Calculate carbonate sediment thickness

Generate carbonate sediment thickness grids from age and bathymetry grids over the time range 0-170Ma (in 1My increments). Pelagic carbonate sediments did not exist before 170Ma.

Dependencies

• GMT (and make sure the 'gmt' executable is in the PATH).
• PyGPlates.
• SciPy.
• And, on Windows platforms, optionally install psutil so that this workflow can use CPU cores in the background (ie, below-normal priority).

Usage

To generate the carbonate thickness grids you can either:

• load the Jupyter notebook carbonate_sediment_thickness.ipynb and run all cells, or
• type python run_carbonate_sediment_thickness.py in a console/terminal window.

In either case there are a bunch of top-level parameters that you can change/configure. By default use_all_cpu_cores is set to True to run on all CPU cores (otherwise it takes too long; up to 25 hours at 0.5 degree resolution using just a single core). Note that you can increase the grid_spacing parameter to reduce the running time.

Note: If you choose the Jupyter notebook and you edit a parameter outside the notebook (such as inside the imported module carbonate_sediment_thickness) then you'll need to restart the notebook kernel after each modification (or insert reload(carbonate_sediment_thickness) after import carbonate_sediment_thickness).

The location of the age and bathymetry will need to be changed to point to your local grids.

The age grids can be downloaded from https://www.earthbyte.org/webdav/ftp/Data_Collections/Muller_etal_2019_Tectonics/Muller_etal_2019_Agegrids/Muller_etal_2019_Tectonics_v2.0_netCDF.zip .

The bathymetry grids can be downloaded from https://www.earthbyte.org/webdav/ftp/Data_Collections/Wright_etal_2020_ESR/Grids/Paleobathymetry_RHCW18/ .

You can either use the supplied topological model (2019_v2) or provide your own. In either case you'll set the topology_model_name variable (in carbonate_sediment_thickness.ipynb or run_carbonate_sediment_thickness.py) to the name of the topological model. If you're using the supplied model you only need to specify topology_model_name = '2019_v2'. However if you're providing your own model then please follow these steps to use your model:

• Create a new sub-directory of input_data/topology_model/ that is the name of your model (eg, my_model).
  • For example: input_data/topology_model/my_model/
• Copy your model files into that directory.
  • For example, copy the model GPML(Z) and ROT files into input_data/topology_model/my_model/.
• Create a new text file called rotation_files.txt that lists the model's rotation files.
  • For example: input_data/topology_model/my_model/rotation_files.txt
  • The paths of the rotation files (listed in rotation_files.txt) should be relative to the base directory. For example:

    input_data/topology_model/my_model/rotations_1.rot
    input_data/topology_model/my_model/rotations_2.rot
    ...
    

  • A convenient way to generate this file is (using the my_model example) is to run the following command from the base directory:

    ls -A1 input_data/topology_model/my_model/*.rot > input_data/topology_model/my_model/rotation_files.txt
    

• Create a new text file called topology_files.txt that lists the model's topology files.
  • For example: input_data/topology_model/my_model/topology_files.txt
  • The paths of the topology files (listed in topology_files.txt) should be relative to the base directory. For example:

    input_data/topology_model/my_model/topologies_1.gpmlz
    input_data/topology_model/my_model/topologies_2.gpmlz
    ...
    

  • A convenient way to generate this file is (using the my_model example) is to run the following command from the base directory. This assumes a mix of .gpml and .gpmlz files (also note the >> on the second command to append):

    ls -A1 input_data/topology_model/my_model/*.gpml > input_data/topology_model/my_model/topology_files.txt
    ls -A1 input_data/topology_model/my_model/*.gpmlz >> input_data/topology_model/my_model/topology_files.txt
    

• Then set the topology_model_name variable to the name of your model (ie, name of the sub-directory).
  • For example: topology_model_name = 'my_model'
• Note: It may be helpful to look at the supplied 2019_v2 model as an example of how to do this.
  • That is, have a look in the input_data/topology_model/2019_v2/ directory.

Reference

Dutkiewicz, A., Müller, R.D., Cannon, J., Vaughan, S. and Zahirovic, S., 2019, Sequestration and subduction of deep-sea carbonate in the global ocean since the Early Cretaceous. Geology, 47(1), pp.91-94. DOI: https://doi.org/10.1130/G45424.1