Currently topo files are restricted to three possible formats as ASCII files. A future project is to allow other formats including NetCDF.
In the descriptions below it is assumed that the topo file gives the elevation of the topography (relative to some reference level) as a value of z at each (x,y) point on a rectangular grid. Only uniformly spaced rectangular topo grids are currently recognized.
More than one topo file can be specified (see Topography data file parameters) that might cover overlapping regions at different resolutions. The union of all the topo files should cover the full computational domain specified (and may extend outside it). Internally in GeoClaw a single piecewise-bilinear function is constructed from the union of the topo files, using the best information available in regions of overlap. This function is then integrated over computational grid cells to obtain the single topo value in each grid cell needed when solving depth averaged equations such as the shallow water equations with these finite volume methods. Note that this has the feature that if a grid cell is refined at some stage in the computation, the topo used in the fine cells have an average value that is equal to the coarse cell value. This is crucial in maintaining the ocean-at-rest steady state, for example.
The recognized topotypes are:
topotype = 1
x,y,z values on each line, progressing from upper left (NW) corner across rows (moving east), then down in standard GIS form. The size of the grid and spacing between the grid points is deduced from the data.
Example: if you want a flat bottom at B = -1000. over a domain 0. <= x <= 10. and 20. <= y <= 30. then the topo file could be simply:0. 30. -1000. 10. 30. -1000. 0. 20. -1000. 10. 20. -1000.
These files are larger than necessary since they store the x,y values at each point even though the points are required to be equally spaced. Many data sets come this way, but note that you can convert a file of this type to one of the more compact types below using clawpack.geoclaw.topotools.converttopotype(inputfile, outputfile, topotypein=1, topotypeout=2, nodata_value=None).
topotype = 2
The file starts with a header consisting of 6 lines containing:mx my xllcorner yllcorner cellsize nodataval
and is followed by mx*my lines containing the z values at each x,y, again progressing from upper left (NW) corner across rows (moving east), then down in standard GIS form. The lower left corner of the grid is (xllcorner, yllcorner) and the distance between grid points in both x and y is cellsize. The value nodataval indicates what value of z is specified for missing data points (often something like 9999. in data sets with missing values).
Example: For the same example as above, the topo file with topotype==2 would be:2 mx 2 my 0. xllcorner 20. yllcorner 10. cellsize 9999. nodatavalue -1000. -1000. -1000. -1000.
topotype = 3
The file starts with a header consisting of 6 lines as for topotype=2, followed by my lines, each containing mx values for one row of data (ordered as before, so the first line of data is the northernmost line of data, going from west to east).
Example: For the same example as above, the topo file with topotype==3 would be:2 mx 2 my 0. xllcorner 20. yllcorner 10. cellsize 9999. nodatavalue -1000. -1000. -1000. -1000.
This is essentially the same as the ESRI ASCII Raster format except that the Fortran code assumes the parameter values come first rather than the labels.
topotype = 4This file type is not ASCII but rather in a NetCDF4 format supported by the CF MetaData conventions (v. 1.6). Files that conform to this standard can be read in by GeoClaw. The topotools module also has support for reading and writing (including therefore conversion) of these types of bathymetry files. To use this functionality you will need to add -DNETCDF to the FFLAGS variable either by the command line or in the Makefile.
The Fortran code will recognize headers for topotype 2 or 3 that have the labels first and then the parameter values. Note that the label strings are ignored in either case, the order of lines is important.
It is also possible to specify values -1, -2, or -3 for topotype, in which case the z values will be negated as they are read in (since some data sets use different convensions for positive and negative values relative to sea level).
For GeoClaw applications in the ocean or lakes (such as tsunami modeling), it is generally assumed that sea_level = 0 has been set in Specifying GeoClaw parameters in setrun.py and that z<0 corresponds to subsurface bathymetry and z>0 to topograpy above sea level.
Downloading topography files¶
The example $CLAW/examples/tsunami/chile2010 is set up to automatically download topo files via:
$ make topo
See the maketopo.py file in that directory.
Other such examples will appear in the future.
Several on-line databases are available for topograpy, see Some sources of tsunami data for some links.
Some Python tools for working with topography files are available, see Python tools for working with topo and dtopo.
Topography displacement files¶
Some problems have recently been observed when trying to specify time-varying topography with dtopo files. Nearly instantaneous displacement occuring at the start seems to work ok, but slowly varying displacement does not always work well when AMR is also being used. A better version of this code is currently being developed, but for now use with caution!
This has been fixed in Clawpack 5.1.0.
For tsunami generation a file dtopo is generally used to specify the displacement of the topography relative to that specified in the topo files.
Currently two formats are supported for this file:
Similar to topo files with topotype=1 as described above, except that each line starts with a t value for the time, so each line contains t,x,y,dz
The x,y,dz values give the displacement dz at x,y at time t. It is assumed that the grid is uniform and that the file contains mx*my*mt lines if mt different times are specified for an mx*my grid.
Similar to topo files with topotype=3 as described above, but the header is different, and contains lines specifying mx, my, mt, xlower, ylower, t0, dx, dy, and dt. These are followed by mt sets of my lines, each line containing mx values of dz.
The Okada model can be used to generate dtopo files from fault parameters, as described in Earthquake sources: Fault slip and the Okada model.
Note that if the topography is moving, it is important to insure that the time step is small enough to capture the motion. Starting in Version 5.1.0, there is a new parameter that can be specified in setrun.py to limit the size time step used during the time when topography is moving. See Topography data file parameters.
qinit data file¶
Instead of (or in addition to) specifying a displacement of the topography it is possible to specify a perturbation to the depth, momentum, or surface elevation of the initial data. This is generally useful only for tsunami modeling where the initial data specified in the default qinit.f90 function is the stationary water with surface elevation equal to sea_level as set in setrun.py (see Specifying GeoClaw parameters in setrun.py).
Of course it is possible to copy the qinit.f90 function to your directory and modify it, but for some applications the initial elevation may be given on grid of the same type as described above. In this case file can be provided as described at qinit data file parameters containing this perturbation.
The file format is similar to what is described above for topotype=1, but now each line contains x,y,dq where dq is a perturbation to one of the components of q as specified by the value of iqinit specified (see qinit data file parameters). If iqinit = 4, the value dq is instead the surface elevation desired for the initial data and the depth h (first component of q) is set accordingly.