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--- software:specfem3d:start [2014/01/03 00:11]
emheien [Tutorial 2: Waterlayered halfspace]
+++ software:specfem3d:start [2015/02/11 17:45] (current)
emheien
@@ Line 2: / Line 2: @@
 [[http://geodynamics.org/cig/software/specfem3d|SPECFEM3D Software Page]]
+===== Development =====
+If you want to contribute to the source code, please refer to [[https://github.com/geodynamics/specfem3d/wiki|https://github.com/geodynamics/specfem3d/wiki]] for details.
 ===== Tutorials =====
+Step-by-step tutorials how to run SPECFEM3D simulations
 ==== Tutorial 1: Homogeneous halfspace ====
@@ Line 433: / Line 439: @@
 {{:software:specfem3d:tutorial:waterlayered_seismograms.jpg?direct&500|}}
+==== Tutorial 3: Mount St. Helens ====
+The following instructions assume that you have installed [[http://geodynamics.org/cig/software/specfem3d/|SPECFEM3D]] and familiarized yourself with how you will run the package based on your computer configuration, as detailed in the "SPECFEM3D User manual":http://www.geodynamics.org/wsvn/cig/seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.pdf?op=file&rev=0&sc=0 (Chapter 2 provides installation help). Additionally, we will make use of an external, hexahedral mesher [[http://cubit.sandia.gov/|CUBIT]]. Please make sure you have these packages installed on your system.
+The example is distributed with the package under the examples/ directory. However, you might need to edit these example scripts slightly to launch them on your system.
+=== Mount St. Helens ===
+This is a step-by-step tutorial how to create a mesh for a region around Mount St. Helens, export it into a [[http://geodynamics.org/cig/software/specfem3d/|SPECFEM3D]] file format and run the mesh partitioning and database generation.
+Change to the example directory
+  []$ cd SPECFEM3D/examples/Mount_StHelens
+Please also see the README file in this example directory. An example topography file "ptopo.mean.utm" is provided as well, in the following we explain in detail how to construct such a file.
+=== Downloading topography data ===
+You can get [[http://srtm.csi.cgiar.org|SRTM]] 90m Digital Elevation Data for a region of interest at: [[http://srtm.csi.cgiar.org|http://srtm.csi.cgiar.org]]
+For this example, we choose Mount St.Helens as region of interest.
+Mount St. Helens is located at: 46.197 N 122.186 W
+This region is contained in a downloadable file ''srtm_12_03.zip'', which you will have to download from
+[[http://srtm.csi.cgiar.org/SELECTION/inputCoord.asp|http://srtm.csi.cgiar.org/SELECTION/inputCoord.asp]]
+using the region of interest:
+  Latitude min: 45 N  max: 50 N
+  Longitude min: 125 W max: 120 W
+unzipping the file
+  [Mount_StHelens]$ unzip srtm_12_03.zip
+leads to:
+  ..
+  srtm_12_03.tif
+  ..
+=== Converting Geotif topography data ===
+To convert the Geotif-file into an ''longitude/latitude/elevation'' format, you can use the package [[http://fwtools.maptools.org/|FWTools]] at: [[http://fwtools.maptools.org/|http://fwtools.maptools.org/]]
+Install the package and use their ''gdal2xyz'' executable to extract the tif file into xyz format:
+  [Mount_StHelens]$ FWTools-2.0.6/bin_safe/gdal2xyz.py srtm_12_03.tif > srtm_12_03.xyz
+the newly created file ''srtm_12_03.xyz'' has now the format:
+  #longitude #latitude #elevation (m)
+the file size is ~ 963 MB.
+=== Extracting the region of interest ===
+To further extract and manipulate the topography data, you can use the package [[http://gmt.soest.hawaii.edu/|GMT]] at: [[http://gmt.soest.hawaii.edu/|http://gmt.soest.hawaii.edu/]]
+For our purpose, the region of interest will be:
+  \ -R-122.3/-122.1/46.1/46.3//
+that is a region of ~23 km x 23 km extent.
