Guided examples using ELMER FEM

Presenter: Matic, Brank, Faculty of Mechanical Engineering, UL Date: 12-03-2021

 Quick software overview
• Elmer FEM
• Finite element software package for multiphysical
problems
• Multiple modules within Elmer FEM:
• Elmer Solver: Kernel of Elmer FEM, which
performs FEM computations
• Elmer Grid: Module for mesh
preparation/conversion
• Elmer GUI: Graphical user interface built around
ElmerSolver with the intention to ease the case
preparation and computation for users
• Open source
• Source code and documentation available at
GitHub - ElmerCSC/elmerfem: Official git repository of Elmer FEM
software
 Quick software overview

• Paraview
• multiple-platform application for interactive, scientific
visualization
• Open source
• Many useful visualization capabilities:
• Contours and isosurfaces for scalar and vector fields
• Streamlines
• Advanced data manipulation through Python
• Support of variety of formats
• VTK, VTU
• CGNS
• Source code and documentation available at
GitHub - Kitware/ParaView: VTK-based Data Analysis and Visualization
Application
 Software loading and running

• On Viz
• Connect to Viz using NoMachine Terminal
• Click bottom left icon on desktop to open the start menu
(See figure)
• Open terminal

Start menu Fig: Start menu of

Fig: Terminal display trinity desktop.
 Software loading and running
• To open Elmer GUI:
• To load Elmer into environment, type into terminal
• module load elmer/foss-2018b
• To run Elmer GUI
• ElmerGUI

• To open ParaView
• To load ParaView into environment, type into terminal
• module load ParaView/5.6.2-foss-2020b-mpi
• To run ParaView
• paraview
 Loaded elastic beam – 2D
• Case definition
• 2D case
• Homogeneous, elastic beam, defined
on 𝑥 − 𝑦 plane
(length 1𝑚 and thickness 0.1𝑚)
• Rigid support at the wall
• Space dependent mechanical load,
which grows linearly from 0 to 𝑞0 = 1𝑒7𝑁
𝐿 = 1𝑚
• Goal
𝑡 = 0.1𝑚
• Obtain the displacement of the beam
Loaded elastic beam – 2D
• Mathematical definition of the problem
• Domain of computation:
• Beam area Ω
• Boundary conditions
• Mechanical load Γ3
• No displacement at Γ4
• Zero load on Γ1 and Γ2

• Problem solution

−∇𝜎 = 0 𝑜𝑛 Ω
𝜎 = 𝜆𝑡𝑟 𝜀 𝑢 𝐼 + 2𝜇𝜀(𝑢) 𝑜𝑛 Ω
𝑢=0 𝑜𝑛 Γ4
𝜎𝑛 = 0 𝑜𝑛 Γ1 𝑎𝑛𝑑 Γ_2
𝜎𝑛 = −𝑞 𝑜𝑛 Γ3
 Case preparation - overview
1. Definition of domain of computation (Elmer GUI)
• Mesh preparation/definition
2. Definition of type of physical problem (Elmer GUI)
• Definition of equation to be solved
3. Definition of material properties (Elmer GUI)
4. Definition of boundary/initial conditions (Elmer GUI)
5. Computation (Elmer GUI)
6. Postprocessing of results (ParaView)
 Case preparation
1. Definition of domain of computation (Elmer GUI)
• Import mesh into Elmer GUI
• File->Open
• Navigate to your folder and select beam.grd
• Use Mouse wheel/left button to rotate and zoom mesh
Case preparation
• Go to Model->summary to observe mesh
information
• Check that mesh contains 3221 nodes
• How many surface elements are in the mesh?
• What is the type of the surface elements?
• Triangles, quadrangles?
• Check Elmer documentation
to see ID numbers for different
elements
 Case preparation
2. Definition of type of physical problem
• In Model->Setup… one can define
properties related to the simulation, such
as results directory, input mesh directory,
name of output file, constants, etc…
• Make sure the simulation type is set
to Steady state
Case preparation
• In Model->Equation->Add… one
can select equations to be solved
during the computation. For the
bending of beam, select Linear
elasticity tab
• Tick checkboxes Active and
Plane stress
• Assign the equation to the Mesh body
(Tick the box in Apply to body)
• In the end, click OK to accept new
changes
 Case preparation
3. Definition of material properties
• The material of the beam in our Study is
iron with Poisson’s ration of 0.29 and
Young’s modulus of 1.93 ∙ 109 𝑁/𝑚2
• Click on Model->Material->Add…
• Click on Material library and
select Iron(generic)
• Click OK
• Tick box Apply to bodies to set the
material to mesh.
• Click OK
 Case preparation
4. Definition of boundary conditions
• To define a boundary condition, click on Model->Boundary condition->Add…
• Navigate to Linear elasticity
• Here, we can define displacements and loads on the mesh boundaries
 Case preparation
• Definition of wall boundary condition
• Set Displacement 1 and Displacement 2 to 0. Identification number 1 refers to x-coordinate
and 2 refers to y-coordinate
• Select appropriate Edge on the Mesh
• Set name of boundary condition to Wall
• Click OK
• Definition of mechanical load 𝑞(𝑥)
• Create a new boundary condition (Model->Boundary condition->Add…)
• Navigate to Linear elasticity
• Now we have to define linear load that points in y-direction and is linearly increasing along x-
direction. To do that:
• Go to Force 2 (remember, 2 refers to y-direction)
• The variable to specify: Variable Coordinate 1; Real; 0 0; 1 -1.0e7; End
• Set boundary condition name to Load
 Case preparation
• Explanation of Force 2 definition
• The semicolon in Elmer FEM specifies the definition of new keyword
• The first keyword (Variable Coordinate 1) specifies that Force 2
is changing its value along coordinate 1 (remember, 1 refers to x-
direction) 𝑦

