Archive for the 'solveur-FEM' Category; python mac OSX, windows; open source software modeling environment and pde solver

CompuCell is an open source software modeling environment and pde solver. It is largely used for cellular modeling (foams, tissues, etc.), however, efforts are being made to include fluid simulation capabilities. Created in collaboration between groups at IU and Notre Dame, CompuCell provides an easy user interface for complex cellular modeling.

Integration with SBW

We have conducted a preliminary integration of CompuCell3D with Systems Biology Workbench (SBW) to link to subcellular models. As a result users can select the level of detail in their models while working within a single integrated framework.

see :


Source Code and ChangeLog

SVN Repository

To download from our repository, use your favorite svn client and download from:

Known Issues and Requirements

  • Python 2.5
  • Ubuntu users must install python-qt4
  • ———
  • Python and MAC OSX

    Python comes pre-installed on Mac OS X, but due to Apple’s release cycle, it’s often one or even two years old. The overwhelming recommendation of the « MacPython » community is to upgrade your Python by downloading and installing a newer version from the Python standard release page.

    If you are using Mac OS X 10.5, see the Leopard wiki page for detailed information.

    If you’re just curious…

    You don’t have to download anything. You can run a Python interpreter by double-clicking on Applications / Utilities / Terminal (here’s a picture), then typing « python » into the window that opens up.

    You’ll see a prompt that looks like this:

    Python 2.3.5 (#1, Mar 20 2005, 20:38:20)
    [GCC 3.3 20030304 (Apple Computer, Inc. build 1809)] on darwin
    Type "help", "copyright", "credits" or "license" for more information.

    (On Mac OS X 10.3 (Panther), it will say « Python 2.3.0 », an older version.)Try typing « 2 + 2 » and hit « Enter »:

    >>> 2 + 2

    You’ve just evaluated your first Python expression. It’s a simple environment, but good enough to work through the Python tutorial.By the way, if you download the recommended upgrade mentioned at the top of this page, the « IDLE » development environment will make working through the tutorial a bit easier.

  • FEM, finite element method, PDE, partial differential equation;mathematica
    This package allows to solve second order elliptic differential equations in two variables:

    div(a*grad u) – b*u = f in the domain domain u = gD Dirichlet boundary conditions on first part of boundary a*du/dn = gN Neumann condition on the other part of the boundary

    If the functions a, b f, gD and gN are given, then a numerical approximation is computed, using the method of finite elements. To generate meshes the programm EasyMesh can be used.

    a starting point for building 3D surface meshes or true volumetric tetrahedral grids

    « nanosecond history »:


    Since William Lorensen and Harvey Cline’s publication of Marching Cubes: A High
    Resolution 3D Surface Construction Algorithm in 1987 Marching Cubes has become the
    defining algorithm for the creation of 3D surface meshes.

    Yet despite the success of Marching Cubes the resulting mesh exhibits several weaknesses, including aliasing and terracing artifacts, less-than-optimal triangle quality, and large numbers of triangles.  A
    multitude of techniques have been introduced to address these issues, including surface
    smoothing and triangle decimation algorithms. Beyond reducing artifacts, smoothing
    improves the effectiveness of triangle decimation algorithms and reduces errors during
    finite element analysis. However, many smoothing techniques fail to eliminate terracing
    because their local filter neighborhood does not encompass the width of the terrace.
    Additionally, smoothing a mesh without consideration of the original data may smooth
    away crucial fine details as well as mesh generation artifacts.


    In 1998 Sarah F. F. Gibson published Constrained Elastic Surface Nets: Generating
    Smooth Surfaces from Binary Segmented Data. Her work attempts to preserve the fine
    detail present in the original data by applying smoothing directly to the binary data and
    introduces the concept of a constraint to limit the deviation of the smoothed data from the
    Modified SurfaceNets attempts to apply Gibson’s SurfaceNet technique to the
    problem of smoothing a Marching Cubes mesh. By defining SurfaceNet nodes on the
    Marching Cubes mesh and constraining their movement to their Voronoi regions,
    Modified SurfaceNets aims to reduce terracing while preserving the fine detail of the
    original image.


    and see this present bog :


    This class of Surface Reconstruction methods is OK for immerged SURFACE and only for SURFACE.

