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Mesh Generation & Grid Generation on the Web

http://www-users.informatik.rwth-aachen.de/~roberts/meshgeneration.html

Mesh Generation & Grid Generation on the Web

The aim of this document is to provide information on mesh and grid generation: people working in the field, research groups, books and conferences. It is maintained by Robert Schneiders.

Mesh generation is an interdisciplinary area, and people from different departments are working on it: Mathematicians, computer scientists, engineers from many disciplines. Despite the fact that surprisingly many people are active in the field, often there are few contacts between researchers. The aim of this page is to improve communication between research groups and to help people to get an overview of the field.

The page is organized as follows:

<!– –>

    People and research groups: Info on meshing research at universities, companies, government labs etc.

    List of people: A directory of people working on mesh generation.

    Latest news: What’s up in mesh generation.

    Software: A list of programs, both public domain and commercial.

    Conferences: Information on conferences, summerschools, short courses etc.

    Literature: Books, reviews, online sources and course materials.

    Open positions: Career opportunities for people with background in mesh generation.

    Information on related topics: Pages with information on CFD, scientific computing, computational geometry and other fields related to mesh generation.

<!– –> Service for frequent readers: You can find all entries, sorted by time of insertion, here (there is also an archive page). <!– Click here to see the latest updates (there is also an archive page). –>

Research on mesh generation is abundant, and I don’t claim to give a complete overview. In order make this page a useful service for the mesh generation community, I need help from other people. So if you are interested in getting put on the list, or if you have any comments or hints on other sources of information on mesh generation in the net, please send me an email (robert.schneiders@arcor.de).

A valuable source of information is the Meshing Research Corner, a comprehensive database with literature on mesh generation. It is maintained by Steve Owen.

ParaView is an application framework as well as a turn-key application; Modeling software OpenFOAM and ParaView ; mesh processing: generation, manipulation, conversion

ParaView is an open source, multi-platform data analysis and visualization application. It has a client-server architecture to facilitate remote visualization of datasets

It is an application built on top of the Visualization Tool Kit (VTK) libraries.

The ParaView code base is designed in such a way that all of its components can be reused to quickly develop vertical applications. This flexibility allows ParaView developers to quickly develop applications.

Input/Output and File Format

  • Supports a variety of file formats including: VTK (new and legacy, all types including parallel, ascii and binary, can read and written).
  • Various polygonal file formats including STL and BYU (by default, read only, other VTK writers can be added by writing XML description).
  • Many other file formats are supported. See ParaView Readers and ParaView Writers for a full list.

CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. ParaView utilizes CMake for the software compilation process.

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ParaView is used as the visualization platform for the Modeling software OpenFOAM (Open Field Operation and Manipulation).It is primarily a C++ toolbox for the customisation and extension of numerical solvers for continuum mechanics problems, including computational fluid dynamics (CFD). It comes with a growing collection of pre-written solvers applicable to a wide range of problems.

First major general-purpose CFD package to use polyhedral cells. This functionality is a natural consequence of the hierarchical description of simulation objects.

OpenFOAM compares favourably with the capabilities of most leading general-purpose commercial closed-source CFD packages. It relies on the user’s choice of third party pre- and post-processing utilities, and ships with:

  • a plugin (paraFoam) for visualisation of solution data and meshes in ParaView.
  • a wide range of mesh converters allowing import from a number of leading commercial packages
  • an automatic hexahedral mesher to mesh engineering configurations

OpenFOAM was conceived as a continuum mechanics platform but is ideal for building multi-physics simulations.

OpenCFD develop OpenFOAM in the Linux/UNIX operating system because: we believe it is the best platform for this kind of high end simulation code development and operation; Linux is efficient, robust, reliable and flexible and undergoes rapid development and improvement; Linux is open source, like OpenFOAM; Linux is very effective for parallel operation on Beowulf clusters.

OpenFOAM is open source software so people can freely compile it on any operating system they choose. Most OpenFOAM users are running Linux, so this site offers the download of binaries for selected Linux systems.

