ElmerGUI A new pre-processor for Elmer

Mikko Lyly

CSC, Finnish IT Center for Science

Elmer User meeting, 29th May 2008, CSC, Espoo

Outline

Backgound Workflow Practical example On input file formats Excercise Custom menus

Background

Intended to replace ElmerFront:• Enhanced mesh generation and mesh manipulation tools• Enhanced visualization routines (based on OpenGL and extensions)• Better compatibility with latest Solver• Programmable/customizable GUI• Less dependencies on external libraries• Portability (Linux, Windows, Mac)

ElmerGUI is not:• A CAD program – complicated 3D-geometries should be modelled by

separate tools and imported into ElmerGUI in an appropriate format• A stand-alone-program – it needs ElmerSolver and ElmerPost (the “elmer-

suite”) in path to solve the problem and visualize the results

Prequisites

Libraries: • Qt Cross-Platform Application Framework (version 4.2 or higher)• Qwt - Qt Widgets for Technical Applications (version 5 or higher)

Qt4: http://trolltech.com/products/qt/

Qwt5: http://qwt.sourceforge.net/

Licence: GPL

Qt4 is pre-installed on most Linux distributions

Binary installation packages available for Windows and Mac

Compilation

Getting the sources:

$ svn co https://elmerfem.svn.sourceforge.net/svnroot/elmerfem elmefem

ElmerGUI is located in ”elmerfem/trunk/misc/Mesh3D”:

$ cd elmerfem/trunk/misc/Mesh3D

$ less LICENCES.txt

Follow the compilation instruction in README.txt:

$ qmake –project

$ qmake

$ make

Mesh generation

Possibility to use the following mesh generators:• Tetgen (libtet compiled as a shared library)• Netgen (libng compiled as a shared library)• ElmerGrid (built-in)

No hard-coded dependencies on external generators

For more information and documentation, see:

http://tetgen.berlios.de/

http://www.hpfem.jku.at/netgen/

http://www.csc.fi/elmer

Mesh generation Tetgen (libtet)

• Developed by Hang Si et al. at the Weierstrass Institute for Applied Analysis and Stochastics

• Fast and efficient unstructured tetrahedral mesh generator• Licenced under the MIT-licence• Not free, but for private, research, and educational purposes it can be used

at no cost and without further arrangements• Due to the commercial restrictions, libtet is not included in the binary

distribution packages of Elmer. • The user has to make sure that he has a valid licence, or right to use the

genarator otherwise, and download /compile the shared library from source:

$ cd elmerfem/trunk/misc/tetgen_patches$ patch < patch_tetgen.h$ g++ -fPIC -c predicates.cxx$ g++ -fPIC -O -DTETLIBRARY -c tetgen.cxx$ g++ -fPIC -c ElmerAPI.cpp$ g++ -shared predicates.o tetgen.o ElmerAPI.o -o libtet.so

Mesh generation

Netgen (libng)• NETGEN was developed mainly by Joachim Schöberl within project grants

from the Austrian Science Fund FWF ( Special Research Project "Numerical and Symbolic Scientific Computing", Start Project "hp-FEM) at the Johannes Kepler University Linz. Significant contributions were made by Johannes Gerstmayr (STL geometry) Robert Gaisbauer (OpenCascade interface).

• Powerful triangular and tetrahedral mesh generator• Licenced under LGPL – included in the binary distribution packages of Elmer• Instructions for compiling libng from source can be found from

$ cd elmerfem/trunk/misc/netgen_patches$ less README

Mesh generation

ElmerGrid• Built-in mesh generator and mesh manipulation tool• Very fast structured 1D/2D/3D-mesh generation• Able to import mesh files in several external formats

Mesh generation

Mesh generator chosen automatically by input-file-format:• STL (stereolitography format) – libtet or libng• SMESH (piecewise linear complex) – libtet• POLY (like SMESH but less restrictions) - libtet• OFF (Geomview's polyhedral file format) - libtet• PLY (polyhedral file format) - libtet• MESH (Medit's surface mesh file format) - libtet• GRD (elmergrid's native input file) - ElmerGrid• FDNET (Fidap's mesh file format) - ElmerGrid• MSH (Gmesh's file format) - ElmerGrid• MPHTXT (Comsol Multiphysic's mesh file format) - ElmerGrid• UNV (Ideas' universal file format) – ElmerGrid• Elmer's native mesh file format

ElmerGUI + ElmerSolver + ElmerPost

Workflow

ElmerGrid

Workflow

Open your input file (example: samples/grd/angle3d.grd):

Workflow

Optionally configure mesh generator and remesh:

