Added setup for the March 11, 2011, M 9.1 Tohoku tsunami event.

.gitattributes

@@ -31,6 +31,9 @@
 # err files (typically archived output of runs)
 *.err filter=lfs diff=lfs merge=lfs -text
 
+# postscript files (typically plots)
+*.ps filter=lfs diff=lfs merge=lfs -text
+
 # PDF files (typically plots)
 *.pdf filter=lfs diff=lfs merge=lfs -text
 

bench/tsunami/tohoku/README.rst

+March 11, 2011, M 9.1 Tohoku tsunami event
+==========================================
+This directory contains input and output for a simulation of the March 11, 2011, M 9.1 Tohoku tsunami event.
+The bathymetry and displacement data were projected to a flat domain using the transverse Mercator projection with a projection center in the vicinity of the epicenter.
+Additionally, a scale factor of 0.9996 was used.
+The mesh-refined considered the wave speeds in the computational domain with the highest resolution at the shore line.
+
+A hard dry tolerance of -50m was used in the simulations.
+Potential aliasing issues when converting and accessing the geo-data were ignored.
+
+* Contact: Alexander Breuer

bench/tsunami/tohoku/configs/tohoku.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  @file This file is part of EDGE.
+
+  @author Alexander Breuer (alex.breuer AT uni-jena.de)
+
+  @section LICENSE
+  Copyright (c) 2020-2021, Friedrich Schiller University Jena
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+  3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+  @section DESCRIPTION
+  Config for the March 11, 2011, M 9.1 Tohoku tsunami event.
+-->
+<edge>
+  <cfr>
+    <mesh>
+        <in>
+          <base>meshes/gen/tohoku</base>
+          <extension>.msh</extension>
+        </in>
+      <boundary>
+        <outflow>105</outflow>
+      </boundary>
+    </mesh>
+
+    <setups>
+      <end_time>7500</end_time>
+    </setups>
+
+    <output>
+      <wave_field>
+        <type>vtk_binary</type>
+        <file>tohoku/wf</file>
+        <int>50</int>
+      </wave_field>
+    </output>
+  </cfr>
+</edge>
+

bench/tsunami/tohoku/meshes/README.rst

+Used commands:
+
+.. code-block: bash
+
+  ./generate.sh 2>&1 | tee generate.sh.log

bench/tsunami/tohoku/meshes/data/README.rst

+This data has been generated using the tools at https://github.com/breuera/tsunami in revision c98e0f8f740d1598623c8573251b9e481035923c.

bench/tsunami/tohoku/meshes/data/grids/CC0.md

+[![CC0](http://i.creativecommons.org/p/zero/1.0/88x31.png)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+To the extent possible under law, [Alexander Nikolas Breuer](http://dial3343.org) has waived all copyright and related or neighboring rights to the following work:
+
+* `tohoku_gebco20_250m_bath.nc`
+* `tohoku_gebco20_50m_bath.nc`
+* `tohoku_ucsb3_250m_displ.nc`
+* `tohoku_usgs_250m_displ.nc`
+
+This work is published from: Germany.

bench/tsunami/tohoku/meshes/data/plots/CC0.md

+[![CC0](http://i.creativecommons.org/p/zero/1.0/88x31.png)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+To the extent possible under law, [Alexander Nikolas Breuer](http://dial3343.org) has waived all copyright and related or neighboring rights to the following work:
+
+* `tohoku_gebco20_ucsb3_250m_displ.pdf`
+* `tohoku_gebco20_ucsb3_250m_overview.ps`
+* `tohoku_gebco20_ucsb3_50m_displ.pdf`
+* `tohoku_gebco20_ucsb3_50m_overview.ps`
+* `tohoku_gebco20_usgs_250m_displ.pdf`
+* `tohoku_gebco20_usgs_250m_overview.ps`
+
+This work is published from: Germany.

