24  Elmer Fundamentals

24.1 Preprocessing steps

  • Other than the native ElmerGrid, several other software can be used for conceiving a geometry and mesh generation workflow. Users are encouraged to use external tools such as gmsh or Salome to generate computational meshes, built-in support in Elmer bein limited to very simple geometries only. For complex geometries FreeCAD is a standout alternative. For more consider reading Geometry and Preprocessing.

  • Not all gmsh standard mesh formats are supported, but only version 2 (as for OpenFOAM); that said, users are encouraged to export mesh in UNV format to avoid compatibility issues, and also because both proposed tools support it. You can control the element orders in command line using option -order <N>; gmsh operates this way so that the same script can generate any supported element type.

  • For importing meshes one uses ElmerGrid <input-format> <output-format>, where the format arguments are documented in the manual sections 1.3 and 1.4. The UNV input is given by number 8 while standard ElmerSolver output by number 2, so that the conversion command would start with ElmerGrid 8 2 <other-arguments...>. Always verify the number of nodes remain untouched after conversion - or if it changed when using option -merge <dist>, merging nodes that are closer than the user-defined <dist>.

  • Remember to use Coherence; with OpenCASCADE factory in gmsh scripts to automatically strip internal faces; that might not be enough for complex cases, see below. Note: I tried doing so and unless Physical Surfaces naming the external boundaries are provided every interface is dumped and imported by Elmer; maybe I misunderstood the use of command!

  • Because faces are not named in Elmer, i.e. no matter what Physical Surface names you provide in gmsh, even for the advanced user working from command line it might be interesting to use the interactive zone grouping capabilities of ElmerGUI. That might even become a requirement as geometric complexity grows.

Software Notes
FreeCAD Geometry only for now, probably the best in the list; good parametric modeling support. Has native Elmer integration.
Salome Can export UNV (8) meshes readable by Elmer. An extension to call Elmer directly from Salome is under development.
gmsh Can export MSH2 (14) and UNV (8) formats readable by Elmer.
netgen Is able to write native Elmer linear meshes; can be used as a plug-in.
tetgen Can be used as a plug-in.

24.2 Using Elmer

  • Newcomers might be interested in ElmerGUI; although very intuitive, the interface is quite limited and for complex programs running from command line is the preferred mode.

  • Most users will finally end setting up an workflow employing both to ElmerSolver (to run the simulations) and ElmerGrid (to prepare the grid and setup parallelization).

  • There is also ViewFactors which might be useful in special cases involving radiation and other executables but they are not mentioned here because they fall in the legacy code family.

  • Users must be aware that Elmer has no default unit system; one must take care that units are coherent across the different models and materials.

  • Support to mathematical operations in SIF through MATC, which has its own syntax and documentation. It can be used, e.g. for computing temperature dependent properties, what can be helpful for simple expressions (instead of writing Fortran 90 code for extensions).

24.3 Parallel computing

  • Before running in parallel a working case running in serial is required; using ElmerGUI this can be enabled in Run > Parallel settings.... Notice that after running postprocessing of .pvtu needs to be done in ParaView directly.

  • To partition the mesh from command line one needs to run ElmerGrid 2 2 <mesh-name> -partdual -metiskway <N>, which will convert <mesh-name> from Elmer mesh format (2) into itself (thus the 2 2 in the command) and dump the resulting mesh in partitions.<N>, with <N> being the number of physical cores to run the simulation.

  • Parallel cases can be run with mpiexec -n <N> ElmerSolver_mpi. Notice that under Linux the MPI runner is called mpirun instead of mpiexec.

24.4 Tips and ideas

  • Use Coordinate Mapping to rotate meshes with oriented particles
  • Scaling of a single direction can be done with Coordinate Scaling
  • Time step can be changed with a list of elements in Timestep Intervals, e.g.
! Run 10 time-steps of 0.1 s, then 100 with 1.0 s.
Timestep Intervals(2) = 10 100
Timestep Sizes(2) = 0.1 1.0
  • Take care with Linear System Abort Not Converged = True for physical consistency; generally continuing a simulation after a failed step is worthless unless one is pseudo-stepping towards a difficult (highly nonlinear) steady-state.

24.5 Material properties

Material properties can be specified as:

  • Constant: just the default numeric input in SIF files

  • Tabulated linearly or using a cubic spline, e.g.

