1. Lukasz Kaczmarczyk Avatar Lukasz Kaczmarczyk
  2. Project created by Lukasz
  3. mofem-joseph

Wiki

Clone wiki

mofem-joseph / MoFEM User Manual

View History

#MoFEM User Manual

    ##1 Introduction

    MoFEM (Mesh Oriented Finite Element Method) is a new open-source finite element analysis code tailored for the solution of multi-physics problems with arbitrary levels of approximation, different levels of mesh refinement and optimised for high-performance computing. MoFEM is the blend of the Boost MultiIndex containers, MOAB (Mesh Oriented Database) and PETSc (Portable, Extensible Toolkit for Scientific Computation).

    MoFEM is written in C++ and it is open-source under the GNU Lesser General Public License (see Legal Stuff). MoFEM currently uses the well-established CUBIT by Sandia National Laboratories for pre-processing, and the open-source ParaView by Kitware for post-processing.

    ####1-1 Release notes The current version of MoFEM is 0.0.1 (codename JosePH). JosePH is a development version.

    ####1-2 Installation MoFEM is open-source and can be compiled and used on any operating system and platform where it is possible and makes sense to do so. So far it has been compiled successfully on several versions of OS X, Ubuntu Linux and Red Hat Linux. Detailed installation instructions are provided by the following links:

    If you have any problems installing MoFEM or would like to share your success installing it on a different system than the above, please contact cmatgu@googlegroups.com.

    ####1-3 MoFEM build directory

    The MoFEM build directory has the following structure:

    File/Folder Description
    /atom_tests
    /benchmarks
    /CMakeFiles
    /examples
    /scripts
    /Testing
    /third_party
    cmake_install.cmake
    CMakeCache.txt
    config.h
    CTestTestfile.cmake
    DartConfiguration.tcl
    Doxyfile
    INSTALL
    libmofem_complex_for_lazy.a
    libmofem_Field.a
    libmofem_student_body.a
    Makefile

    ####1-4 Testing your build

    ####1-5 Legal Stuff

    MoFEM is copyright by Lukasz Kaczmarczyk and has received contributions by several people. MoFEM can be used freely for educational and research purposes by other institutions. If you use this software please cite our work.

    MoFEM is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

    MoFEM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public License along with MoFEM. If not, please see http://www.gnu.org/licenses.

    Go to Contents

    ##2 Pre-Processing

    ####2-1 Introduction

    CUBIT (https://cubit.sandia.gov)

    TRELIS (http://www.csimsoft.com)

    ####2-5 Importing models from other software

    Current limitations of working with mesh-based models

    ...

    At present, the following approaches are recommended:

    1. Import an external geometry into CUBIT using a supported CAD format such as ACIS or IGES. Then work on your model as normal using the imported geometry
    2. Import geometry into CUBIT directly from a supported mesh-based file. Use the imported mesh or automatically generated geometry as guide to re-create the geometry in CUBIT from scratch. Then delete the imported data.
    3. Create the geometry in CUBIT from scratch.

    Go to Contents

    ##3 Post-Processing

    Go to Contents

    ##4 Running an Analysis

    Go to Contents

    ##5 Materials

    ####5-1 Introduction

    ####5-2 Constitutive materials

    • Elasticity

    • Transverse Isotropy

    #####Elastic material

    #####Transverse isotropic material

    #####Linear interface

    More information is provided in the Theory Manual.

    ####5-3 Defining materials for MoFEM using CUBIT/Trelis

    MoFEM materials are defined with CUBIT or Trelis using Blocks (i.e. sets of entities). Normally, Blocks which consist of tets or volumes are used. A Block signifies a MoFEM material when the Block name starts with MAT_ (upper case) followed by the material name, e.g. MAT_ELASTIC (see Section 5-4 for a list of material Blocks). Optionally, the Block name can include descriptive text in the end, e.g. MAT_ELASTIC1, or MAT_ELASTIC_Steel.

    CUBIT/Trelis Blocks can have up to 10 attributes (numbers). When a Block is specified as a MoFEM material using MAT_, the attributes are read in MoFEM as real numbers.