Workflow

The values in the config dialog are inherited from cmd line tools:

Workflow

Remeshing is perfomed in a separate thread:

Workflow Manipulate boundaries: Select a boundary by double clicking and

choose ”divide surface” to split it by ”sharp edges”:

Workflow Manipulate boundaries: Select boundaries by holding down the

CTRL-key while double clicking. Choose ”unify surface” to join:

Workflow Turn on/off boundary index numbering for verification:

Workflow Define an equation (PDE-system) to solve:

Workflow Let us define the ”heat equation” as an example:

Workflow The equation can later be activated for modification from menu:

Workflow Similarly, we can next define material properties and parameters:

Workflow Data is given in the ”General” and ”Heat equation” tabs:

Workflow Add body force:

Workflow Add boundary conditions:

Workflow Generate solver input file (sif):

Workflow Edit the solver input file (if needed):

Workflow Save the model:

Workflow

Run solver:

Workflow Convergence monitor reveals possible problems:

Workflow Invoke post processor:

Workflow Visualize the results by Elmerpost:

Workflow You can alternatively define/edit body properties by holding down

the SHIFT-key and by double clicking any surface of the body:

Workflow Similarly, boundary conditions may be (re)defined by holding

down the ALT-key while double clicking a boundary:

Workflow The SHIFT / ALT –functionality may also be activated from menu:

Workflow

There are some useful functions available from menu:• View -> Surface mesh (toggles the visibility of surface mesh)• View -> Sharp edges (show the ”sharp edges” separating boundaries)• View -> Compass (show coordinates)• View -> Hide/show selected (toggle the visibility of current selection)• View -> Numbering (useful for debugging and verification of the model)• View -> Reset model view (clear view)• Model -> Summary (get an overview of the model)• File -> Save picture as… (save the image in several formats)• Mesh -> Terminate (kills the meshing thread, if blocked)• Run -> Show convergence (toggles the visibility of convergece monitor)• Run -> Kill solver (kills the solver process, if necessary)• Run -> Kill postprocessor (kills ElmerPost, if necessary)

Input file formats

SMESH• Part 1 - node list• First line: <# of points> <dimension (must be 3)> <# of attributes> <# of boundary

markers (0 or 1)> • Remaining lines list # of points:

<point #> <x> <y> <z>[attributes] [boundary marker]...

• Part 2 - facet list• One line: <# of facets> <boundary markers (0 or 1)> • Following lines list # of facets:

<# of corners> <corner 1> <corner 2> ... <corner #> [boundary marker]...

• Part 3 - hole list• One line: <# of holes> • Following lines list # of holes:

<hole #> <x> <y> <z>...

• Part 4 - region attributes list• One line: <# of region> • Following lines list # of region attributes:

<region #> <x> <y> <z><region number><region attribute>...

Input file formats

Example (”L.smesh”):• 12 3 0 1• 1 0 0 0 1• 2 4 0 0 1• 3 4 2 0 1• 4 2 2 0 1• 5 2 6 0 1• 6 0 6 0 1• 7 0 0 2 1• 8 4 0 2 1• 9 4 2 2 1• 10 2 2 2 1• 11 2 6 2 1• 12 0 6 2 1• 8 1• 6 1 2 3 4 5 6 1• 6 7 8 9 10 11 12 1• 4 1 2 8 7 1• 4 2 3 9 8 2• 4 3 4 10 9 1• 4 4 5 11 10 1• 4 5 6 12 11 3• 4 6 1 7 12 1• 0• 0

Input file formats The previous smesh-file should produce the following output:

Input file formats Mesh density control by volume constaints (see tetgen’s manuals

for more details about command relevant line arguments):

Input file formats It is possible to control the density locally by ”mtr-files” Example (”L.mtr”):

• 12 1• 0.25• 0.25• 0.25• 0.025• 0.25• 0.25• 0.25• 0.25• 0.25• 0.025• 0.25• 0.25

Input file formats

Activate local mesh density control by introducing argument ”m”:

Input file formats

Input file formats

Examples can be found from

• Tetgen’s site at

http://tetgen.berlios.de/

• INRIA’s mesh database at

http://www-c.inria.fr/gamma/download/disclaimer.php

Customizing the GUI

The menus of ElmerGUI are constructed dynamically when the process is initiated

Menus are described by ”edf-files” (elmer-definition-file) which are written in XML containing problem specific information about dialog styles and dependencies on model data

The files are located in directory ”edf” (with respect to ElmerGUI) An example of customizing the menus can be found from the

course material and from Elmer’s web site

Finally…

ElmerGUI will be evolving in the near future Tutoirials available from Elmer’s web site User feedback is more than welcome