Topography data¶
See also
The GeoClaw Description and Detailed Contents software for flow over topography requires at least one topo file to be input, see Specifying GeoClaw parameters in setrun.py.
Currently topo files are restricted to three possible formats as ASCII files, or NetCDF files are also allowed.
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 Description and Detailed Contents 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.
Warning
Some changes were made in version 5.5.0 that affect how topofiles with topo_type in [2,3] are interpreted for files with a header specifying xllcorner and yllcorner. This may cause computed results to differ from previous results using the same topofiles if the header contains this specification. See Grid registration for more details on this llcorner registration. The description below has been modified to use lower registration, equivalent to llcenter registration.
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: The data below would be used in the GeoClaw code to define a bilinear function over the domain 0. <= x <= 10. and 20. <= y <= 30. that decreases (deeper water) as you move to the east or to the south:
0. 30. -1000. 10. 30. -2000. 0. 20. -3000. 10. 20. -4000.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 e.g.:
from clawpack.geoclaw import topotools topo = topotools.Topography(input_path, topo_type=1) topo.write(output_path, topo_type=3)topotype = 2
The file starts with a header consisting of 6 lines containing:
XXX mx XXX my XXX xlower | xllcenter | xllcorner XXX ylower | yllcenter | yllcorner XXX cellsize XXX nodatavaland 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 (xlower, ylower) 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).
Note:
The value XXX and the label (e.g. xlower) can appear in either order in each of the header lines.
the cellsize line can include two values dx, dy rather than a single value, in case the spacing is different in x and y.
Example: For the same example as above, the topo file with topotype==2 and lower registration would be:
2 mx 2 my 0. xlower 20. ylower 10. cellsize -9999 nodatavalue -1000. -2000. -3000. -4000.This file would be interpreted the same way if llcenter registration was specified on lines 3 and 4, but differently if llcorner was specified – see Grid registration.
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 and lower registration would be:
2 mx 2 my 0. xlower 20. ylower 10. cellsize -9999 nodatavalue -1000. -2000. -3000. -4000.This file would be interpreted the same way if llcenter registration was specified on lines 3 and 4, but differently if llcorner was specified – see Grid registration.
Note:
The value XXX and the label (e.g. xlower) can appear in either order in each of the header lines.
the cellsize line can include two values dx, dy rather than a single value, in case the spacing is different in x and y.
This is essentially the same as the ESRI ASCII Raster format, but it is important to note which grid registration is used. NCEI and etopo1 data sets generally have this format with llcorner registration! See Grid registration for more details.
topotype = 4
This 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 (see NetCDF format below). 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. 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 Description and Detailed Contents 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.
NetCDF format¶
Topofiles can be read in netCDF format, either from local .nc files or from some online databases that provide netCDF servers, e.g. the NOAA THREDDS server. Use the topotools.read_netcdf function. Note that this also allows reading in only a subset of the data, both limiting the extent and the resolution, e.g. by sampling every other point (by setting coarsen=2). This is particularly useful if you only want a subset of a huge online netCDF file (e.g. coastal DEMs at 1/3 arcsecond resolution are typically several gigabytes).
The dictionary topotools.remote_topo_urls contains some useful URLs for etopo1 and a few other NOAA THREDDS datasets. This allows reading etopo1 data, for example, via:
>>> from clawpack.geoclaw import topotools
>>> topo1 = topotools.read_netcdf('etopo1',...)
See $CLAW/geoclaw/tests/test_etopo1.py for one example, in which a very small patch from the global etopo1 database (which has 1 arcminute resolution) is downloaded at different resolutions.
Note: Earlier versions of clawpack included etopotools.py providing a different way to download subsampled etopo1 topography. That has been deprecated since the old way is no longer supported by NOAA and did not always do the subsampling properly.
Note: Data in the NOAA THREDDS server is referenced to NAVD88, not to MHW!
See also Grid registration for important information about the manner in which the data downloaded should be interpreted. For netCDF files the data points are generally interpreted as pointwise values at the points specified in the lat and lon arrays included in the file (or as cell-averaged values with these points as the cell centers).
Topography displacement files¶
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:
dtopotype=1:
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.
dtopotype=3:
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. See also dtopotools module for moving topography.
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 qinit_type specified (see qinit data file parameters). If qinit_type = 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.
