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femb: basic FEM with Graphite

This is a Graphite plugin that implements P1 FEM for Poisson equation on tetrahedral meshes.

The interest of this code is mainly to show how to use the Geogram and Graphite APIs, functions and classes. The FEM part is very basic and simple.

If you want to learn how to develop a plugin for Graphite and Geogram, please use the tutorial associated to this plugin.

If you are only interested in the FEM implementation (~200 lines), you can directly look at the file algo/femb.cpp

Validation: same results than with MFEM on sinbump_test.lua and neumann_test.lua

Installation

Assuming that you have a working Graphite setup, the steps are:

// get the plugin source code
mkdir /path/to/this/plugin
git clone https://github.com/mxncr/femb.git /path/to/this/plugin

// tell graphite to build the new plugin
ln -s /path/to/this/plugin /path/to/graphite/plugins/OGF/femb
echo "add_subdirectory(femb)" >> /path/to/graphite/plugins/OGF/Plugins.txt

Now you should:

  • configure and build Graphite (which will build this plugin)
  • launch Graphite, go to Files > Preferences > Plugins, enter femb and click Add, then Save configuration file
  • restart Graphite, from now on you should have the femb plugin working (right click on a mesh in Scene and check if the FEM command menu is present)

Run FEM simulations

Two possibilities:

a) From command line, you can load a mesh and run a Lua script. See the Lua scripts in data/ for examples. This will open Graphite with the simulation output.

graphite  data/cube_s12.meshb data/sinbump_test.lua 
graphite  data/cube_s12.meshb data/neumann_test.lua

b) From the Graphite GUI: open Graphite, load a mesh (right click on Scene), right click on the new mesh and use the FEM menu.

After the simulation, a new mesh is created in the scene (with the suffix _fem) with the solution as a vertex attribute (named u by default). Right click on the new mesh and use the Properties menu to visualize the attributes.

Problem specification

The Poisson problem is specified via explicit formulas thanks to the powerful math parsing and evaluation library ExprTk. See ExptTk documentation for the complete list of supported functions.

Dirichlet BCs are specified by a region formula and by an evaluation formula. A mesh facet is considered Dirichlet if the dirichlet region formula is positive at its center. E.g.:

dirichlet_region = "if (x < 0.1){1.} else if (z > 0.99){1.} else {-1.}"
dirichlet_value  = "cos(x) * sin(z) - x^2"

Same for Neumann BCs:

neumann_region = "if (x^2 + y^2 < 0.3^,1,-1)"
neumann_value  = "cos(x) * sin(z) - x^2"

Diffusion coefficient and source term use only the evaluation formula:

diffusion_value  = "if (z > 0.5, 10., 1.)"
sourceterm_value = "if ( (x-0.5)^2 + (y-0.5)^2 + (z-0.5)^2 < 0.1^2, 1., 0.)"

As ExprTk allows complicated evaluation functions, it is possible to define complicated Poisson problems with this simple API. There is no need to tags the mesh facets before import. Regions are solely determined by the math formulas of the problem definition.

Example

In the following example, we start with the point cloud of an ancient amphora (data/amphora_pts.meshb). The mesh preprocessing step of the plugin takes care of building the tetrahedral mesh (surface reconstruction of the boundary with Geogram algorithms and interior volume meshing with TetGen). We apply the following Poisson problem:

{
    dirichlet_region="if(y > 0.95, 1, -1)", 
    dirichlet_value="0", 
    neumann_region="if(y < 0.10, 1, -1)",
    neumann_value="1.", 
    sourceterm_value="0", 
    diffusion_value="1", 
    solution_name="u"
}

Results:

See data/amphora_test.lua to launch the problem from command line.