This repository contains the code used to set up and run the examples in the manuscript

Implicit Adaptive Mesh Refinement for Dispersive Tsunami Propagation
by Marsha J. Berger and Randall J. LeVeque, submitted, 2023
(Revised manuscript submitted March, 2024 with updated examples)

which is available as a preprint. [v2]

This paper has now been accepted for publication in the SIAM Journal on Scientific Computing.

The python scripts setrun.py in each directory may be useful to see more clearly how each run was set up.

Notes: (Revised June 2024)

• The version of GeoClaw needed to run the code in this repository was recently released in Clawpack v5.10.0. See https://www.clawpack.org/releases.html for links and release notes.

  All releases of Clawpack are also permanently archived on Zenodo and at this DOI: https://doi.org/10.17605/osf.io/kmw6h.

• Clawpack v5.10.0 includes both:

  • A 2D version of GeoClaw with implicit timestepping coupled with AMR, and applied to the Boussinesq-type equations described in the paper. See https://www.clawpack.org/bouss2d.html.

  • A 1D version of GeoClaw that also supports the solution of some Boussinesq-type equations, along with shallow water equations. The 1D code is used to compute reference radially-symmetric solutions for comparison with the 2D simulations for the example in radial_shelf_beach_nonlinear. See https://www.clawpack.org/geoclaw1d.html.

• To run the codes using MPI for the implicit solves via PETSc, combined with OpenMP for the explicit time stepping in the shallow water steps (distributing grid patches between threads), it is necessary to use PETSc Version 3.20 (or later) with enhancements added by Barry Smith.

• The file setenv_rjl.sh is a bash script for the environment variables as set by RJL on the laptop where the timings were performed. These environment variables must be set properly for your computer.

• The file petscMPIoptions lists the PETSc options used for the linear solvers. You must set an environment variable PETSC_OPTIONS to be the full path to this file.

• Alternatively, rather than setting environment variables, you can modify the Makefile in each example directory as indicated in the lines that are commented out.

• The version of this repository used for the resubmitted paper is tagged as resubmitted_march2024. This code was cleaned up a bit more and tagged publication for the version to be archived in the Supplementary Materials for the paper, and is also archived at DOI 10.5281/zenodo.12709453.