bench/tsunami/tohoku/meshes/generate.sh

+mkdir gen
+
+# generate initial mesh
+echo "####################"
+echo "### initial mesh ###"
+echo "####################"
+echo $(date)
+gmsh -2 tohoku.geo -o gen/tohoku_refined.msh
+
+# perform mesh refinemnt steps
+for l_re in $(seq 1 10)
+do
+  echo "###########################"
+  echo "### refinement #${l_re} ###"
+  echo "###########################"
+  echo $(date)
+  edge_v -x tohoku.xml
+  gmsh -2 tohoku.geo -bgm gen/tohoku_bgm.msh -o gen/tohoku_refined.msh
+done
+
+echo "##################"
+echo "### final mesh ###"
+echo "##################"
+echo $(date)
+edge_v -x tohoku.xml

bench/tsunami/tohoku/meshes/tohoku.geo

+cl = 10000;
+
+
+// domain
+Point(1) = { -195000, -745000,    0, cl };
+Point(2) = { 1500000, -745000,    0, cl };
+Point(3) = { 1500000, 745000, 0, cl };
+Point(4) = { -195000, 745000, 0, cl };
+
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+
+Line Loop(101) = { 1, 2, 3, 4};
+Plane Surface(201) = {101};
+
+// volume
+Physical Surface("region_0") = {201};
+
+// periodic boundaries
+//Periodic Line {1} = {-3};
+//Periodic Line {2} = {-4};
+
+// here's the boundary tag.
+Physical Line(105) = {1, 2, 3, 4};
\ No newline at end of file

bench/tsunami/tohoku/meshes/tohoku.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  @file This file is part of EDGE.
+
+  @author Alexander Breuer (alex.breuer AT uni-jena.de)
+
+  @section LICENSE
+  Copyright (c) 2020-2021, Friedrich Schiller University Jena
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+  3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+  @section DESCRIPTION
+  EDGE-V configuration for the depth-adapted mesh of the pacific for the 2011 Tohoku event.
+-->
+<edge_v>
+  <mesh>
+    <periodic>no</periodic>
+    <write_element_annotations>0</write_element_annotations>
+    <n_partitions>1</n_partitions>
+    <files>
+      <in>gen/tohoku_refined.msh</in>
+      <out>
+        <base>gen/tohoku</base>
+        <extension>.msh</extension>
+      </out>
+    </files>
+  </mesh>
+
+  <velocity_model>
+    <tsunami>
+      <dry_tolerance>-100</dry_tolerance>
+      <bathymetry>data/grids/tohoku_gebco20_50m_bath.nc</bathymetry>
+      <displacements>data/grids/tohoku_ucsb3_250m_displ.nc</displacements>
+      <displacements>data/grids/tohoku_usgs_250m_displ.nc</displacements>
+      <expression>
+        <![CDATA[
+          var shore_speed := sqrt( 9.81 * 100 ) / 5;
+
+          if( data < -1500 ) {
+            var speed := sqrt( 9.81 * -data );
+            min_speed := speed;
+            max_speed := speed;
+          }
+          else if( data < -100 ) {
+            var speed := sqrt( 9.81 * -data );
+            min_speed := speed / ( 1 + (data + 1500)/(1400*0.25) );
+            max_speed := speed / ( 1 + (data + 1500)/(1400*0.25) );
+          }
+          else if( data < 50 ) {
+            min_speed := shore_speed;
+            max_speed := shore_speed;
+          }
+          else {
+            var dry_speed := shore_speed + sqrt( 9.81 * (data-50) ) * 2.5;
+            min_speed := dry_speed;
+            max_speed := dry_speed;
+          }
+      ]]>
+      </expression>
+    </tsunami>
+  </velocity_model>
+  <refinement>
+    <expression>
+      <![CDATA[
+        edges_per_wave_length := 2.5;
+        frequency := 0.01;
+
+        // decrease edge length at discontinuities
+        if( maximum_wave_speed_ratio > 1.5 ) {
+          edges_per_wave_length *= 2; 
+        }
+      ]]>
+    </expression>
+    <out>gen/tohoku_bgm.msh</out>
+  </refinement>
+
+  <time>
+    <n_groups>1</n_groups>
+    <files>
+      <out>
+        <time_steps>gen/time_steps.csv</time_steps>
+      </out>
+    </files>
+  </time>
+</edge_v>

bench/tsunami/tohoku/runs/README.rst

+Used commands:
+
+.. code-block: bash
+
+   OMP_NUM_THREADS=4 edge -x configs/tohoku.xml 2>&1 | tee edge.log

