Sea surface

# ReadTsunami read ChEESE Tsunami files ## Purpose This module is designed to read [TsunamiHySEA](https://edanya.uma.es/hysea/index.php/models/tsunami-hysea) files. [TsunamiHySEA](https://edanya.uma.es/hysea/index.php/models/tsunami-hysea) is a numerical model for quake generated tsunami simulation. 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**: Latitdude array which specifies one dimension of the sea domain - **grid_lat**: Latitdude array of the topography - **grid_lon**: Longitude array of the topography - **time**: Timesteps used for the simulation - **eta**: Wave amplitude per timestep ## How the reader works The reader is able to read netCDF files which uses a [PnetCDF](https://parallel-netcdf.github.io/) 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. --- ## 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| |-|-|-| |first_step|first timestep to read|Int| |last_step|last timestep to read (-1: last)|Int| |step_increment|number of steps to increment|Int| |first_rank|rank for first partition of first timestep|Int| |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| ### 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. ```{figure} ../../../module/read/ReadTsunami/simple.png --- 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. ![](../../../module/read/ReadTsunami/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. [MapDrape](MapDrape.md) is used in this context to make a coordinate system conversion of the dataset from WGS84 to Mercator. [IndexManifolds](IndexManifolds.md) needs to be used here to specify which layer of the LayerGrid needs to be used as input for MapDrape. [LoadCover](LoadCover.md) loads the google data as VRML file while the [Variant](Variant.md) modules allows the user to disable data later in COVER. ```{figure} ../../../module/read/ReadTsunami/cadiz.png --- 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. ![](../../../module/read/ReadTsunami/tsunamiCadizNcTopo.png) In comparison to the previous topographic data the same simulation data with the additional google maps data is shown in the following pictures. ![](../../../module/read/ReadTsunami/tsunamiCadiz.png) ![](../../../module/read/ReadTsunami/tsunamiCadizClose.png) ![](../../../module/read/ReadTsunami/tsunamiCadizClose2.png) ## Related Modules ### Often Used With - [Color](Color.md) - [MapDrape](MapDrape.md) - [IndexManifolds](IndexManifolds.md) - [Variant](Variant.md) ## Build Requirements - PnetCDF: build with --enable-thread-safe flag as described on [PnetCDF-GitHub](https://github.com/Parallel-NetCDF/PnetCDF) 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. ::: ## Acknowledgements - [TsunamiHySEA](https://github.com/edanya-uma/TsunamiHySEA) - [ChEESE](https://cheese-coe.eu/) - [Google Maps](https://www.google.com/maps/place/C%C3%A1diz,+Provinz+C%C3%A1diz,+Spanien/@36.5163851,-6.2999767,14z/data=!3m1!4b1!4m5!3m4!1s0xd0dd25724ec240f:0x40463fd8ca03b00!8m2!3d36.5210142!4d-6.2804565?hl=de)