== Work in progress / ToDo list =====
 +  * AMR using AGRIF on membrane2d and then membrane3d code. Collaboration with Laurent Debreu.
 +  * Device stable numerical schemes for stiff elastic interactions.
 +  * Adaptation of codes to model the motion of a cell on a substrate.
 +  * Motion of red blod cells in small vessels: behavior of vesicles in Poiseuille flow.
 +
 +
 +
  
  
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bombec.txt ยท Last modified: 2011/02/09 00:04 by maitre