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--- software:specfem3d:start [2014/01/02 22:47]
emheien
+++ 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 226: / Line 232: @@
 . change your working directory to the example folder:
-  <pre>
+  []$ cd SPECFEM3D/examples/waterlayered_halfspace
-  []$ cd SPECFEM3D/examples/waterlayered_halfspace </pre>
-. start the graphical user interface (GUI) of "CUBIT":http://cubit.sandia.gov:
+. start the graphical user interface (GUI) of [[http://cubit.sandia.gov/|CUBIT]]:
-  <pre>
+  [waterlayered_halfspace]$ claro
-  [waterlayered_halfspace]$ claro </pre>
-  <p align="center"><a href="figures/cubit12.jpg/image_view"><img src="figures/cubit12.jpg" width=640 ></a></p>
+{{:software:specfem3d:tutorial:cubit12.jpg?direct&640|}}
 . run the python file:
-  <pre>
+  use the (Play Journal File) button and open the file "waterlayer_mesh_boundary_fig8.py"
-  use the (Play Journal File) button and open the file "waterlayer_mesh_boundary_fig8.py"</pre>
 . in case the script executed successfully, it should create you three volumes with a refined mesh for the top layer, a triplication layer and a coarser mesh layer at the bottom:
-  <p align="center"><a href="figures/cubit_waterlayered.jpg/image_view"><img src="figures/cubit_waterlayered.jpg" width=640 ></a></p>
+{{:software:specfem3d:tutorial:cubit_waterlayered.jpg?direct&640|}}
-  check that the script created a new folder "MESH/" containing the files:
+check that the script created a new folder "MESH/" containing the files:
-  <pre>
   [waterlayered_halfspace]$ ls -1 MESH/
   absorbing_surface_file_bottom
@@ Line 256: / Line 257: @@
   mesh_file
   nodes_coords_file
-  nummaterial_velocity_file</pre>
+  nummaterial_velocity_file
+you can also check if the export was successful by examining the output in the Command line window of CUBIT. The sensitive part should look like
-  you can also check if the export was successful by examining the output in the Command line window of CUBIT. The sensitive part should look like
+{{:software:specfem3d:tutorial:cubit_commandline_waterlayered.jpg?direct&400|}}
-  <p align="center"><a href="figures/cubit_commandline_waterlayered.jpg/image_view"><img src="figures/cubit_commandline_waterlayered.jpg" width=400 ></a></p>
+. optionally, you could modify the material properties of the model, either in CUBIT or in the newly created material file:
+* changing the block properties in CUBIT
+{{:software:specfem3d:tutorial:cubit_properties_waterlayered.jpg?direct&400|}}
-. optionally, you could modify the material properties of the model,
+the following table applies for **acoustic** material properties:
-  either in CUBIT or in the newly created material file:
-  * changing the block properties in CUBIT
+^ **Name** ^ block name must start with "acoustic" for acoustic materials followed by a unique identifier ''material_id'' ^
+| **Attribute 1**  | Material ID |
+| **Attribute 2**  | P-wave speed |
+| **Attribute 3**  | S-wave speed is ignored, set to zero |
+| **Attribute 4**  | Density |
-    <p align="center"><a href="figures/cubit_properties_waterlayered.jpg/image_view"><img src="figures/cubit_properties_waterlayered.jpg" width=400 ></a></p>
+the following table applies for **elastic** material properties:
-    the following table applies for **acoustic** material properties:
+^ **Name** ^ block name must start with "elastic" for elastic materials followed by a unique identifier ''material_id'' ^
+| **Attribute 1**  | Material ID |
+| **Attribute 2**  | P-wave speed |
+| **Attribute 3**  | S-wave speed |
+| **Attribute 4**  | Density |
+| **Attribute 5**  | Quality factor |
+| **Attribute 6**  | Anisotropy flag |
-    |------------------------------------------------------------------------------------------|
+Once you changed the properties, you will have to re-export the mesh. This can be done, using the script ''run_cubit2specfem3d.py'':
-    | **Name**         | block name must start with "acoustic"                                 |
+  use the (Play Journal File) button and open the file "run_cubit2specfem3d.py"
-    |                  | for acoustic materials followed by a unique identifier ''material_id''|
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 1**  | Material ID                                                           |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 2**  | P-wave speed                                                          |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 3**  | S-wave speed is ignored, set to zero                                  |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 4**  | Density                                                               |
-    |------------------------------------------------------------------------------------------|
-    the following table applies for **elastic** material properties:
+This should refresh the files in directory "MESH/".
