How to install bone remodelling module and run simple example?

[Lukasz Kaczmraczyk]

Hello Karol,

Student using docker installation on mac os x, we have basic mofem installation working already. We need to add bone remodelling module and run a simple example. How to do it? Also, do you have links to some simple meshses for testing? 

Regards,

Lukasz

[Lukasz Kaczmraczyk]

The web-page to start is here,

http://mofem.eng.gla.ac.uk/mofem/html/um_bone_remodelling_readnme.html

There is a way to how you can install precompiled version? Can you also show how to run example with bike frame?

[Karol Lewandowski]

To install bone remodelling on docker go to users modules source directory e.g.: 

cd $MOFEM_INSTALL_DIR/um/users_modules/users_modules/

Next, clone the repository with the following command: 

git clone https://bitbucket.org/likask/mofem_um_bone_remodelling.git bone_remodelling

go back to users modules build and re-configure with METAIO library: 

cd ..

cmake -DCMAKE_BUILD_TYPE=Release -DWITH_METAIO=1  -DCMAKE_C_FLAGS="-Wall"  \

-DCMAKE_CXX_FLAGS="-Wall -Wno-bind-to-temporary-copy -Wno-overloaded-virtual" \

-DCMAKE_EXE_LINKER_FLAGS="-L$MOFEM_INSTALL_DIR/local/lib" users_modules

on docker command is slightly different: 

cmake -DWITH_METAIO=1 -DBUILD_SHARED_LIBS=yes -DCMAKE_BUILD_TYPE=Release users_modules

At last, compile user modules with:

make -j2 

To run the code use command: 

./bone_adaptation -my_file frame_bike.cub -my_order 2 -my_output_prt 5 -ksp_type fgmres -pc_type lu -pc_factor_mat_solver_package mumps -ksp_atol 1e-12 -ksp_rtol 1e-12 -snes_monitor -snes_type newtonls -snes_linesearch_type basic -snes_max_it 20 -snes_atol 1e-8 -snes_rtol 1e-8 -ts_type beuler -ts_dt 0.01 -ts_final_time 1 -ts_max_snes_failures -1 -my_load_history load_history2.in -young_modulus 1000 -poisson_ratio 0.3 -rho_ref 0.1 -psi_ref 2.0 -c 1.0 -m 3 -n 2 -mass_postproc -ts_monitor | tee log

VTK files can be generated using script:

./do_vtk.sh

I added the .cub file. I also presented similar procedure with basic post-processing in Youtube video.

For bike frame optimisation mesh can be generated in cubit: 

reset

set geometry engine acis

set duplicate block elements on

#

#{height=0.5}

#{width=0.01}

#

brick x 1 y 0.5 z 0.03

brick x 0.03 y 0.03 z 0.03

move volume 2 location surface 5 include_merged

chop volume 2 with volume 1 keep

imprint volume 1 with curve 37 39

delete volume 2 3 4

brick x 0.03 y 0.03 z 0.03

move volume 5 location surface 27 include_merged

chop volume 5 with volume 1 keep

imprint volume 1 with curve 71 81

delete volume 5 6 7

brick x 0.03 y 0.03 z 0.03

move volume 8 location surface 25 include_merged

chop volume 8 with volume 1 keep

imprint volume 1 with curve 127 125

delete volume 8 9 10

#MESH ALL

volume all size auto factor 6

#volume all size auto factor 5

volume all scheme tetmesh

mesh volume all

volume all scale 2

#DEFINE BOUNDARY CONDITIONS

#{area1=SurfaceArea(46)}

#{area2=SurfaceArea(26)}

#{area3=SurfaceArea(69)}

#{area6=TriArea(2478)+TriArea(2448)}

#{area4=TriArea(2350)+TriArea(2383)}

#{area5=TriArea(2511)+TriArea(2514)}

#{length=Length(11)}

#{load=1.5}

block 4 surface 46

block 4 name "FORCE_01"

block 4 attribute count 3

block 4 attribute index 1 0

block 4 attribute index 2 {-load/area1}

block 4 attribute index 3 0

block 5 surface 69

block 5 name "FORCE_02"

block 5 attribute count 3

block 5 attribute index 1 0

block 5 attribute index 2 {-load/area2}

block 5 attribute index 3 0

block 6 surface 26

block 6 name "FORCE_03"

block 6 attribute count 3 0

block 6 attribute index 2 {-load/area3}

block 6 attribute index 3 0

#DEFINE BOUNDARY CONDITIONS 

block 2 curve 10

block 2 name "DISPLACEMENT"

block 2 attribute count 6

block 2 attribute index 1 0

block 2 attribute index 2 0

block 2 attribute index 3 0

block 2 attribute index 4 1

block 2 attribute index 5 1

block 2 attribute index 6 1

block 3 curve 9

block 3 name "DISPLACEMENT_2"

block 3 attribute count 6

block 3 attribute index 1 0

block 3 attribute index 2 0

block 3 attribute index 3 0

block 3 attribute index 4 1

block 3 attribute index 5 1

block 3 attribute index 6 1

block 9 surface 1 2

block 9 name "DISPLACEMENT_3"

block 9 attribute count 6

block 9 attribute index 1 0

block 9 attribute index 2 0

block 9 attribute index 3 0

block 9 attribute index 4 0

block 9 attribute index 5 0

block 9 attribute index 6 1

block 8 volume all

block 8 name "MAT_ELASTIC"

block 8 attribute count 6

block 8 attribute index 1 1000

block 8 attribute index 2 0.2

save as "/Users/karollewandowski/moFEM/users_modules/bone_remodelling/frame_bike.cub" overwrite

While in docker you can copy the file above from Downloads folder with: 

cp  $HOSTHOME/Downloads/frame_bike.cub ./