• Then the user can define a table of x (coordinate), F (force) values. So

the next keywords look like 𝑥
Real;
0 0;
1 -1.0e7;
𝑥 = 0𝑚, 𝑥 = 1𝑚,
End 𝐹 = 0𝑁 𝐹 = −1.0𝑒 7 𝑁
• Keyword Real defines the type of numbers in a table
• Keyword 0 0 specifies that at 𝑥 = 0𝑚, the force is 𝐹 = 0𝑁
• Keyword 1 -1.0e7 specifies that at 𝑥 = 1𝑚, the force is 𝐹 = −1.0𝑒 7 𝑁
• Keyword End specifies end of table
 Case preparation
• In case of elasticity solver, the Mesh boundaries are automatically set to 0 load
• Thus it is not necessary to define zero force on remaining two edges
• As an exercise, one can set the forces at these two edges to 0
 Running the case
5. Computation
• Before running the case, one can observe the solver input file (extension .sif)
• SIF file is a file, generated by Elmer GUI.
• The file contains the case set-up with all the parameters specified by the user in Elmer
GUI
• This file is then taken as input by the Elmer kernel (ElmerSolver), which then computes
the solution based on these parameters
• Click on Sif->Generate and then Sif->Edit…
• Here you can manually change properties in the
editor
 Running the case
• To run the case, click “Save and run” button (see figure)
• This button will then ask you to select a project folder. Then it will save the changes and
run the case.
• Two windows open:
• Convergence monitor
• Solver log
 Post-processing
• Use mouse wheel/right button to rotate and zoom result
 Post-processing
• To change coordinate of • To get the maximum displacement, navigate
displacement, navigate to to Edit->Find data…
Properties->coloring- • In the dialog, select Point(s) and set
>displacement displacement(1) to “is min”
 Exercise 1

• Change maximum load on the right edge (at 𝑥 = 1𝑚) to 𝐹 = −1.0𝑒 8 𝑁

and run the case again.
• Change the load again to 𝐹 = −1.0𝑒 9 𝑁. Run the case and observe the
maximum displacement with increase of load
 Exercise 2
• Add a new wall boundary condition to the right side of the beam (where 𝑥 =
1𝑚, set displacement in x and y direction to 0)
• Modify the load at the top to have the following dependency in x-direction.
What is the maximum displacement in y-direction?