As the present time we are unaware of any binary distributions for Windows or MacOSX. However, ports to these operating systems have been the subject of debate on the OpenFOAM discussion site, which may provide the best source of information on the matter.

http://www.opencfd.co.uk/openfoam/

OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells.

Mesh generation

OpenFOAM applications handle unstructured meshes of mixed polyhedra with any number of faces: hexahedra, tetrahedra, degenerate cells, basically anything.

Mesh generation is made simple by the fact that a cell is simply represented as a list of faces and a face as a list of vertices: this makes mesh handling very easy even for complex meshes with, say, embedded refinement or complex shapes near the boundary.

OpenFOAM is supplied with the following mesh generator tools that run in parallel.

Mesh generation tools


blockMesh A multi-block mesh generator
extrude2DMesh Takes 2D mesh (all faces 2 points only, no front and back faces) and creates a 3D mesh by extruding with specified thickness
extrudeMesh Extrude mesh from existing patch (by default outwards facing normals; optional flips faces) or from patch read from file
snappyHexMesh Automatic split hex mesher. Refines and snaps to surface

The main mesh generators cover two extremes: snappyHexMesh, that can mesh to complex CAD surfaces; blockMesh a simple file-driven block mesh generator.

Mesh manipulation

OpenFOAM is supplied with several utilties that perform mesh checking and manipulation. The full list of utilties is given below

Mesh manipulation


attachMesh Attach topologically detached mesh using prescribed mesh modifiers
autoPatch Divides external faces into patches based on (user supplied) feature angle
cellSet Selects a cell set through a dictionary
checkMesh Checks validity of a mesh
createBaffles Makes internal faces into boundary faces. Does not duplicate points, unlike mergeOrSplitBaffles
createPatch Utility to create patches out of selected boundary faces. Faces come either from existing patches or from a faceSet
deformedGeom Deforms a polyMesh using a displacement field U and a scaling factor supplied as an argument
faceSet Selects a face set through a dictionary
flattenMesh Flattens the front and back planes of a 2D cartesian mesh
insideCells Picks up cells with cell centre ’inside’ of surface. Requires surface to be closed and singly connected
mergeMeshes Merge two meshes
mergeOrSplitBaffles Detects faces that share points (baffles). Either merge them or duplicate the points
mirrorMesh Mirrors a mesh around a given plane
moveDynamicMesh Mesh motion and topological mesh changes utility
moveEngineMesh Solver for moving meshes for engine calculations.
moveMesh Solver for moving meshes
objToVTK Read obj line (not surface!) file and convert into vtk
pointSet Selects a point set through a dictionary
refineMesh Utility to refine cells in multiple directions
renumberMesh Renumbers the cell list in order to reduce the bandwidth, reading and renumbering all fields from all the time directories
rotateMesh Rotates the mesh and fields from the direcion n1   \special {t4ht= to the direction n2   \special {t4ht=
setSet Manipulate a cell/face/point set interactively
setsToZones Add pointZones/faceZones/cellZones to the mesh from similar named pointSets/faceSets/cellSets
splitMesh Splits mesh by making internal faces external. Uses attachDetach
splitMeshRegions Splits mesh into multiple regions
stitchMesh ’Stitches’ a mesh
subsetMesh Selects a section of mesh based on a cellSet
transformPoints Transforms the mesh points in the polyMesh directory according to the translate, rotate and scale options
zipUpMesh Reads in a mesh with hanging vertices and zips up the cells to guarantee that all polyhedral cells of valid shape are closed

Mesh motion

OpenFOAM adopts a novel approach to mesh motion by defining it in terms of the boundary motion which is extremely robust.

The solver need only define the the motion of the boundary and everything else will be done automatically. The open architecture of OpenFOAM solver codes allows quick and efficient implementation: mesh motion can be based on any solution variable, either local or integrated and by dynamically adjusted during the run.