! Linear interpolation
Viscosity = Variable Temperature
  Real
    298.15 1.0
    ! ... more data here
    373.15 2.0
End

! Cubic spline interpolation
Viscosity = Variable Temperature
  Real cubic
    298.15 1.0
    315.15 1.1
    345.15 1.5
    ! ... more data here
    373.15 2.0
End
  • Arrays: for representing anisotropic bodies, e.g.
Heat Conductivity(3,3) = 1 0 0\
                         0 1 0\
                         0 0 2

  • Using MATC as explained below in this page. Notice that sourcing files in MATC is the recommended way to get reusable code; coding MATC in SIF files requires to escape all lines and quickly becomes messy.

  • User-defined functions (UDF) can also be provided in Fortran; notice that even when MATC can be used, this may lead to a speed-up of calculations with the inconvenient of needing more code. So for cases that are intended to be reused, it is important to consider writing proper extensions in Fortran. The following example illustrates a temperature dependent thermal conductivity function which is evaluated by Elmer at all nodes. In most cases a simple USE DefUtils is enough to get the required Elmer API to write the extension.

FUNCTION conductivity(model, n, time) RESULT(k)
    !**************************************************************
    ! Load Elmer library.
    !**************************************************************

    USE DefUtils
    IMPLICIT None

    !**************************************************************
    ! Function interface.
    !**************************************************************

    TYPE(Model_t) :: model
    INTEGER       :: n
    REAL(KIND=dp) :: time, k

    !**************************************************************
    ! Function internals.
    !**************************************************************

    TYPE(Variable_t), POINTER :: varptr
    REAL(KIND=dp) :: T
    INTEGER :: idx

    !**************************************************************
    ! Actual implementation
    !**************************************************************

    ! Retrieve pointer to the temperature variable.
    varptr => VariableGet(model%Variables, 'Temperature')

    ! Access index of current node.
    idx = varptr%Perm(n)

    ! Retrieve nodal temperature.
    T = varptr%Values(idx)

    ! Compute heat conductivity from NodalTemperature, k=k(T)
    k = 2.0 - T * (2.5e-03 - 1.0e-06 * T)
END FUNCTION conductivity

In order to compile the above assume it is written to properties.f90 file; then one can call elmerf90 properties.f90 –o properties to generate the required shared library that is loaded in runtime by Elmer. Below we illustrate the use of Procedure to attach this library to a given material; first one provides the name of the shared library then the name of the function. A single library can in fact contain several functionalities.

Material 1
  Name = "Solid"
  Heat Conductivity = Variable Time
    Procedure "properties" "conductivity"
  Heat Capacity = 1000
  Density = 2500
End

24.6 Postprocessing

For postprocessing the recommended way is by using external tools as ParaView and PyVista, both handling well the VTK format of outputs. Nonetheless there are a some in-solver processing utilities that are worth knowing, especially in what concerns extracting and filtering data from certain regions, creating new fields, and computing fluxes.

  • Creating a new scalar

The keyword set of materials is actually not fixed; one can, for instance, create composition field in different units with MATC, as illustrated below (case here):

MoleFraction = Variable Concentration
  Real MATC "carbonmolefraction(tx)"

Then in solver SaveMaterials, this new name MoleFraction can be used as a variable:

Solver 1
  Equation = SaveMaterials
  Parameter 1 = Concentration Diffusivity
  Parameter 2 = MoleFraction
  Procedure = "SaveData" "SaveMaterials"
  Exec Solver = After Timestep
End

Another situation that can be frequently found is unit conversion for temperature. It was chosen to implement it in this case because it is multi-material; that is a reminder that in such cases the new variable needs to be created for all materials (as this is a tweak, since the temperature is not a material property, but a global field). If forgotten in one material, an error will show up in ParaView telling you that the field is not available in some regions.

24.7 User-defined functions

Upcoming

24.7.1 Derived fields

  • StreamSolver

  • FluxSolver

#elmer/models/flux-solver

  • VorticitySolver

  • DivergenceSolver

  • ScalarPotentialSolver

  • ArtificialCompressibility

  • FluidicForce

  • ElectricForce

  • RigidBodyReduction

  • FilterTimeSeries

  • DataToFieldSolver

  • ProjectToPlane

  • StructureProjectToPlane

  • FindOptimum

24.7.2 Saving data modules

Note: coupling to OpenFOAM is discussed separately in another section.

  • SaveData

  • SaveScalars

#elmer/models/save-scalars

  • SaveLine

#elmer/models/save-line

  • SaveMaterials

  • SaveBoundaryValues

  • ResultOutputSolve

  • ResultOutputSolver

#elmer/models/result-output-solver

  • SaveGridData

  • SaveGridData

  • Isosurface

  • IsosurfaceSolver

24.7.3 OpenFOAM coupling

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