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:


    MeshLab is an open source, portable, and extensible system for the processing and editing of unstructured 3D triangular meshes.



    The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

    The system is heavily based on the VCG library developed at the Visual Computing Lab of ISTI – CNR, for all the core mesh processing tasks and it is available for Windows, Linux (src) and MacOSX (intel only).

    The MeshLab system started in late 2005 as a part of the FGT course of the Computer Science department of University of Pisa and most of the code (~15k lines) of the first versions was written by a handful of willing students. The following years FGT students have continued to work to this project implementing more and more features. The proud MeshLab developers are listed below.
    This project have been supported by the European Networks of Excellence Epoch and (partially) by Aim@Shape

    Remember that, whenever you use MeshLab in a official/commercial project or in any kind of research, you should:

    • Explicitly cite in your work that you have used MeshLab, a tool developed with the support of the Epoch NOE,
    • Post a couple of lines in the users’ forum describing the project where MeshLab was used.

    Adopted License, acknowlegments and other legal issues are detailed here.


    • Interactive selection and deletion of portion of the mesh. Even for large models.
    • Painting interface for selecting, smoothing and coloring meshes.
    • Input/output in many formats:
      • import:PLY, STL, OFF, OBJ, 3DS, COLLADA, PTX
      • export:PLY, STL, OFF, OBJ, 3DS, COLLADA, VRML, DXF
      • Point Clouds support. Now 3D files that are composed only by points are well supported in PLY and OBJ format.
      • U3D support; MeshLab is the first open source tool to provide direct conversion of 3D meshes into the U3D format. Now you can create pdf, like this with 3D objects with just MeshLab and LaTeX.
    • Mesh Cleaning Filters:
      • removal of duplicated, unreferenced vertices, null faces
      • removal of small isolated components
      • coherent normal unification and flipping
      • erasing of non manifold faces
      • automatic filling of holes
    • Remeshing filters:
      • High quality edge collapse simplification (even with texture coords preservation)
      • Surface reconstruction from points (a ball pivoting variant)
      • Subdivision surfaces (loop and butterfly)
      • Feature preserving smoothing and fairing filters
    • Various Colorization/Inspection filters
      • Gaussian and mean curvature
      • Border edges, geodesic distance, from borders
      • Non two-manifold edges and vertices
      • Self intersecting faces
      • Ambient Occlusion. An ambient occlusion field can be computed and stored per vertex
    • Interactive Mesh Painting
      • Color Painting
      • Selection paint
      • Smoothing
    • Measuring tool. You can take linear measures between points of the displayed meshes
    • Slicing tool. A new tool that allows to export planar sections of a mesh in SVG format
    • 3D Scanning tools
      • Alignment ICP based range map alignment tool, for putting meshes into the same reference space.
      • Merging of multiple meshes the Poisson surface reconstruction source code (kindly provided by by Michael Kazhdan and Matthew Bolitho) have been included in.
    • OpenGL Shader based rendering (write your own shader!) compatible with Typhoon Lab’s Shader Designer
    • Large rendering (up to 16k x 16k) for high quality printing
    • The history of the all performed cleaning/editing actions can be re-played on different meshes or saved and for archival purposes.
    • Extendible plugins based architecture, writing new mesh processing functions, colorization filters and support for different file formats is quite easy! Look at PlugIn Samples

    Bug reports and feature requests should be filed using the sourceforge service ->
    General questions can be posted on the help public forums

    STL openSource et autres


    MeshLab is an open source Windows and Linux application for visualizing, processing and converting three dimensional meshes to or from the STL file format.

    MeshLab Homepage

    MeshLab, started in late 2005, is a free and open-source general-purpose mesh processing software program; the system is aimed to help the processing of the typical not-so-small unstructured models that arise in the pipeline of processing of the data coming from 3D scanning. MeshLab is oriented to the management and processing of unstructured large meshes and provides a set of tools for editing, cleaning, healing, inspecting, rendering and converting these kinds of meshes.

    The automatic mesh cleaning filters includes removal of duplicated, unreferenced vertices, non manifold edges and null faces. Remeshing tools support high quality simplification based on quadric error measure, various kinds of subdivision surfaces and two surface reconstruction algorithms from point clouds based on the ball pivoting technique and on the Poisson surface reconstruction approach. For the removal of noise, usually present in acquired surfaces, MeshLab supports various kinds of smoothing filters and tools for curvature analysis and visualization.

    MeshLab also includes an interactive direct paint-on-mesh system that allows to interactively change the color of a mesh, to define selections and to directly smooth out noise and small features.

    Version 1.1.0 also includes a tool for the registration of multiple range maps based on the Iterative Closest Point algorithm.

    MeshLab is available for most platforms, including Windows, Linux and Mac OS X intel only. The system support input/output in the following formats: PLY, STL, OFF, OBJ, 3DS and COLLADA.

    ————Art of Illusion

    Art of Illusion is a free, open source 3D modelling and rendering studio. It is written entirely in Java, and should be usable on any Java Virtual Machine which is compatible with J2SE 1.4 or later.

