use seissol v1.3/Rusanov fluxes/ vtkhdf/ extend tpv13 (#52)

* use rusanov

* fix Dockerfile_jupyterlab

* small improvements on tpv13_training.geo

* update to msh4

* switch to main

* update both dockers

* use latest releases of SeisSol and PUMGen

* use vtk output for fault

* add rupture speed exercise

* combine subsidence plots and fix typo in geo

* close plotter to avoid memory leak

* precise exercise and input file

* disable vtk fault output for now

* add small exercice related with the initial stress

* add sympy

* fix dictionnary

* more precise instructions

* fix missing import module and format files naemes and variables with

* add subtitle for ground deformation exercise

* improve exercise with varying dip

* add pandas (for moment rate release)

* fix bug intoduced previously

* change task title

* fix clim for Vr

Dockerfile

@@ -86,20 +86,15 @@ RUN git clone --recursive https://github.com/TUM-I5/ASAGI.git \
     && CC=mpicc CXX=mpicxx cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DSHARED_LIB=off -DSTATIC_LIB=on -DNONUMA=on \
     && make -j$(nproc) && make install
 
-RUN git clone https://github.com/uphoffc/ImpalaJIT.git \
-    && cd ImpalaJIT \
-    && mkdir build && cd build \
-    && cmake .. && make -j $(nproc) install 
-
 RUN git clone https://github.com/SeisSol/easi \
     && cd easi \
     && mkdir build && cd build \
-    && CC=mpicc CXX=mpicxx cmake .. -DEASICUBE=OFF -DLUA=ON -DCMAKE_PREFIX_PATH=/home/tools -DCMAKE_INSTALL_PREFIX=/home/tools -DASAGI=ON -DIMPALAJIT=ON .. \
+    && CC=mpicc CXX=mpicxx cmake .. -DEASICUBE=OFF -DLUA=ON -DCMAKE_PREFIX_PATH=/home/tools -DCMAKE_INSTALL_PREFIX=/home/tools -DASAGI=ON -DIMPALAJIT=OFF .. \
     && make -j$(nproc) && make install
 
 RUN pip install numpy && docker-clean
 
-RUN git clone --recursive --depth 1 --single-branch --branch v1.1.3 https://github.com/SeisSol/SeisSol.git \
+RUN git clone --recursive --depth 1 --single-branch --branch v1.3.0 https://github.com/SeisSol/SeisSol.git \
     && cd SeisSol \
     && mkdir build_hsw && cd build_hsw \
     && export PATH=$PATH:/home/tools/bin \
@@ -116,13 +111,7 @@ RUN cd SeisSol/preprocessing/science/rconv \
     && CC=mpicc CXX=mpicxx cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_PREFIX_PATH=/home/tools \
     && make -j$(nproc) && cp rconv /home/tools/bin/
 
-RUN git clone --recursive --depth 1 --single-branch --branch v2.2.7 https://github.com/SCOREC/core.git \
-    && cd core \
-    && mkdir build && cd build \
-    && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release -DSCOREC_CXX_FLAGS="-Wno-error=array-bounds" \
-    && make -j$(nproc) && make install
-
-RUN git clone --recursive --branch v1.0.1 https://github.com/SeisSol/PUMGen.git \
+RUN git clone --recursive --branch v1.1.0 https://github.com/SeisSol/PUMGen.git \
     && cd PUMGen \
     && mkdir build && cd build \
     && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release \
@@ -163,6 +152,8 @@ RUN conda install \
     matplotlib \
     gmsh \
     python-gmsh \
+    sympy \
+    pandas \
     && docker-clean
 ENV PATH=/home/tools/bin:$PATH
 ENV OMP_PLACES="cores"

Dockerfile_jupyterlab

@@ -93,7 +93,7 @@ RUN git clone https://github.com/SeisSol/easi \
     && CC=mpicc CXX=mpicxx cmake .. -DEASICUBE=OFF -DLUA=ON -DCMAKE_PREFIX_PATH=/home/tools -DCMAKE_INSTALL_PREFIX=/home/tools -DASAGI=ON -DIMPALAJIT=OFF .. \
     && make -j$(nproc) && make install
 