    The procedure to define a MoFEM material using CUBIT/Trelis is as follows:

    ####5-4 Description of CUBIT/Trelis Material Blocks

    #####MAT_ELASTIC: Elastic material 

    Block name: MAT_ELASTIC
Number of attributes: 10
Attribute 1:  Young's modulus
Attribute 2:  Poisson's ratio
Attribute 3:  User defined attribute 1
...
Attribute 10: User defined attribute 10

Note: Attributes 3-10 are for future use and can be left at the default value of 1

    #####MAT_TRANSISO: Transverse isotropic material 

    Block name: MAT_TRANSISO
Number of attributes: 5
Attribute 1:  Young's modulus in xy plane (Ep)
Attribute 2:  Young's modulus in z-direction (Ez)
Attribute 3:  Poisson's ratio in xy plane (vp)
Attribute 4:  Poisson's ratio in z-direction (vpz)
Attribute 5:  Shear modulus in z-direction (Gzp)

    #####MAT_INTERF: Linear interface 

    Block name: MAT_INTERF
Number of attributes: 1
Attribute 1:  Elastic modulus multiplier

    Go to Contents

    ##6 Elements

    ####6-1 Introduction MoFEM uses 4-node linear or high-order tetrahedra (up to 5th order). Tetrahedra can fit any 3D geometry and are suitable for local mesh refinement. High-order tetrahedra offer improved deformability and overcome the limitations of linear elements. Information on the underlying theory is provided in the Theory Manual.

    CUBIT crack geometry

    Figure 6.1 4-node tetrahedron

    With MoFEM the Finite Element approximation can be improved in four principal ways and manually or automatically, or using combinations of these:

    • Global mesh refinement (remeshing)
    • Local mesh refinement
    • Global high-order enhancement
    • Local high-order enhancement

    Figure 6.2 Global mesh refinement

    Figure 6.3 Local mesh refinement

    Figure 6.4 Global high-order enhancement

    Figure 6.5 Local high-order enhancement

    ####6-2 Pre-processing

    ####6-3 Post-processing

    Go to Contents

    ##7 Linear Elasticity

    ... Modelling problems with 2 or more different materials ...

    Go to Contents

    ##8 Nonlinear Elasticity

    Go to Contents

    ##9 Potential Flow

    Go to Contents

    ##10 Fracture

    ####10-1 Introduction This section describes how to undertake fracture analysis using MoFEM, e.g. in order to calculate stress intensity factors at crack tips. Fracture analysis in MoFEM is three-dimensional and nonlinear as it takes into account large deformations and nonconservative loading. The theory behind Fracture Analysis with MoFEM is outlined in the Theory Manual. All pre-processing is undertaken using CUBIT, whereas post-processing is undertaken using ParaView and/or output text files. ####10-2 Analysis workflow

    1. Create FE model geometry [CUBIT]
    2. Create the crack geometry; each crack is represented by a single geometrical surface [CUBIT]
    3. Apply loads & boundary conditions [CUBIT]
    4. Define BlockSet with linear elastic material MAT_ELASTIC and apply material properties [CUBIT]
    5. Mesh model [CUBIT]
    6. Specify fracture constraints using NodeSets and SideSets [CUBIT]
    7. Run fracture analysis [MoFEM]
    8. Post-process [ParaView & MoFEM txt output files]

    Note that the modelling procedure for fracture analysis is similar to the procedure for creating a simple elastic model. The only difference is the creation of surfaces which represent cracks, and the application of fracture constraints (Section 10-4).

    ####10-3 Modelling of cracks Cracks for fracture analysis are modelled in CUBIT using simple geometry surfaces. Each crack is represented by a single surface, partially or fully enclosed within a volume. The nodes associated with the crack surface are split automatically by MoFEM. Unlike traditional procedures, MoFEM does not require the user to take any special mesh considerations (e.g. radial meshing) around the crack tip for integration purposes. There are no restrictions for the geometry of crack surfaces.

    The user is free to adopt any procedure convenient for the creation of geometry and the meshing of crack surfaces in CUBIT. However, it is often convenient to define a tool volume enclosure and cut it to create the crack surface (see Figure 10.1 below). This approach also allows better control of the mesh in the vicinity of the crack.

    CUBIT crack geometry

    Figure 10.1 Example of geometrical definition of a crack in CUBIT

    A good example of MoFEM fracture modelling is the plate with horizontal crack benchmark test.

    ####10-4 Fracture constraints

    In order to run a fracture analysis, it is necessary to inform MoFEM about the crack surface, crack tip and domain boundary. This is achieved completely during pre-processing in CUBIT using Nodesets and Sidesets with fixed numbers which are identifiable by MoFEM.

    The procedure will be simplified and automated in future releases of MoFEM.