-    |------------------------------------------------------------------------------------------|
+* directly modifing the file ''nummaterial_velocity_file'' in the ''MESH/'' directory:
-    | **Name**         | block name must start with "elastic"                                  |
+   1          1028.000000          1480.000000             0.000000             0.000000  0
-    |                  | for elastic materials followed by a unique identifier ''material_id'' |
+   2          3200.000000          7500.000000          4300.000000          9000.000000  0
-    |------------------------------------------------------------------------------------------|
+   3          3200.000000          7500.000000          4300.000000          9000.000000  0
-    | **Attribute 1**  | Material ID                                                           |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 2**  | P-wave speed                                                          |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 3**  | S-wave speed                                                          |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 4**  | Density                                                               |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 5**  | Quality factor                                                        |
-    |------------------------------------------------------------------------------------------|
-    | **Attribute 6**  | Anisotropy flag                                                       |
-    |------------------------------------------------------------------------------------------|
-    Once you changed the properties, you will have to re-export the mesh. This can be done, using the script ''run_cubit2specfem3d.py'':
+this file defines the material properties. the format is:
-    <pre>
-    use the (Play Journal File) button and open the file "run_cubit2specfem3d.py"</pre>
-    This should refresh the files in directory "MESH/".
+^ **Domain_id**                  ^ **Material_id** ^ **Density**         ^ **P-wave speed**  ^ **S-wave speed**      ^ **Quality factor**  ^ **Anisotropy_flag**            ^
+| 1 = acoustic, | unique material | density             | wave speed in m/s | wave speed in m/s | Quality factor, | flag for anisotropy model, |
+| 2 = elastic       | identifier      | in kg/m<sup>3</sup> |                   | (ignored for acoustic materials) | 0 = no attenuation  | 0 = no anisotropy              |
-  * directly modifing the file ''nummaterial_velocity_file'' in the ''MESH/'' directory:
+----
-    <pre class="file">
-   1          1028.000000          1480.000000             0.000000             0.000000  0
-   2          3200.000000          7500.000000          4300.000000          9000.000000  0
-   3          3200.000000          7500.000000          4300.000000          9000.000000  0
-    </pre>
-    this file defines the material properties. the format is:
+=== Setting up example folder for simulations ===
-    |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+We will set up the example folder for simulation runs:
-    | **Domain_id**                  | **Material_id** | **Density**         | **P-wave speed**  | **S-wave speed**      | **Quality factor**  | **Anisotropy_flag**            |
-    |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-    | <code>1</code> = acoustic,<br> | unique material | density             | wave speed in m/s | wave speed in m/s <br>| Quality factor,<br> | flag for anisotropy model,<br> |
-    | <code>2</code> = elastic       | identifier      | in kg/m<sup>3</sup> |                   | (ignored for acoustic | 0 = no attenuation  | 0 = no anisotropy              |
-    |                                |                 |                     |                   | materials)            |                     |                                |
-    |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-<hr>
-Setting up example folder for simulations
- We will set up the example folder for simulation runs:
 * databases directory:
-  create a directory ''in_out_files/DATABASES_MPI/'' into which you will put the mesh partitions:
+create a directory ''in_out_files/DATABASES_MPI/'' into which you will put the mesh partitions:
-  <pre>
   []$ cd SPECFEM3D/examples/waterlayered_halfspace
-  [waterlayered_halfspace]$ mkdir -p in_out_files/DATABASES_MPI </pre>
+  [waterlayered_halfspace]$ mkdir -p in_out_files/DATABASES_MPI
 * parameter files:
-  make sure you have the parameter files in a local directory ''in_data_files/'' for the example:
+make sure you have the parameter files in a local directory ''in_data_files/'' for the example:
-  <pre>
   [waterlayered_halfspace]$ ls -1 in_data_files/
   Par_file
   CMTSOLUTION
-  STATIONS </pre>
+  STATIONS
-  these files should already be provided in the example folder.
+these files should already be provided in the example folder.
 * executables:
-  compile the executables in the root directory:
+compile the executables in the root directory:
-  <pre>
   []$ cd SPECFEM3D/
-  [SPECFEM3D]$ make </pre>
+  [SPECFEM3D]$ make
-  in case the compilation was successful, it will create the executables ''xdecompose_mesh_SCOTCH'', ''xgenerate_databases'' and ''xspecfem3D'' in the ''bin/'' directory
+in case the compilation was successful, it will create the executables ''xdecompose_mesh_SCOTCH'', ''xgenerate_databases'' and ''xspecfem3D'' in the ''bin/'' directory
-  and create a local directory ''bin/'' to link the executables from the root directory:
+and create a local directory ''bin/'' to link the executables from the root directory:
-  <pre>
   []$ cd SPECFEM3D/examples/waterlayered_halfspace
   [waterlayered_halfspace]$ mkdir -p bin
@@ Line 366: / Line 336: @@
   [bin]$ ln -s ../../../bin/xdecompose_mesh_SCOTCH
   [bin]$ ln -s ../../../bin/xgenerate_databases
-  [bin]$ ln -s ../../../bin/xspecfem3D </pre>
+  [bin]$ ln -s ../../../bin/xspecfem3D
 All these steps and the following decomposition, database generation and solver run are put in a ''process.sh'' bash script file in the example folder. You can simply run the script:
-  <pre>
+  [waterlayered_halfspace]$ ./process.sh
-  [waterlayered_halfspace]$ ./process.sh </pre>
 to do the setup and following steps for you. Please modify and adapt the script to your needs.
