software:specfem3d:start
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software:specfem3d:start [2014/01/03 00:19] emheien |
software:specfem3d:start [2015/02/11 17:45] (current) emheien |
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| [[http://geodynamics.org/cig/software/specfem3d|SPECFEM3D Software Page]] | [[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 ===== | ===== Tutorials ===== | ||
| + | |||
| + | Step-by-step tutorials how to run SPECFEM3D simulations | ||
| ==== Tutorial 1: Homogeneous halfspace ==== | ==== Tutorial 1: Homogeneous halfspace ==== | ||
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| ==== Tutorial 3: Mount St. Helens ==== | ==== Tutorial 3: Mount St. Helens ==== | ||
| - | The following instructions assume that you have installed "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 "CUBIT":http://cubit.sandia.gov. Please make sure you have these packages installed on your system. | + | 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. | 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. | ||
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| === Mount St. Helens === | === 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 "SPECFEM3D":../../specfem3d file format and run the mesh partitioning and database generation. | + | 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 | Change to the example directory | ||
| - | <pre> | + | []$ cd SPECFEM3D/examples/Mount_StHelens |
| - | []$ cd SPECFEM3D/examples/Mount_StHelens</pre> | + | |
| 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. | 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 | + | === Downloading topography data === |
| - | You can get "SRTM":http://srtm.csi.cgiar.org 90m Digital Elevation Data for a region of interest at: "http://srtm.csi.cgiar.org":http://srtm.csi.cgiar.org | + | 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. | For this example, we choose Mount St.Helens as region of interest. | ||
| Mount St. Helens is located at: 46.197 N 122.186 W | 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 | + | 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: | using the region of interest: | ||
| Latitude min: 45 N max: 50 N | Latitude min: 45 N max: 50 N | ||
| Line 462: | Line 467: | ||
| unzipping the file | unzipping the file | ||
| - | <pre> | + | [Mount_StHelens]$ unzip srtm_12_03.zip |
| - | [Mount_StHelens]$ unzip srtm_12_03.zip</pre> | + | |
| leads to: | leads to: | ||
| Line 470: | Line 474: | ||
| .. | .. | ||
| + | === Converting Geotif topography data === | ||
| - | 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/]] |
| - | To convert the Geotif-file into an ''longitude/latitude/elevation'' format, you can use the | + | Install the package and use their ''gdal2xyz'' executable to extract the tif file into xyz format: |
| - | package "FWTools":http://fwtools.maptools.org/ at: "http://fwtools.maptools.org/":http://fwtools.maptools.org/ | + | [Mount_StHelens]$ FWTools-2.0.6/bin_safe/gdal2xyz.py srtm_12_03.tif > srtm_12_03.xyz |
| - | + | ||
| - | Install the package and use their ''gdal2xyz'' executable to extract | + | |
| - | the tif file into xyz format: | + | |
| - | <pre> | + | |
| - | [Mount_StHelens]$ FWTools-2.0.6/bin_safe/gdal2xyz.py srtm_12_03.tif > srtm_12_03.xyz </pre> | + | |
| the newly created file ''srtm_12_03.xyz'' has now the format: | the newly created file ''srtm_12_03.xyz'' has now the format: | ||
| - | <pre> | + | #longitude #latitude #elevation (m) |
| - | #longitude #latitude #elevation (m)</pre> | + | |
| the file size is ~ 963 MB. | the file size is ~ 963 MB. | ||
| + | === Extracting the region of interest === | ||
| - | 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/]] |
| - | To further extract and manipulate the topography data, you can use the | + | For our purpose, the region of interest will be: |
| - | package "GMT":http://gmt.soest.hawaii.edu/ at: "http://gmt.soest.hawaii.edu/":http://gmt.soest.hawaii.edu/ | + | \ -R-122.3/-122.1/46.1/46.3// |
| - | + | ||
| - | For our purpose, the region of interest will be: | + | |
| - | <pre> | + | |
| - | -R-122.3/-122.1/46.1/46.3//</pre> | + | |
| that is a region of ~23 km x 23 km extent. | that is a region of ~23 km x 23 km extent. | ||
| - | <p align="center"><a href="figures/mount-sthelens.jpg/image_view"><img src="figures/mount-sthelens.jpg" width=300 ></a></p> | + | {{: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): | 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): | ||
| - | <pre> | + | [Mount_StHelens]$ blockmean srtm_12_03.xyz -R-122.3/-122.1/46.1/46.3 -I0.006/0.006 > ptopo.mean.xyz |
| - | [Mount_StHelens]$ blockmean srtm_12_03.xyz -R-122.3/-122.1/46.1/46.3 -I0.006/0.006 > ptopo.mean.xyz </pre> | + | |
| - | This will create a new file ''ptopo.mean.xyz'' with a ''longitude/latitude/elevation'' format | + | This will create a new file ''ptopo.mean.xyz'' with a ''longitude/latitude/elevation'' format of the region of interest |
| - | of the region of interest | + | |
| + | === Converting to Cartesian coordinates === | ||
| - | 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. |
| - | + | ||
| - | 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). | Mount St.Helens lies in the UTM zone: 10 (T). | ||
| Use the script "convert_lonlat2utm.pl" provided in this example folder: | Use the script "convert_lonlat2utm.pl" provided in this example folder: | ||
| - | <pre> | + | [Mount_StHelens]$ ./convert_lonlat2utm.pl ptopo.mean.xyz 10 > ptopo.mean.utm |
| - | [Mount_StHelens]$ ./convert_lonlat2utm.pl ptopo.mean.xyz 10 > ptopo.mean.utm </pre> | + | |
| | | ||
| to create a new file ''ptopo.mean.utm'' which will have a file format: | to create a new file ''ptopo.mean.utm'' which will have a file format: | ||
| - | <pre> | + | #UTM_X (m) #UTM_Y (m) #Z (m) |
| - | #UTM_X (m) #UTM_Y (m) #Z (m)</pre> | + | |
| - | + | {{:software:specfem3d:tutorial:mount-sthelens-views.jpg?direct&400|}} | |
| - | <p align="center"><a href="figures/mount-sthelens-views.jpg/image_view"><img src="figures/mount-sthelens-views.jpg" width=400 ></a></p> | + | |
| ---- | ---- | ||
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| === Meshing === | === Meshing === | ||
| - | In the following, we will run a python script within "CUBIT":http://cubit.sandia.gov to create the needed mesh files for the partitioner. | + | In the following, we will run a python script within [[http://cubit.sandia.gov/|CUBIT]] to create the needed mesh files for the partitioner. |
| 1. if not done so yet, change your working directory to the example folder: | 1. if not done so yet, change your working directory to the example folder: | ||
| []$ cd SPECFEM3D/examples/Mount_StHelens | []$ cd SPECFEM3D/examples/Mount_StHelens | ||
| - | 2. start the graphical user interface (GUI) of "CUBIT":http://cubit.sandia.gov: | + | 2. start the graphical user interface (GUI) of [[http://cubit.sandia.gov/|CUBIT]]: |
| [Mount_StHelens]$ claro | [Mount_StHelens]$ claro | ||
| Line 563: | Line 554: | ||
| nummaterial_velocity_file | nummaterial_velocity_file | ||
| - | you can also check if the export was successful by examining the output in the Command line window of CUBIT. | + | 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 | + | === 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. | + | 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. |
| 1. In case you can run parallel programs on your desktop (needs an MPI installation), you can simply run the script: | 1. In case you can run parallel programs on your desktop (needs an MPI installation), you can simply run the script: | ||
software/specfem3d/start.1388708381.txt.gz · Last modified: 2014/01/03 00:19 by emheien
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