    If you want to generate not only surface models from your data but also to create true
    volumetric tetrahedral grids suitable for advanced 3D finite-element simulations, then open your mind… Usually, these grids are constructed using a flexible advancing-front algorithm. Again, special care is taken to obtain meshes of high quality, i.e., tetrahedra with bad aspect ratio are avoided…

    see a commercial software (with a quite good link with matlab):


    In biophotonics, we have this process:

    1/produce your images (exactly a stack of 2D images)

    2/perform many image cleaning and many img processes with or without informations from the other images in the stack (often it is only a process for each image with imageJ)

    3/the final step is segmentation & binarisation also with or without informations from the other images in the stack

    4/generation of surface ( a/isosurface for rendering; b/ 3D surface mesh)

    5/generation true  3D volumetric tetrahedral grids suitable for advanced 3D finite-element simulations

    6/a 4D solver with time

    7/statistics and comparison between biology, medical and multiphysics data and 4D simulations

    FEM et éléments finis-english and « Francais »

    Some examples of FEM software available on the market

    Some examples of explicit software:

    See also


    1. ^ Clough, Ray W.; Edward L. Wilson. Early Finite Element Research at Berkeley (PDF). 2007

    External links


    Quelques exemples de logiciels d’éléments finis appliqués à la mécanique des structures

    Quelques exemples de logiciels généralistes utilisant la méthode des éléments finis en mécanique des structures

    • ABAQUS: logiciel américain
    • CosmosWorks : Logiciel Franco-Américain appartenant à SolidWorks qui lui même appartient à Dassault CosmosWorks
    • ANSYS: logiciel américain
    • CAST3M: logiciel français mis à disposition gratuitement pour l’enseignement et la recherche CASTEM
    • SYSTUS: logiciel français, traite des calculs mécaniques, thermiques et thermo-mécaniques linéaires et non-linéaires
    • SYSWELD: logiciel français, basé sur SYSTUS et permettant le calcul de traitement thermique, thermo-chimique, soudage, avec couplage mécanique/thermique/métallurgique voir éléctromagnétisme (trempe par induction)
    • Code Aster: logiciel libre français Aster
    • Nastran: logiciel américain
    • PERMAS: logiciel allemand PERMAS
    • SAMCEF: logiciel belge SAMCEF
    • Morfeo: logiciel belge Morfeo
    • JMAG: logiciel Japonais (distribué en Europe par Powersys Powersys) permet un couplage entre les analyses électromagnétiques et structurelles.

    Quelques exemples de logiciels de dynamique non linéaire (explicite) des structures utilisant la méthode des éléments finis en mécanique des structures



    comsol finite element CAD import module

    Getting your CAD geometries ready for FEA modeling is easier than ever with the CAD Import Module. It facilitates the reading of industry-standard formats such as STEP, IGES, ACIS® (SAT®) or Parasolid®. Extra add-ons support file formats for packages that have their own geometry kernel.

    The CAD Import Module goes beyond just the reading of file formats. The interactive repair feature assures that imported geometries are mathematically correct for FEA modeling. And, in order to cut down on unnecessary details in your CAD geometries, defeaturing tools that remove fillets, small faces, sliver faces, as well as spikes or short edges are included.

    The CAD Import Module also provides a bidirectional interface to SolidWorks® that maintains associativity with the CAD system. This means that parameters can be changed in COMSOL models, which result in automatically updating the CAD geometry in SolidWorks that then updates the COMSOL geometry for a new model.

    File formats supported by COMSOL products

    Product File format (file extensions) Supported versions
    COMSOL Multiphysics STL (.stl)
    VRML (.wrl, .wml) 1.0
    DXF (.dxf) up to R14
    GDS (.gds)¹ 2
    CAD Import Module Parasolid (.x_t, .x_b) up to V18
    SAT (.sat, .sab) up to R17
    STEP (.step, .stp) AP203, AP214
    IGES (.igs, .iges) up to 5.3
    CATIA V4 Import Module CATIA V4 (.model) 4.1.9 to 4.2.4
    CATIA V5 Import Module CATIA V5 (.CATPart, .CATProduct) R2 to R17
    Inventor Import Module Autodesk Inventor (.ipt)² 6 to 11
    Pro/E Import Module Pro/Engineer (.prt, .asm) 16 to Wildfire 3
    VDA-FS Import Module VDA-FS (.vda) 1 and 2

    ¹ GDS Import requires COMSOL Script.
    ² Only import of parts is supported.

    autres formats:


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