bench/tsunami/tohoku/runs/configs

+../configs
\ No newline at end of file

bench/tsunami/tohoku/runs/meshes

+../meshes
\ No newline at end of file

bench/tsunami/tohoku/runs/vis/first_sim/CC0.md

+[![CC0](http://i.creativecommons.org/p/zero/1.0/88x31.png)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+To the extent possible under law, [Alexander Nikolas Breuer](http://dial3343.org) has waived all copyright and related or neighboring rights to the following work:
+
+* `wf.0000.png`
+* `wf.0001.png`
+* `wf.0002.png`
+* `wf.0003.png`
+* `wf.0004.png`
+* `wf.0005.png`
+* `wf.0006.png`
+* `wf.0007.png`
+* `wf.0008.png`
+* `wf.0009.png`
+* `wf.0010.png`
+* `wf.0011.png`
+* `wf.0012.png`
+* `wf.0013.png`
+* `wf.0014.png`
+* `wf.0015.png`
+* `wf.0016.png`
+* `wf.0017.png`
+* `wf.0018.png`
+* `wf.0019.png`
+* `wf.0020.png`
+* `wf.0021.png`
+* `wf.0022.png`
+* `wf.0023.png`
+* `wf.0024.png`
+* `wf.0025.png`
+* `wf.0026.png`
+* `wf.0027.png`
+* `wf.0028.png`
+* `wf.0029.png`
+* `wf.0030.png`
+* `wf.0031.png`
+* `wf.0032.png`
+* `wf.0033.png`
+* `wf.0034.png`
+* `wf.0035.png`
+* `wf.0036.png`
+* `wf.0037.png`
+* `wf.0038.png`
+* `wf.0039.png`
+* `wf.0040.png`
+* `wf.0041.png`
+* `wf.0042.png`
+* `wf.0043.png`
+* `wf.0044.png`
+* `wf.0045.png`
+* `wf.0046.png`
+* `wf.0047.png`
+* `wf.0048.png`
+* `wf.0049.png`
+* `wf.0050.png`
+* `wf.0051.png`
+* `wf.0052.png`
+* `wf.0053.png`
+* `wf.0054.png`
+* `wf.0055.png`
+* `wf.0056.png`
+* `wf.0057.png`
+* `wf.0058.png`
+* `wf.0059.png`
+* `wf.0060.png`
+* `wf.0061.png`
+* `wf.0062.png`
+* `wf.0063.png`
+* `wf.0064.png`
+* `wf.0065.png`
+* `wf.0066.png`
+* `wf.0067.png`
+* `wf.0068.png`
+* `wf.0069.png`
+* `wf.0070.png`
+* `wf.0071.png`
+* `wf.0072.png`
+* `wf.0073.png`
+* `wf.0074.png`
+* `wf.0075.png`
+* `wf.0076.png`
+* `wf.0077.png`
+* `wf.0078.png`
+* `wf.0079.png`
+* `wf.0080.png`
+* `wf.0081.png`
+* `wf.0082.png`
+* `wf.0083.png`
+* `wf.0084.png`
+* `wf.0085.png`
+* `wf.0086.png`
+* `wf.0087.png`
+* `wf.0088.png`
+* `wf.0089.png`
+* `wf.0090.png`
+* `wf.0091.png`
+* `wf.0092.png`
+* `wf.0093.png`
+* `wf.0094.png`
+* `wf.0095.png`
+* `wf.0096.png`
+* `wf.0097.png`
+* `wf.0098.png`
+* `wf.0099.png`
+* `wf.0100.png`
+* `wf.0101.png`
+* `wf.0102.png`
+* `wf.0103.png`
+* `wf.0104.png`
+* `wf.0105.png`
+* `wf.0106.png`
+* `wf.0107.png`
+* `wf.0108.png`
+* `wf.0109.png`
+* `wf.0110.png`
+* `wf.0111.png`
+* `wf.0112.png`
+* `wf.0113.png`
+* `wf.0114.png`
+* `wf.0115.png`
+* `wf.0116.png`
+* `wf.0117.png`
+* `wf.0118.png`
+* `wf.0119.png`
+* `wf.0120.png`
+* `wf.0121.png`
+* `wf.0122.png`
+* `wf.0123.png`
+* `wf.0124.png`
+* `wf.0125.png`
+* `wf.0126.png`
+* `wf.0127.png`
+* `wf.0128.png`
+* `wf.0129.png`
+* `wf.0130.png`
+* `wf.0131.png`
+* `wf.0132.png`
+* `wf.0133.png`
+* `wf.0134.png`
+* `wf.0135.png`
+* `wf.0136.png`
+* `wf.0137.png`
+* `wf.0138.png`
+* `wf.0139.png`
+* `wf.0140.png`
+* `wf.0141.png`
+* `wf.0142.png`
+* `wf.0143.png`
+* `wf.0144.png`
+* `wf.0145.png`
+* `wf.0146.png`
+* `wf.0147.png`
+* `wf.0148.png`
+* `wf.0149.png`
+* `wf.0150.png`
+
+This work is published from: Germany.