How to run the examples with fossils

Overview of the Graphical User Interface (GUI)

Double click on the desktop icon.

A console appears as well as a small window with 2 parameters.

The first option is the input file. The program takes a python file as input. Several examples are provided with the program binaries in the installation folder (which is %USERPROFILE%\AppData\Local\Programs\Fossils if you have kept the default folder). Example files are stored in the models sub-folder.

By default others\dolicorhynchops\dolicorhynchops_10k.py (a Dolicorhynchops mandible with a very coarse surface mesh) is selected. If it is not, you can reset the parameter to its default value by clicking on the yellow arrow on the right of the same line.

The second option is the workspace. This is a folder where the results will be stored after computation, so that they can be reloaded later.

The default workspace is %USERPROFILE%\workspace but you can change it to any other convenient location. Use the folder icon to browse your harddrive.

The results will be gathered in a subfolder of the workspace whose name is the same as the name of the input file (it will be thus %USERPROFILE%\workspace\dolicorhynchops_10k for the default model).

Running the simulation

Click on the "Run" button to start the finite element analysis. The calculation steps can be followed in the console.

Interesting information can be retreived from this output. For example, the number of finite elements of the default model is 16384. The number of degrees of freedom is 15377.

At the end of the calculation, some interesting values are calculated and displayed (internal energy, reaction forces and components of the applied forces on each muscle surface):

extracting results...
        internal energy = 95.219 N.mm
        axis_pt1_Fx = 61.538 N
        axis_pt1_Fy = -0.720 N
        axis_pt1_Fz = -44.509 N
        axis_pt2_Fx = 50.742 N
        axis_pt2_Fy = 0.000 N
        axis_pt2_Fz = -31.293 N
        contact_pts_Fx = 17.915 N
        contact_pts_Fy = 0.000 N
        contact_pts_Fz = 0.000 N
        Lmuscle_Fx = -64.914 N
        Lmuscle_Fy = -65.403 N
        Lmuscle_Fz = 38.840 N
        Rmuscle_Fx = -65.281 N
        Rmuscle_Fy = 66.123 N
        Rmuscle_Fz = 36.961 N
Total Execution time: 2.9s

The total CPU time is also given. Note that some parts of the solver have been parallelised. This is the case of the assembly of the system of equations and the resolution of this system. By default the program uses a number of threads equal to the number of virtual cores available on the PC running the simulation.

Analysing results with Gmsh

When the finite element computation is completed, the results are automatically displayed using Gmsh.

Various fields (strains, stresses, displacements) can be displayed on the mesh by selecting a View under the "Post-processing" tab (click on the cross next to "Post-processing" to unfold the list of available fields)

View options (colours, scalar ranges, lighting, etc) can be easily changed by clicking on the small arrow and selecting "Options" in the menu. The user can refer to the Gmsh documentation.

The program ends when the user closes the Gmsh window.

Viewing results later

Once the simulation has been run, the results can be reloaded from the harddrive using the "View" button instead of the "Run" button.

The workspace folder can be easily explored by clicking on the magnifying glass icon on the workspace line in the GUI.

All the results are stored using Gmsh format (.msh) and can be easily reloaded into the classical Gmsh application (without fossils).

The file named stdout.txt contains the messages that were displayed in the console during the calculation.