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README

Scripts to mesh Marmousi model:

The scripts here can be used with CUBIT/Trelis to create a mesh for the Marmousi model. Just run in consecutive order, or open in CUBIT/Trelis -> run script:

./1_create_surfaces.py

this will create a CUBIT model of the Marmousi model using all vertices from the horizons to create mesh surfaces.

./2_mesh_marmousi.py

this will mesh the surfaces. due to some small edges for a few surfaces, this initial mesh needs to be tweaked a bit in a subsequent step.

./3_smooth_mesh.py

this step will try to improve the mesh by running a smoothing operation on the mesh surface - takes a while to finish...

./4_export_mesh.py

as it says, it will export the CUBIT mesh into SPECFEM readible files stored in folder MESH/

For assigning velocities to the surfaces, run script:

./5_convert_surface_rock_to_velocities.py

to create a file nummaterial_velocity_file_marmousi2. This will assign the original water layer to the mesh. To replace the water layer with solid velocities as in Capdeville et al. 2010, use

./5_convert_surface_rock_to_velocities.py --without-water

Installation:

To run these python scripts in the command line, instead of opening the Cubit application and use the "run script"-Button, you will need to make sure that within the python environment you can load the "cubit" module.

The most recent Coreform-Cubit version is 2023.11. It uses internally a python3.10 version. The details below describe how such a installation setup could look like for MacOS.

  • for MacOS: it requires to run this python script with the shipped Cubit version python (due to different architecture compilations).

    Cubit Coreform version 2023.11:

    • the cubit python version is here /Applications/Coreform-Cubit-2023.11.app/Contents/lib/python3/Python.framework/Versions/3.10/python3.10

    • either create an alias which can be set in ~/.alias or ~/.bashrc:

      export CUBITDIR=/Applications/Coreform-Cubit-2023.11.app
function python-cubit() { ${CUBITDIR}/Contents/lib/python3/Python.framework/Versions/3.10/python3.10 "$@" ; }
export -f python-cubit

      or create a symbolic link to the python version in /usr/local/bin:

      sudo ln -s /Applications/Coreform-Cubit-2023.11.app/Contents/lib/python3/Python.framework/Versions/3.10/python3.10 python-cubit

      I ended up using this latter approach, as the export option didn't work properly.

    • to import the cubit module, this also requires to add the Cubit library path to the PYTHONPATH environment variable, in ~/.bashrc use:

      export PYTHONPATH=$PYTHONPATH:${CUBITDIR}/Contents/lib/