-RUN pip install numpy && pip install git+https://github.com/SeisSol/PSpaMM.git@davschneller/compile-fixes && docker-clean
+RUN pip install numpy && pip install git+https://github.com/SeisSol/PSpaMM.git && docker-clean
 
 #RUN git clone --depth 1 --single-branch --branch main https://github.com/libxsmm/libxsmm.git \
 #    && cd libxsmm \
@@ -104,7 +104,7 @@ RUN pip install numpy && pip install git+https://github.com/SeisSol/PSpaMM.git@d
 #       -j$(nproc) generator \
 #    && cp bin/libxsmm_gemm_generator /home/tools/bin
 
-RUN git clone --recursive --depth 1 --single-branch --branch v1.1.3 https://github.com/SeisSol/SeisSol.git \
+RUN git clone --recursive --depth 1 --single-branch --branch v1.3.0 https://github.com/SeisSol/SeisSol.git \
     && cd SeisSol \
     && mkdir build_hsw && cd build_hsw \
     && export PATH=$PATH:/home/tools/bin \
@@ -121,13 +121,7 @@ RUN cd SeisSol/preprocessing/science/rconv \
     && CC=mpicc CXX=mpicxx cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_PREFIX_PATH=/home/tools \
     && make -j$(nproc) && cp rconv /home/tools/bin/
 
-RUN git clone --recursive --depth 1 --single-branch --branch v2.2.7 https://github.com/SCOREC/core.git \
-    && cd core \
-    && mkdir build && cd build \
-    && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release -DSCOREC_CXX_FLAGS="-Wno-error=array-bounds" \
-    && make -j$(nproc) && make install
-
-RUN git clone --recursive https://github.com/SeisSol/PUMGen.git \
+RUN git clone --recursive --branch v1.1.0 https://github.com/SeisSol/PUMGen.git \
     && cd PUMGen \
     && mkdir build && cd build \
     && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release \
@@ -169,6 +163,8 @@ RUN conda install \
     matplotlib \
     gmsh \
     python-gmsh \
+    sympy \
+    pandas \
     && docker-clean
 ENV PATH=/home/tools/bin:$PATH
 ENV OMP_PLACES="cores"

kaikoura/parametersLSW.par

@@ -7,6 +7,8 @@ Tv=0.05
 !Attenuation parameters (ignored if not compiled with attenuation)
 FreqCentral=0.5
 FreqRatio=100
+numflux = 'rusanov' ! The numerical flux. Values: 'godunov', 'rusanov'
+numfluxnearfault = 'rusanov' ! The numerical flux for faces of cells adjacent to the fault (on cells which have at least one DR face), excluding the DR faces themselves. Values: 'godunov', 'rusanov'
 /
 
 &IniCondition

kaikoura/parametersRS.par

@@ -7,6 +7,9 @@ Tv=0.05
 !Attenuation parameters (ignored if not compiled with attenuation)
 FreqCentral=0.5
 FreqRatio=100
+
+numflux = 'rusanov' ! The numerical flux. Values: 'godunov', 'rusanov'
+numfluxnearfault = 'rusanov' ! The numerical flux for faces of cells adjacent to the fault (on cells which have at least one DR face), excluding the DR faces themselves. Values: 'godunov', 'rusanov'
 /
 
 &IniCondition

sulawesi/parametersLSW.par

@@ -7,6 +7,8 @@ Tv=0.05
 !Attenuation parameters (ignored if not compiled with attenuation)
 FreqCentral=0.3
 FreqRatio=100
+numflux = 'rusanov' ! The numerical flux. Values: 'godunov', 'rusanov'
+numfluxnearfault = 'rusanov' ! The numerical flux for faces of cells adjacent to the fault (on cells which have at least one DR face), excluding the DR faces themselves. Values: 'godunov', 'rusanov'
 /
 
 &IniCondition

sulawesi/parametersRS.par

@@ -7,6 +7,8 @@ Tv=0.05
 !Attenuation parameters (ignored if not compiled with attenuation)
 FreqCentral=0.3
 FreqRatio=100
+numflux = 'rusanov' ! The numerical flux. Values: 'godunov', 'rusanov'
+numfluxnearfault = 'rusanov' ! The numerical flux for faces of cells adjacent to the fault (on cells which have at least one DR face), excluding the DR faces themselves. Values: 'godunov', 'rusanov'
 /
 