@@ Line 380: / Line 349: @@
 run the mesh partitioner:
-  <pre>
+  [waterlayered_halfspace]$ ./bin/xdecompose_mesh_SCOTCH 4 MESH/ in_out_files/DATABASES_MPI/
-  [waterlayered_halfspace]$ ./bin/xdecompose_mesh_SCOTCH 4 MESH/ in_out_files/DATABASES_MPI/   </pre>
 check that this created the mesh partitions:
-  <pre>
   [waterlayered_halfspace]$ ls -1 in_out_files/DATABASES_MPI/
   proc000000_Database
   proc000001_Database
   proc000002_Database
-  proc000003_Database </pre>
+  proc000003_Database
-<p align="center"><a href="figures/scotch_partitions_waterlayered.jpg/image_view"><img src="figures/scotch_partitions_waterlayered.jpg" width=400 ></a></p>
+{{:software:specfem3d:tutorial:scotch_partitions_waterlayered.jpg?direct&400|}}
 You are done.
-<hr>
+----
+=== Database generation ===
-Database generation
+Next, you will need to create the mesh databases.
- Next, you will need to create the mesh databases.
 . in case you can run parallel programs on your desktop (needs an MPI installation), you can run the executable like:
-  <pre>
   [waterlayered_halfspace]$ cd bin/
-  [bin]$ mpirun -np 4 ./xgenerate_databases </pre>
+  [bin]$ mpirun -np 4 ./xgenerate_databases
-  otherwise, you will need to modify and adapt one of the cluster scripts provided in the ''SPECFEM3D/utils/Cluster/'' directory.
+otherwise, you will need to modify and adapt one of the cluster scripts provided in the ''SPECFEM3D/utils/Cluster/'' directory.
 . check the output file ''in_out_files/OUTPUT_FILES/output_mesher.txt'' to see if the databases were generated successfully.
   The output file contains the suggested time step for your mesh:
-  <pre class="file">
   Verification of simulation parameters
   ...
   Minimum period resolved =   1.632425
   **Maximum suggested time step =   5.1801954E-03**
-  </pre>
-<hr>
+----
-Forward simulation
+=== Forward simulation ===
+To run a forward simulation, do the following:
- To run a forward simulation, do the following:
+. make sure, you have the parameter files in the directory ''in_data_files/''.
+Most parameters in the ''Par_file'' should be set before running the database generation.
+The following may be changed after running ''xgenerate_databases'':
-. make sure, you have the parameter files in the directory ''in_data_files/''.
-  Most parameters in the ''Par_file'' should be set before running the database generation.
-  The following may be changed after running ''xgenerate_databases'':
-  <pre class="file">
   # forward or adjoint simulation
   SIMULATION_TYPE                 = 1   # 1 = forward, 2 = adjoint, 3 = both simultaneously
   NOISE_TOMOGRAPHY                = 0   # 0 = earthquake simulation,  1/2/3 = three steps in noise simulation
   SAVE_FORWARD                    = .false.
   # time step parameters
   NSTEP                           = 4500
   DT                              = 0.005
   # absorbing boundary conditions for a regional simulation
   ABSORBING_CONDITIONS            = .true.
   # save AVS or OpenDX movies
   MOVIE_SURFACE                   = .false.
@@ Line 448: / Line 411: @@
   USE_HIGHRES_FOR_MOVIES          = .false.
   HDUR_MOVIE                      = 0.0
   # interval at which we output time step info and max of norm of displacement
   NTSTEP_BETWEEN_OUTPUT_INFO      = 500
   # interval in time steps for writing of seismograms
   NTSTEP_BETWEEN_OUTPUT_SEISMOS   = 10000
   # interval in time steps for reading adjoint traces
   NTSTEP_BETWEEN_READ_ADJSRC      = 0      # 0 = read the whole adjoint sources at the same time
-  # print source time function
-  PRINT_SOURCE_TIME_FUNCTION      = .false.  </pre>
+  # print source time function
+  PRINT_SOURCE_TIME_FUNCTION      = .false.
 . in case you can run parallel programs on your desktop (needs an MPI installation), you can run the executable like:
-  <pre>
   [waterlayered_halfspace]$ cd bin/
-  [bin]$ mpirun -np 4 ./xspecfem3D  </pre>
+  [bin]$ mpirun -np 4 ./xspecfem3D
-  note, this example should take about 1 hour 45 minutes to finish the simulation.
+note, this example should take about 1 hour 45 minutes to finish the simulation.
@@ Line 473: / Line 435: @@
   the seismograms will look like this, using gnuplot:
-  <pre>
+  gnuplot> plot "X10.DB.BXZ.semd" w l,"X20.DB.BXZ.semd" w l,"X30.DB.BXZ.semd" w l
-  gnuplot> plot "X10.DB.BXZ.semd" w l,"X20.DB.BXZ.semd" w l,"X30.DB.BXZ.semd" w l  </pre>
+{{: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
-  <p align="center"><a href="figures/waterlayered_seismograms.jpg/image_view"><img src="figures/waterlayered_seismograms.jpg" width=500 ></a></p>
+{{:software:specfem3d:tutorial:mountsthelens_seismograms.jpg?direct&500|}}

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