    File Handling

    Mac OS X

    Art of Illusion requires Mac OS X 10.4 or later with all software updates installed.

    1. Download the Art of Illusion installer.
    2. Double-click it to mount the disk image, then copy the « Art of Illusion » folder to your Applications folder.
    3. (optional) Download the Java Media Framework. Select the « Cross-platform Java » version. After you download it, find the file jmf.jar and move it to /Library/Java/Extensions. The rest of the downloaded files are not needed, and can be deleted. (This step is not required, and most of Art of Illusion will work normally without JMF. You will not be able to save animations in Quicktime format, however, if it is not installed.)
    4. To launch the program, double-click the Art of Illusion icon.


    RepRap is an OpenSource project that uses STL file input and generates solid objects as output.

    On peut utiliser des parties de ce projet pour la gestion et modif des STL.


    • The STL Format – Standard Data Format for Fabbers: The STL Format
    • How to Create an STL file Guide to exporting STL files from various CAD packages (courtesy of ProtoCAM)
    • SolidView SolidView is a commercial STL manipulation package that has a Lite version available (under provision of a business email address) for STL viewing.
    • Freesteel with a web-interface where you can upload an STL file and render it into an image in your browser.
    • ADMesh is a GPLed text-based program for processing triangulated solid meshes, and reads and writes the STL file format.


    • remarque: Mathematica sait lire du STL.


    SolidView lite

    Version Up to
    ACIS/SAT .sat, .sab ACIS/SAT Data v18 Yes*
    Assembly Component Definition .acd SolidView Any Yes
    Autodesk DXF .dxf 2004 Yes
    Autodesk DWG .dwg 2004 Yes
    Catia V4 .cat, .exp, .model Native Catia V4 Data V4 Yes*
    Catia V5 .catpart, .catproduct Native Catia V5 Data R7 to R17 Yes*
    I-Deas Web Access .mca, .idi I-Deas MCA v11NX Yes*
    Initial Graphics Exchange Specification .igs, .iges IGES 3D Any Yes*
    Object File .obj Any Yes Yes
    Parasolid .x_t, .x_b Parasolid text and binary Data v19 Yes*
    Pro/Engineer .prt, .asm Native PTC Pro/E Data WildFire 4 Yes*
    SolidEdge .par, .dft., .asm, .psm Native SolidEdge Data v20 Yes*
    Solid File Exchange .SFX SolidView Any Yes Yes
    SolidView Solid .sv SolidView Any Yes
    SolidWorks .sldprt, .sldasm Native SolidWorks Data 2008 Yes Yes
    Step .step Native PTC AP203/AP214 Yes*
    Stereolithography .stl Any Yes Yes
    Unigraphics .prt Native UG Data
    parts and assemblies
    NX 5 Yes*
    VDAFS .vda Any Yes*
    VRML .wrl 1.0 / 2.0 Yes Yes

    *Optional add on for SolidView/Pro. Click here for pricing.

    SolidView/Lite SolidView SolidView/Pro SolidView/Pro RP
    All Versions Have Fully Functional Demos N/A Free for 15 days Free for 15 days Free for 15 days
    Description FREE Low Cost Markup Import CAD data Import CAD data &
    Rapid Prototyping Tools
    View STL, VRML, OBJ, SolidWorks Yes Yes Yes Yes
    Print STL, VRML, OBJ, SolidWorks Yes Yes Yes Yes
    Measure STL, VRML, OBJ, SolidWorks Yes Yes Yes
    Modify STL, VRML, OBJ Yes Yes Yes
    Save STL, VRML, OBJ Yes Yes
    View, Print, Measure, Modify, and Save DXF Yes Yes
    View SFX files Yes Yes Yes Yes
    Print SFX files Yes Yes Yes Yes
    Measure SFX files Yes Yes Yes Yes
    Combine 3D data Yes Yes Yes
    Edit/Save SFX files Yes Yes Yes
    Replay SFX 3D Slide Shows Yes Yes Yes Yes
    Create new SFX files Yes Yes
    Modify SFX data Yes Yes Yes Yes
    Publish SFX files Yes Yes
    Export section data Yes Yes
    View 2D raster files (tif, bmp, jpeg, etc.) Yes Yes
    View 2D vector files (cgm, hpgl, wmf, etc.) Yes Yes
    Optional CAD Interfaces Yes Yes
    Optional Network Licensing Yes Yes
    Move, copy and scale 3D data Yes Yes
    Verify STL data Yes Yes
    Repair STL data Yes
    Split STL data Yes
    Shell STL data Yes
    Create drain holes Yes
    Automatic RP part layout Yes
    Manual RP part layout Yes
    RP build time estimator Yes
    Optional automatic RP support generator


    STL interchanging data between CAD/CAM system


    There are many other file formats capable of encoding triangles available, such as VRML, DXF, but they have the disadvantage that it’s possible to put things other than triangles into it, and thus produce something ambiguous or unusable.


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