+{{:software:specfem3d:tutorial:mount-sthelens.jpg?direct&300|}}
+Using the ''blockmean'' executable from the GMT package, we extract and interpolate the topography data for the detailed region, using an interpolated grid spacing of 0.006 degrees (~ 700 m):
+  [Mount_StHelens]$ blockmean srtm_12_03.xyz -R-122.3/-122.1/46.1/46.3 -I0.006/0.006 > ptopo.mean.xyz
+This will create a new file ''ptopo.mean.xyz'' with a ''longitude/latitude/elevation'' format of the region of interest
+=== Converting to Cartesian coordinates ===
+Since the CUBIT mesh will need Cartesian coordinates, we convert the topography file from ''longitude/latitude/elevation'' to ''X/Y/Z'' coordinates using a UTM projection.
+Mount St.Helens lies in the UTM zone: 10 (T).
+Use the script "convert_lonlat2utm.pl" provided in this example folder:
+  [Mount_StHelens]$ ./convert_lonlat2utm.pl ptopo.mean.xyz 10 > ptopo.mean.utm
+to create a new file ''ptopo.mean.utm'' which will have a file format:
+  #UTM_X (m) #UTM_Y (m) #Z (m)
+{{:software:specfem3d:tutorial:mount-sthelens-views.jpg?direct&400|}}
+----
+=== Meshing ===
+In the following, we will run a python script within [[http://cubit.sandia.gov/|CUBIT]] to create the needed mesh files for the partitioner.
+. if not done so yet, change your working directory to the example folder:
+  []$ cd SPECFEM3D/examples/Mount_StHelens
+. start the graphical user interface (GUI) of [[http://cubit.sandia.gov/|CUBIT]]:
+  [Mount_StHelens]$ claro
+{{:software:specfem3d:tutorial:cubit12.jpg?direct&640|}}
+. run the python file "read_topo.py":
+  use the (Play Journal File) button and open the file 'read_topo.py'
+The script creates a topography surface ''topo.stl'' in STL file format as well as ''topo.cub'' based on file ''ptopo.mean.utm''.
+. run the python file "mesh_mount.py":
+  use the (Play Journal File) button and open the file 'mesh_mount.py'
+In case the script executed successfully, it should create you a single volume with a refined mesh for the top layer, a triplication layer and a coarser mesh at the bottom.
+{{:software:specfem3d:tutorial:cubit_mountsthelens.jpg?direct&640|}}
+check that the script created a new folder "MESH/" containing the files:
+  [Mount_StHelens]$ ls -1 MESH/
+  absorbing_surface_file_bottom
+  absorbing_surface_file_xmax
+  absorbing_surface_file_xmin
+  absorbing_surface_file_ymax
+  absorbing_surface_file_ymin
+  free_surface_file
+  materials_file
+  mesh_file
+  nodes_coords_file
+  nummaterial_velocity_file
+you can also check if the export was successful by examining the output in the Command line window of CUBIT.
+----
+=== Setting up example folder for simulations ===
+We will set up the example folder for simulation runs: All the steps and following decomposition, database generation and solver run are put in a ''process.sh'' bash script file in the example folder.
+. In case you can run parallel programs on your desktop (needs an MPI installation), you can simply run the script:
+  [Mount_StHelens]$ ./process.sh
+to do the setup and following steps for you. The simulation will run on 4 CPU cores by default. Please modify and adapt the script to your needs.
+{{:software:specfem3d:tutorial:mountsthelens_partitions.jpg?direct&400|}}
+Note, this example should take about 15 minutes to finish the simulation.
+. check the output file ''output_solver.txt'' in the output directory ''in_out_files/OUTPUT_FILES/'' to see if the forward simulation was successfully finishing.
+the seismograms will look like this, using gnuplot:
+  gnuplot> plot "X10.DB.HXZ.semd" w l,"X20.DB.HXZ.semd" w l,"X30.DB.HXZ.semd" w l,"X40.DB.HXZ.semd" w l
+{{:software:specfem3d:tutorial:mountsthelens_seismograms.jpg?direct&500|}}

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