𝑥 = 0.5𝑚,
𝑥 = 0𝑚, 𝐹 = −1𝑒8𝑁
𝐹 = 0𝑁 𝑥 = 1𝑚,
𝐹 = 0𝑁
 Exercise 3

• Transient loading
• Change Simulation Type to Transient (Setup->simulation type)
• Set the Time Stepping Method to bdf
• Set the Time step intervals to 200
• Set the Time Step Sizes to 1𝑒 −4
 Loaded elastic beam – 3D
• Case definition
• A homogeneous, elastic beam is rigidly supported on
one end. On the other end, the force is 2000N due to
an attached object. The weight of the beam itself is wall
also included as additional load.
• The length of the beam is 1m, thickness is 0.05 m and
width is 0.1m
• Young’s modulus is 10 ∙ 109 𝑁/𝑚2 and Poisson’s ratio 𝑤 = 0.1𝑚
is 0.37
• Density of the material is 550𝑘𝑔/𝑚2
• Goal
• Calculate displacement field of the beam
• Obtain the location and value of the maximum 𝑡 = 0.05𝑚
displacement
• Calculate stress field
𝐹 = 2000𝑁
 Loaded elastic beam – 3D
1. Definition of domain of computation
• Import mesh into Elmer GUI
• Navigate to your folder and select beam3d.grd
• Use Mouse wheel/left button to rotate and zoom mesh
• Verify that mesh consists of 6073 nodes and of 1200 quadratic hexahedral
elements
 Loaded elastic beam – 3D
2. Definition of type of physical problem
• Set the simulation type to Steady
state
• Set equation to Linear elasticity
• In Linear elasticity, set checkbox
next to Active
• We also want to compute stresses as a
post-processing step, so set checkbox of
Calculate Stresses
• Click on Edit solver settings:
Edit Solver Settings
• check Iterative method and set it to
GCR
• Set Preconditioning to ILU1
 Loaded elastic beam – 3D

3. Definition of material properties

• Create a new material and define:
• Density,
• Poisson’s ratio and
• Young’s modulus
• Assign the material to 3D beam
 Loaded elastic beam – 3D
4. Definition of boundary conditions
• Define zero displacement on left face that lies in
x-z plane (at the wall – refer to figure on slide
24)
• Note that second boundary condition distributes
the load of 2000N uniformly on the area of 𝑡 ∙
𝑤 = 0.05𝑚 ∙ 0.1𝑚 = 5.0𝑒 −3 𝑚2
• The weight of the beam should be defined
through Body Force
• Navigate to Model->Body force->Add…->Linear
elasticity
• Set the force in negative y-direction through mass of
beam and gravitational acceleration
• Apply the body force to the mesh body
 Loaded elastic beam – 3D
5. Computation
• Generate and check SIF file
• Save the case and run it
 Loaded elastic beam – 3D
5. Post processing
• What is the maximum displacement and where is its location
• Plot displacements and Von mises stresses
 Exercise
Gravity in x-direction
• The beam should be more rigid if the beam is orientated differently
• Change the direction of gravity and force of attached object in the negative x-
direction
 Heat equation
• Case definition
• A structure in L-shape is heated by
internal source with magnitude of Internal
1𝑊/𝑚3 . The density of the structure is heat
source
1𝑘𝑔/𝑚3 and the heat conductivity is
1𝑊/𝑚𝐾. The temperature of boundaries
of the structure is set to 0.
• Goal
• Obtain temperature distribution in the
structure
𝑇𝑏𝑜𝑢𝑛𝑑𝑎𝑟𝑦 = 0℃
 Heat equation
• Mathematically the problem to be solved
is
−𝑘Δ𝑇 =𝜌𝑓 𝑜𝑛 Ω
ቊ
𝑇 =0 𝑜𝑛 Γ
• Parameters
• 𝑘 … heat conductivity
• 𝑇 … temperature
• 𝑓 … heat source
 Heat equation