    The Nodesets and Sidesets required to specify a fracture problem are as follows:

    Nodeset/Sideset No Description
    100 (Sideset) Sideset 100 contains curves which define the problem exterior
    101 (Nodeset) Nodeset 101 contains vertices which define the problem exterior
    102 (Sideset) Sideset 102 contains surfaces which define the problem exterior
    200 (Sideset) Sideset 200 contains the crack surfaces
    201 (Sideset) Sideset 201 contains the crack tip curves

    The Sidesets and Nodesets can be specified in two ways: using the CUBIT GUI or the command line/journal editor. It is usually convenient to identify the geometrical entities of interest by 'picking' them using the GUI, and then specify the fracture Sidesets and Nodeset using the journal editor (see Example 10.1 below).

    Example 10.1 How to specify fracture constraints for MoFEM in CUBIT

    Say that we first want to define Sideset 100 which contains all exterior curves of the problem of Figure 10.1.

    • Step 1 - Identify geometrical entities of interest using the GUI: We can easily identify the curves which define the boundary by creating a mock displacement boundary condition and picking the curves of interest. See Figure 10.2.
    CUBIT Command Panel: Materials and BCs --> Create Boundary Conditions
--> Displacement --> select 'Curve' from the Entity List and then
pick the curves of interest

    CUBIT fracture constraints

    Figure 10.2 Identification of curve IDs for Sideset 100. All curves highlighted in amber have been selected.

    • Step 2 - Copy command line output to the journal editor: Once we pick all the entities, the CUBIT command line will display something similar to the following, which we can copy and paste to the journal editor.
      Current entity is Curve 11.
  Current entity is Curve 8.
  Current entity is Curve 12.
  Current entity is Curve 2.
  Current entity is Curve 7.
  Current entity is Curve 3.
  Current entity is Curve 5.
  Current entity is Curve 1.
  Current entity is Curve 6.
  Current entity is Curve 9.
  Current entity is Curve 4.
  Current entity is Curve 10.
    • Step 3 - Define Sideset 100 using the journal editor: Since we now have all the entity IDs we need to define the Sideset, we can write in the journal editor the following and then delete the command line output we previously pasted
    sideset 100 curve 11 8 12 2 7 3 5 1 6 9 4 10

    The same procedure can be used to define Nodeset 101 and Sidesets 102, 200 & 201. You can copy the following in the journal editor and complete the entity IDs for your case:

    sideset 100 curve ...
nodeset 101 vertex ...
sideset 102 surface ...
sideset 200 surface ...
sideset 201 curve ...
    Sometimes it may be quicker to define a Nodeset/Sideset with all entities of a type and then remove the ones that we identify using alland removeas follows:

    sideset 102 surface all
sideset 102 surface ID1 ID2 ... IDn remove

    ####10-5 Meshing

    There are no particular meshing requirements for fracture analysis. It is worthwhile to note the following:

    • Tetrahedral elements are used, of any available order
    • The crack is modelled in CUBIT as a single surface, which is part of the main body geometry. Therefore the crack mesh is generated automatically by meshing the enclosing volumes. The crack nodes are duplicated automatically by MoFEM to represent two crack surfaces.
    • Prior to generating a mesh, ensure that you imprint and merge the crack tool volumes with each other and with the surrounding volumes in CUBIT. You can do so using the GUI or by using imprint volume all and merge volume all in the CUBIT command line or journal editor

    CUBIT crack mesh

    Figure 10.3 Example of mesh with a crack surface in CUBIT

    ####10-6 Fracture analysis

    Analysis is initiated from a terminal using two executables in the following order:

    1. spatial_problem : calculates the displacement and stress field

    2. material_force : calculates the griffith energy and material forces at the crack front

    The input and output files of spatial_problem and material_force are shown in the Table below.

    Module Input Output
    spatial_problem .cub file out_spatial.h5m
    out.vtk
    out_stresses.vtk
    material_force out_spatial.h5m out_material.h5m
    out.vtk

    The .h5m files contain all the model and output data from the execution of the respective modules in HDF5 format.

    The out.vtk files contain post-processing data (except stresses) in ASCII VTK format and can be read directly by ParaView. The out_stresses.vtk file contains stress results for post-processing.

    The post-processing data available in out.vtk and out_stresses.vtk are described in Section 10-7.

    spatial_problem input parameters

    material_force input parameters

    It is usually convenient to use a shell script to run the fracture analysis. The following link provides a general script which can be adapted accordingly.

    The script can be invoked from a terminal as follows:

    ./fracture.sh
    If it is desired to save all terminal output to a log file with filename "log_filename" the following can be used instead:

    ./fracture.sh |tee log_filename

    ####10-7 Post-processing

    Post-processing of a fracture analysis can be undertaken in two complimentary ways:

    1. Post-processing using ParaView

    2. Post-processing using data from the output of the terminal. This requires a log file (see Section 10-6) and can be used to create plots of the fracture analysis results.

