Setting up and running GeoClaw

This is a rough outline with some pointers to existing documentation and examples. More will be added.

See also the GeoClaw documentation and Other learning resources.

Things to set/adjust in setrun.py¶

Computational domain¶

• How large should it be? (Outflow boundaries)

• Should edges be adjusted so that cells on some fine level are aligned to match some desired grid?

Choosing grid resolutions and refinement factors¶

• How coarse should the initial (Level 1) grid be?

• How many AMR levels are needed, what refinement factors are best?

Topography DEMs (topofiles)¶

• Topography data documentation

• Sources of data (needs updating)

• Grid registration documentation

• topotools_examples notebook

• Topography file ordering documentation

Adjusting background sea level¶

• Relation to vertical datum of the topography files.

• Choice of tide level for simulation(s), e.g. MHW is often used for modeling onshore inundation, MLW for modeling drawdown in marinas.

• Incorporating future sea level projections.

• Setting sea_level documentation

• How sea_level is adjusted by ground deformation for initializing water level on fine grids, see Set Eta Init documentation

Specifying ground motion (dtopofiles)¶

• Coastal subsidence / uplift

• Choice of dtopo_data.dt_max_dtopo for static vs. kinematic sources

• dtopo file documentation

• dtopotools_examples notebook

• Okada notebook

• CSZ_example notebook

Refinement criteria and flagregions¶

• Finite volume methods, cell-averaged values, and consistency between levels

• Adaptive mesh refinement (AMR) algorithms documentation

• AMR refinement criteria documentation

• Specifying flagregions for adaptive refinement documentation

• Using Ruled Rectangles for refinement regions, e.g. MakeFlagregionsCoast notebook

• Guiding AMR with adjoint flagging See also the example in $CLAW/geoclaw/examples/tsunami/chile2010_adjoint and its README in the Clawpack Gallery. Additional examples in the paper Davis & LeVeque (2016).

Duration of simulation and time between outputs¶

• Size of output files, ascii vs binary output

• Time frame output (full AMR solution) vs. fgout output (on fixed grids)

• Choice of Courant number, cfl_desired

Synthetic gauges¶

• Centering gauges in grid cells

• Capturing pre-seismic and/or final topography at gauge points

• When to turn gauges on

• General Gauges documentation

fgmax grids to capture maxima¶

• Centering fgmax grid points in computational grid cells

• What levels to monitor, when to turn on

• Capturing pre-seismic and/or final topography at grid points

• Fixed grid monitoring documentation

fgout grids for frequent output on fixed grids¶

• Fixed grid output documentation

Bottom friction and the Manning Coefficient¶

• Manning friction term documentation

Other topics¶

Initializing some land below sea level as dry¶

Land that is behind a dike or levee should be forced to be dry initially. This can be done with a force_dry array.

• Force Cells to be Dry Initially documentation

• Force Cells to be Dry Initially notebook.

Initializing some land above sea level as wet¶

A lake that is near the coast may have an initial surface elevation that is different from sea_level.

• Modifying set_eta_init.f90 to change sea_level over specified region.

• Set Eta Init documentation

• See the sample code commented out in the default set_eta_init.f90

• Modifying Makefile to used your version of this Fortran code, see Makefile documentation

Adding river flow, precipitation, overland flooding¶

• Sample results for Quillayute River flooding notebook from Tutorial from CSDMS 2024

Landslide generated tsunamis¶

• Landslides documentation

• Need for dispersive modeling, see Boussinesq solver documentation

Running GeoClaw¶

Basic workflow and output¶

Using OpenMP, how many threads?¶

• See Using OpenMP documentation

Checkpoint files and restarts¶

• See Checkpointing and restarting documentation

Running on cluster / supercomputer¶

• Sending output to a scratch directory

• SLURM scripts

• Running dispersive (Boussinesq) code with MPI, PETSc on TACC