1. Definition of domain of computation

• Import mesh into Elmer GUI
• Navigate to your folder and select angle.grd
• Use Mouse wheel/left button to rotate and zoom mesh
• Verify that mesh was successfully imported and that it consists of 341 nodes
and of 300 bilinear elements
 Heat equation
2. Definition of type of physical
problem
• Set the simulation type to
Steady state
• Set equation to Heat equation
• In Heat equation check checkbox
next to Active
 Heat equation
3. Definition of material properties
• Create a new material and define:
• Density,
• Heat conductivity (in Heat)
• Assign the material to the body
 Heat equation
4. Definition of boundary conditions
• Define zero temperature on boundaries
• Temperature is defined under Dirichlet
conditions
• Apply temperature to all boundaries
 Heat equation
4. Definition of boundary conditions
• Define volumetric heat source in the structure
• A Body force represents the right-hand side of
the equation which in this case represents the
heat source
• Navigate to Body force
• Set Heat Source to 1 and apply the condition
to a body, then click OK
 Heat equation
5. Computation
• Generate and check SIF file
• Save the case and run it
 Heat equation
6. Post-processing
• Open the result in ParaView
• What is the value of maximum temperature
• Plot temperature as a function of y-coordinate at 𝑥 = 0.5𝑚
• Go to Filters->Alphabetical->Plot On Intersection Curves
• In Properties, specify the intersection plane and then click Apply

𝑇[℃]

𝑥[𝑚]
 Exercise
6. Post-processing
• Examination of computational time vs. number of
mesh nodes
• Check output of Solver Log and read second line
from bottom to get the CPU time (see below)

• Let’s increase the mesh density (i.e. increase the

number of nodes and elements) and rerun the
case
• Navigate to Mesh->Configure…
• In elmergrid->String:, change –autoclean
–relh 1.0 to –autoclean –relh 0.6
• Click Apply
• Click Mesh->Remesh to recompute mesh
 Exercise
• Run the case with denser mesh and observe the time difference
• Try to increase the density even more, for example change the value of
0.6 to 0.1
• Compare CPU times vs. number of mesh nodes
Overview of commands
• elmerf ... Command to compile user defined Fortran routines
• ElmerGrid ... Command to generate and convert mesh data
• ElmerGUI ... Command to run the user interface
• ElmerSolver ... Command that reads SIF file and mesh data
and performs FEM calculations
• ElmerSolver_mpi ... Command that performs parallel FEM
calculations
Overview of commands
elmerf
• Users can define their own functions in Fortran that are then
passed to ElmerSolver
• User defined functions are defined in files with .f90 extension
• In SIF file, the reference to this file can be defined in boundary
condition block, material block,...
• ElmerSolver then calls this function by reading reference in SIF
file
Overview of commands
• Let’s examine the zero temperature boundary condition in Heat transfer case
• In SIF file, the boundary condition block is defined as:
Boundary Condition 1
Target Boundaries(1) = 1
Name = "zero_temp"
Temperature = 0
End
• Here, the temperature of the whole target boundary is set to 0.
• To call an external function, delete the Temperature = 0 line and add these two lines
Temperature = Variable Coordinate 2
Real Procedure "define_temp" "defineTemp“
• The first line means that temperature will be a variable of y-coordinate
• The second line means that we are calling a function "defineTemp“ that is located in
define_temp.f90 file.
 Overview of commands
• File define_temp.f90 should look like this:
FUNCTION defineTemp(Model, elmer_node, t, y) RESULT(elmer_temperature)
USE DefUtils
TYPE(Model_t) :: Model
TYPE(Nodes_t) :: Nodes, EdgeNodes
INTEGER :: elmer_node, i
REAL(KIND=dp) :: t, y
.
. $ Do your own calculations
.
END FUNCTION defineTemp
 Overview of commands
The name of the function is defineTemp
• Input parameters are:
• Model -> structure of ElmerSolver, it contains different
parameters that we can access during function execution
• elmer_node -> ID of the node that is currently being processed
• t-> current timestep
• y-> variable specified in SIF file, in our case y-coordinate
• Output parameter is temperature, as defined in SIF file
• Inside this function we can now write different routines and specify
our own boundary condition
 Thank you for you attention!

This project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant
agreement No 951732. The JU receives support from the European Union’s Horizon 2020 research and innovation
programme and Germany, Bulgaria, Austria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, Greece, Hungary,
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