Elmer GUI A new preprocessor for Elmer Mikko

Elmer. GUI A new pre-processor for Elmer Mikko Lyly CSC, Finnish IT Center for Science Elmer User meeting, 29 th May 2008, CSC, Espoo

Outline Backgound Workflow Practical example On input file formats Excercise Custom menus

Background Intended to replace Elmer. Front: • • • Enhanced mesh generation and mesh manipulation tools Enhanced visualization routines (based on Open. GL and extensions) Better compatibility with latest Solver Programmable/customizable GUI Less dependencies on external libraries Portability (Linux, Windows, Mac) Elmer. GUI is not: • • A CAD program – complicated 3 D-geometries should be modelled by separate tools and imported into Elmer. GUI in an appropriate format A stand-alone-program – it needs Elmer. Solver and Elmer. Post (the “elmersuite”) 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) Qt 4: http: //trolltech. com/products/qt/ Qwt 5: http: //qwt. sourceforge. net/ Licence: GPL Qt 4 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 Elmer. GUI is located in ”elmerfem/trunk/misc/Mesh 3 D”: $ cd elmerfem/trunk/misc/Mesh 3 D $ 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) Elmer. Grid (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++ -f. PIC -c predicates. cxx $ g++ -f. PIC -O -DTETLIBRARY -c tetgen. cxx $ g++ -f. PIC -c Elmer. API. cpp $ g++ -shared predicates. o tetgen. o Elmer. API. 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 (Open. Cascade 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 Elmer. Grid • • • Built-in mesh generator and mesh manipulation tool Very fast structured 1 D/2 D/3 D-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) - Elmer. Grid FDNET (Fidap's mesh file format) - Elmer. Grid MSH (Gmesh's file format) - Elmer. Grid MPHTXT (Comsol Multiphysic's mesh file format) - Elmer. Grid UNV (Ideas' universal file format) – Elmer. Grid Elmer's native mesh file format

Workflow Elmer. GUI + Elmer. Grid Elmer. Solver + Elmer. Post

Workflow Open your input file (example: samples/grd/angle 3 d. 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 Elmer. Post, 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 0001 2 4001 3 4201 4 2201 5 2601 6 0601 7 0021 8 4021 9 4221 10 2 2 2 1 11 2 6 2 1 12 0 6 2 1 8 1 6 123456 1 6 7 8 9 10 11 12 1 4 1287 1 4 2398 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. 025 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 Elmer. GUI 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 Elmer. GUI) An example of customizing the menus can be found from the course material and from Elmer’s web site

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