Mesh motion is also transparently integrated with top-level models: the model writer does not see the additional complexity, which is conveniently packaged within the discretisation operators.

For examples of automated mesh motion in OpenFOAM, see Solutions

Mesh conversion

OpenFOAM accepts meshes generated by any of the major mesh generators and CAD systems. Listed below are converter utlities for the major commercial mesh generators. Note that it is also possible to import the meshes from most general purpose mesh generators since they will export in a format read by one of the converters.

Mesh converters


ansysToFoam Converts an ANSYS input mesh file, exported from I-DEAS, to OPENFOAM®format
cfx4ToFoam Converts a CFX 4 mesh to OPENFOAM®format
fluent3DMeshToFoam Converts a Fluent mesh to OPENFOAM®format
fluentMeshToFoam Converts a Fluent mesh to OPENFOAM®format including multiple region and region boundary handling
foamMeshToFluent Writes out the OPENFOAM®mesh in Fluent mesh format
foamToStarMesh Reads an OPENFOAM®mesh and writes a PROSTAR (v4) bnd/cel/vrt format
gambitToFoam Converts a GAMBIT mesh to OPENFOAM®format
gmshToFoam Reads .msh file as written by Gmsh
ideasUnvToFoam I-Deas unv format mesh conversion
kivaToFoam Converts a KIVA grid to OPENFOAM®format
mshToFoam Converts .msh file generated by the Adventure system
netgenNeutralToFoam Converts neutral file format as written by Netgen v4.4
plot3dToFoam Plot3d mesh (ascii/formatted format) converter
polyDualMesh Calculate the dual of a polyMesh. Adheres to all the feature and patch edges
sammToFoam Converts a STAR-CD SAMM mesh to OPENFOAM®format
star4ToFoam Converts a STAR-CD (v4) PROSTAR mesh into OPENFOAM®format
starToFoam Converts a STAR-CD PROSTAR mesh into OPENFOAM®format
tetgenToFoam Converts .ele and .node and .face files, written by tetgen
writeMeshObj For mesh debugging: writes mesh as three separate OBJ files which can be viewed with e.g. javaview

FEM, finite element method, PDE, partial differential equation;mathematica

http://library.wolfram.com/infocenter/MathSource/4478/
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 general finite element environment;mathematica

http://library.wolfram.com/infocenter/TechNotes/6635/

The Mathematica application package AceFEM is a general finite element environment designed to solve multi-physics and multi-field problems. Using Mathematica, the program provides both extensive symbolic capabilities and the numeric efficiency of a commercial finite element environment.

AceFEM consists of two components. The main module performs tasks such as processing user-input data, mesh generation, control of solution procedures, and graphic post-processing of results. A fully integrated second module handles numerically intensive operations such as evaluation and assembly of finite element quantities, solution of linear systems of equations, contact search procedures, and more.

alliance for medical image computing Kit = free open source software platform

Overview

The NA-MIC Kit is a free open source software platform. The NA-MIC Kit is distributed under a BSD-style license without restrictions or « give-back » requirements and is intended for research, but there are not restrictions on other uses. It consists of the 3D Slicer application software, a number of tools and toolkits such as VTK and ITK, and a software engineering methodology that enables multiplatform implementations. It also draws on other « best practices » from the community to support automatic testing for quality assurance. The NA-MIC kit uses a modular approach, where the individual components can be used by themselves or together. The NA-MIC kit is fully-compatible with local installation (behind institutional firewalls) and installation as an internet service. Significant effort has been invested to ensure compatibility with standard file formats and interoperability with a large number of external applications.

See this presentation on the NA-MIC Kit for more information.

Download Central

Please go here to download Slicer software, documentation and data.

