ReadTsunami

read ChEESE Tsunami files

Purpose

This module is designed to read TsunamiHySEA files in NetCDF format. TsunamiHySEA is a numerical model for quake generated tsunami simulations.

Ports

The first two ports output the geometry for the sea surface and bathymetry as an LayerGrid/Heightmap object. The other ports are providing a vistle scalar object which representing the corresponding in the parameter browser selected attributes.

Parameters

name	description	type
file_dir	NC File directory	String
ghost	Show ghostcells.	Int
fill	Replace filterValue.	Int
VerticalScale	Vertical Scale parameter sea	Float
blocks_latitude	number of blocks in lat-direction	Int
blocks_longitude	number of blocks in lon-direction	Int
fillValue	ncFile fillValue offset for eta	Float
fillValueNew	set new fillValue offset for eta	Float
bathymetry	Select bathymetry stored in netCDF)	String
scalar_0	Select scalar.)	String
scalar_1	Select scalar.)	String
scalar_2	Select scalar.)	String
scalar_3	Select scalar.)	String

Supported Reader Parameters

name	description	type
first_step	first timestep to read	Int
last_step	last timestep to read (-1: last available)	Int
step_increment	number of steps to increment	Int
first_rank	rank for first partition of first timestep	Int

The meaning of these parameters is described in more detail in the Reader Parameters documentation.

Supported System Parameters

name	description	type
_openmp_threads	number of OpenMP threads (0: system default)	Int
_benchmark	show timing information	Int
_concurrency	number of tasks to keep in flight per MPI rank (-1: #cores/2)	Int
_prioritize_visible	prioritize currently visible timestep	Int
_validate_objects	validate data objects before sending to port (Disable, Quick, Thorough)	Int

The meaning of these parameters is described in more detail in the System Parameters documentation.

How the reader works

The reader is able to read NetCDF files which uses a PnetCDF supported file type. In general the module will fetch the longitude and latitude values for the sea (lon, lat) and the bathymetry (grid_lon, grid_lat) from the NetCDF file. Based on each longitude-latitude pair the reader creates a 2D grid, varies the wave height (eta - orthogonal to longitude and latitude coordinates) per timestep and creates a 3D surface representing the sea surface out of it. If an attribute bathymetry is provided with the NetCDF file the reader will build a ground surface as well. Additional attributes like scalar data will be mapped onto the sea surface.

File Format

The raw data output of the simulation is a NetCDF file which contains the following mandatory attributes:

lon: Longitude array which specifies one dimension of the sea domain
lat: Latitude array which specifies one dimension of the sea domain
grid_lat: Latitude array of the topography
grid_lon: Longitude array of the topography
time: Timesteps used for the simulation
eta: Wave amplitude per timestep

Important to note

This module distributes the data into domain blocks per spawned mpi process. With the parameters blocks latitude and blocks longitude an user needs to specify the distribution of the simulation domain. The parameter fill enables the option to replace in the NetCDF file used fillValues for the attribute eta with a new fillValue to reduce the height dimension of the sea surface. If fill is enabled an user need to specify the current fillValue with the parameter fillValue (default fillValue: -9999) along with the replacement with fillValueNew. A NetCDF file read by this reader which does not contain a bathymetry attribute named with a string containing atleast the substring “bathy” won’t get noticed as bathymetry data and therefore not providing output data for the second port. In this case the parameter browser will show None for the parameter bathymetry. Otherwise there will be a selection of bathymetry options available.

Example Usage

Simple cases

In the simplest and most cases a visualization of the simulation result can be done like shown in figure 1.

align: center width: 150px

Fig 1: Simple vizualization pipeline.

In this example the second port will be used to visualize the topography. For the third port the additional scalar data **max_height** is selected which will directly mapped onto the sea surface. The following picture shows the result of executing this visualization pipeline.

![](simpleResult.png)

### Cádiz Tsunami

Visualizing simulation data next to additional topographic data assumes that coordinates are set up for a specific coordinate system. In the next example google maps data of the city Cádiz is used to generate a more immersive experience in VR. In such an example the tsunami data needs to be converted into another coordinate system because google maps uses a certain type of map projection called Mercator. The figure 2 shows the visualization pipeline of this example. [](project:#mod-MapDrape) is used in this context to make a coordinate system conversion of the dataset from WGS84 to Mercator. [](project:#mod-IndexManifolds) needs to be used here to specify which layer of the LayerGrid needs to be used as input for MapDrape. [](project:#mod-LoadCover) loads the google data as VRML file while the [](project:#mod-Variant) modules allows the user to disable data later in COVER.

---
align: center
width: 500px
---
Fig 2: Cádiz pipeline.

The first picture shows the result of executing the visualization pipeline from above with the topographic data which comes with the NetCDF data.

In comparison to the previous topographic data the same simulation data with the additional google maps data is shown in the following pictures.

Build Requirements

PnetCDF: build with –enable-thread-safe flag as described on PnetCDF-GitHub or installed via packagemanager

Note

The PnetCDF install directory should be added to your $PATH environment variable in order to be found by CMake, otherwise it won’t be build.