 &IniCondition

tpv13/parameters.par

@@ -4,6 +4,8 @@ MaterialFileName = 'tpv12_13_material.yaml'
 !enable off-fault plasticity (ignored in Plasticity=0)
 Plasticity = 1
 Tv = 0.03
+numflux = 'rusanov' ! The numerical flux. Values: 'godunov', 'rusanov'
+numfluxnearfault = 'rusanov' ! The numerical flux for faces of cells adjacent to the fault (on cells which have at least one DR face), excluding the DR faces themselves. Values: 'godunov', 'rusanov'
 /
 
 &IniCondition
@@ -34,6 +36,7 @@ printtimeinterval_sec = 1.0                    ! Time interval at which output w
 OutputMask = 1 1 1 1 1 1 1 1 1 1 1             ! turn on and off fault outputs
 refinement_strategy = 2
 refinement = 1
+!vtkorder = 3
 /
 
 !parameterize ascii fault file outputs
@@ -68,8 +71,9 @@ refinement = 1
 
 ! Free surface output
 SurfaceOutput = 1
-SurfaceOutputRefinement = 1
+SurfaceOutputRefinement = 0
 SurfaceOutputInterval = 2.0
+surfacevtkorder = 2
 
 pickdt = 0.005                       ! Pickpoint Sampling
 RFileName = 'tpv12_13_receivers.dat'      ! Record Points in extra file

tpv13/tpv12_13_fault.yaml

@@ -1,26 +1,30 @@
 !Switch
 [s_xx, s_yy, s_zz, s_xy, s_yz, s_xz]: !Include tpv12_13_initial_stress.yaml
-[mu_s, mu_d, d_c, cohesion]: !IdentityMap
-  components:
-    # Inside nucleation patch
-    - !AxisAlignedCuboidalDomainFilter
-      limits:
-        x: [-1500, 1500]
-        y: [-.inf, .inf]
-        z: [-11691.34295108992, -9093.266739736605]
-      components: !ConstantMap
-        map:
-          mu_s:        0.54
-          mu_d:        0.10
-          d_c:         0.50
-          cohesion: -200000
-    # Outside nucleation patch
-    - !ConstantMap
+[mu_d, d_c, cohesion]: !ConstantMap
       map:
-        mu_s:        0.70
         mu_d:        0.10
         d_c:         0.50
         cohesion: -200000
+[mu_s]: !LuaMap
+  returns: [mu_s]
+  function: |
+    function f(x)
+        mu_s = 0.7
+        nucleation_size = 3000.0
+        along_width_nucleation_center = 12000.0
+        sinDip = math.sin(60 * math.pi / 180)
+        x_in_nucleation = (math.abs(x["x"]) <= 0.5 * nucleation_size)
+        z_in_nucleation = (
+            math.abs(x["z"] + along_width_nucleation_center * sinDip) <= 
+            0.5 * nucleation_size * sinDip
+        )     
+        if x_in_nucleation and z_in_nucleation then
+            mu_s = 0.54
+        end
+        
+        return { mu_s = mu_s }
+    end
+        
 [Tnuc_n, Tnuc_s, Tnuc_d, forced_rupture_time]: !ConstantMap
     map:
         Tnuc_n: 0

tpv13/tpv12_13_initial_stress.yaml

@@ -11,9 +11,10 @@
         depth = math.abs(x["z"])
         s_max_minus_Pf = 9.8 * (2700.0 - 1000.0);
         if (depth<=11951.15) then
+          s3_to_s1 = 0.3496
           -- math.floor(a+0.5) is round
-          s_xx =  -0.01 * math.floor(100.0 * (0.5 * (1.0 + 0.3496) * s_max_minus_Pf) + 0.5) * depth
-          s_yy =  -0.01 * math.floor(100.0 *               (0.3496 * s_max_minus_Pf) + 0.5) * depth
+          s_xx =  -0.01 * math.floor(100.0 * (0.5 * (1.0 + s3_to_s1) * s_max_minus_Pf) + 0.5) * depth
+          s_yy =  -0.01 * math.floor(100.0 *               (s3_to_s1 * s_max_minus_Pf) + 0.5) * depth
           s_zz = -s_max_minus_Pf * depth
         else
           s_xx = -s_max_minus_Pf * depth