Software Packages

3D Slicer

3D Slicer is a software package for visualization and medical image computing. A tutorial for prospective users of the program can be found on the web. See our tutorials page for an introduction to the use of 3D Slicer. More…


The Visualization Toolkit VTK

The Visualization Toolkit is an object-oriented toolkit for processing, viewing and interacting with a variety of data forms including images, volumes, polygonal data, and simulation datasets such as meshes, structured grids, and hierarchical multi-resolution forms. It also supports large-scale data processing and rendering. More…


The Insight Toolkit ITK

The Insight Segmentation and Registration Toolkit (ITK) is an open-source software toolkit for performing registration and segmentation. Segmentation is the process of identifying and classifying data found in digitally sampled representations. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be registered with a MRI scan in order to combine the information contained in both. More…


KWKidgets GUI Toolkit

KWWidgets is an Open Source library of GUI classes based on Tcl/Tk with a C++ API. This library was originally developed by Kitware for ParaView, and now has been extended in functionality and architecture thanks to NAMIC support. More…


Teem Libraries and Command Line Tools

Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. More…


XNAT Web-based Image Informatics Server

The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.

NA-MIC is working to provide a portable, easy-to-install and easy-to-administer version of XNAT that can be deployed as part the Kit. These efforts will build on ongoing work in the BIRN community to integrate Slicer with XNAT.


Batchmake

BatchMake is a cross platform tool for batch processing of large amount of data. BatchMake can process datasets locally or on distributed systems using Condor (a grid computing tool that enables distributed computing across the network). Some of the key features of BatchMake include: 1) a BSD License, 2) CMake-like scripting language, 3) distributed scripting via Condor, 4) a centralized remote website for online statistical analysis. 4) a user Interface using FLTK, and 5) BatchMake is cross platform. More…


CMake The Cross-platform Make Tool

CMake is used to control the software build process using simple platform, compiler and operating system independent configuration files. CMake generates native makefiles and workspaces that can be used in the development environment of your choice. That is, CMake does not attempt to replace standard development tools such as compilers and debuggers, rather it produces build files and other development resources that can benefit from automated generation. Further, once CMake configuration files are created, they can be used to produce developer resources across the many platforms that CMake supports. CMake is quite sophisticated: it is possible to support complex environments requiring system configuration, pre-processor generation, code generation, and template instantiation. More…

New: CMake has been adopted by KDE, one of the world’s largest open source software systems.


CDash, CTest, CPack Software Process Tools

As an adjunct to CMake the tools CDash, CTest, CPack are used to test and package all components of the NAMIC kit. CTest is a testing client that locally performs testing on a software repository, and then communicates the results of the testing to CDash (and other testing, dashboard servers such as DART2). CPack is a cross-platform tool for packaging, distributing and installing the NAMIC kit on various systems including Linux, Windows, and Mac OSX. More…


DART Testing Server

DART is a testing server, meaning that it gathers the results of testing from clients (such as CTest) and aggregates them on the testing « dashboard ». This dashboard is central to the NAMIC software process; it provides a centralized web site where NAMIC Kit developers and users can ascertain the day-to-day health of the software, and repair the software immediately if faults are discovered. It facilitates distributed development, and provides the stability that complex software such as the NAMIC Kit requires to support a large community of users. More…

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Ref.

http://www.na-mic.org/Wiki/index.php/NA-MIC-Kit

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NA-MIC Kit in Numbers

The numbers in this table are statistics characterizing the NA-MIC kit. They provide an estimate of the scale of the Kit, including approximate costs to create and total effort expended. Note that estimates such as these are required because large open-source software systems cannot be tracked via direct investment since much of the effort is voluntary in nature, and distributed across the world through a variety of organizations.
Source: http://www.ohloh.org. Captured on May 30 2008. See the Ohloh website for an explanation of how the numbers were computed.

Package Lines of code Person years Price tag at 100k per person year
Slicer 587,919 161 $16,068,440
KWW 189,627 49 $ 4,925,590
VTK 1,344,989 385 $38,521,873
ITK 711,474 197 $19,712,495
CMAKE 213,671 56 $ 5,586,895
Total 3,047,680 848 $84,815,293

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