    Some typical post-processing operations that can be done using ParaView with the results of a fracture analysis:

    • Plot displacement contours. You can calculate displacements from any out.vtk file using the ParaView Calculator. The displacement vector is equal to SPATIAL_POSITION_VAL (Vector) - coords (Vector).
    • Plot the deformed shape using the Warp By Vector tool and calculated displacement vector [out.vtk].
    • Plot the vector of material resistance forces using the Glyph tool and MATERIAL_FORCE_PROJECTED vector [out.vtk].
    • Plot stresses [out_stresses.vtk]

    The Mode I stress intensity factor (KI) can be calculated directly from the terminal/log output using the computed Griffith forces and the following relationship:

    KI

    where G is the computed Griffith force.

    Alternatively, the user can plot contours of nodal Griffith forces in Paraview using the G result set. The following Table outlines the different results that are output for post-processing with Paraview.

    #####Description of out.vtk data

    Result Description Type Components
    G Strain energy release rate. Expresses energy release associated with unit increase of crack surface area. It can be used directly in calculations of stress intensity factors. Scalar N/A
    GRIFFITH_FORCE Indicates the direction of crack propagation at nodes (i.e. mesh-dependent). Energy can be calculated from the dot product of GRIFFITH_FORCE and nodal displacements. Vector X, Y, Z
    MATERIAL_FORCE Force conjugate to displacements in material space. It is used to express work of topological changes of body geometry in material space. Vector X, Y, Z
    MATERIAL_FORCE_PROJECTED Material force projected on surface area Vector X, Y, Z
    SPATIAL_POSITION_VAL Current nodal position of the body in the deformed configuration. Displacements equal this minus the original coordinates (coords). Vector X, Y, Z
    SPATIAL_RESIDUAL It expresses out-of-balance nodal forces. When the correct solution is obtained, its value should converge to zero. Vector X, Y, Z

    #####Description of out_stresses.vtk data

    Result Description Type Components
    CAUCHY_STRESS_VAL Cauchy stress Tensor 0, 1, 2 ... 8
    ESHELBY_STRESS_VAL Eshelby stress. It is the counterpart of Cauchy stress in material space. Tensor 0, 1, 2 ... 8
    J_VAL Jacobian. It expresses volume change. It is the determinant of the gradient of deformation Scalar N/A
    PIOLA1_STRESS_VAL Piola-Kirchhoff stress Tensor 0, 1, 2 ... 8
    PSI_VAL Density of energy Scalar N/A
    SPATIAL_POSITION_VAL Current nodal position of the body in the deformed configuration. Displacements equal this minus the original coordinates (coords). Vector X, Y, Z

    ####10-8 Quick reference This section summarises tools that you can use to streamline fracture modelling, analysis and post-processing.

    Pre-Processing

    To define fracture constraints in the journal editor:

    sideset 100 curve ID1 ID2 ...     # Boundary curves
nodeset 101 vertex ID1 ID2 ...    # Boundary vertices
sideset 102 surface ID1 ID2 ...   # Boundary surfaces
sideset 200 surface ID1 ID2 ...   # Crack surface
sideset 201 curve ID1 ID2 ...     # Crack tip
    In addition, the following may be useful:

    sideset 102 surface all
sideset 102 surface ID1 ID2 ... IDn remove

    Analysis

    Go to Contents

    ##11 Crack Propagation

    ####11-1 Introduction

    This section describes how to undertake discrete crack propagation analysis in MoFEM with automatic remeshing and without the use of interface elements. This is currently limited to isotropic materials. The theory for this type of crack propagation analysis is described in the Theory Manual.

    All pre-processing is undertaken using CUBIT, whereas post-processing is undertaken using ParaView and/or output text files.

    ####11-2 Analysis workflow

    1. Set up a model for fracture analysis [CUBIT]
    2. Define points for output of load-displacement results for post-processing [CUBIT]
    3. Run crack propagation analysis [MoFEM]
    4. Post-process [ParaView & MoFEM txt output files]

    ####11-3 Load-displacement output

    ####11-4 Crack propagation analysis

    ####11-5 Post-processing

    ####11-6 Quick reference

    This section summarises tools that you can use to streamline modelling, analysis and post-processing of crack propagation.

    Go to Contents

    ##20 Dynamics

    Go to Contents

    ##30 Interface Modelling

    Go to Contents

    ##40 Verification

    Go to Contents

    Back to Top | Back to Home Page

    Updated