Merge pull request #241 from PrincetonUniversity/issue-158

Fluid solid bathymetry
PrincetonUniversity · Dec 17, 2024 · 8c5acab · 8c5acab
2 parents d11bc97 + 0e55182
commit 8c5acab
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diff --git a/docs/source_description/source_discription.rst b/docs/source_description/source_discription.rst
@@ -84,7 +84,7 @@ Force Source Description
 Moment Tensor Source Description
 ================================
 
-**Parameter Name** : ``sources.moment_tensor``
+**Parameter Name** : ``sources.moment-tensor``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -93,7 +93,7 @@ Moment Tensor Source Description
 
 **Description** : Definition of moment tensor source
 
-**Parameter Name** : ``sources.moment_tensor.x``
+**Parameter Name** : ``sources.moment-tensor.x``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -102,7 +102,7 @@ Moment Tensor Source Description
 
 **Description** : X coordinate location of the moment tensor source.
 
-**Parameter Name** : ``sources.moment_tensor.z``
+**Parameter Name** : ``sources.moment-tensor.z``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -111,7 +111,7 @@ Moment Tensor Source Description
 
 **Description** : Z coordinate location of the moment tensor source.
 
-**Parameter Name** : ``sources.moment_tensor.Mxx``
+**Parameter Name** : ``sources.moment-tensor.Mxx``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -120,7 +120,7 @@ Moment Tensor Source Description
 
 **Description** : Mxx moment tensor component.
 
-**Parameter Name** : ``sources.moment_tensor.Mzz``
+**Parameter Name** : ``sources.moment-tensor.Mzz``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -129,7 +129,7 @@ Moment Tensor Source Description
 
 **Description** : Mzz moment tensor component.
 
-**Parameter Name** : ``sources.moment_tensor.Mxz``
+**Parameter Name** : ``sources.moment-tensor.Mxz``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -138,7 +138,7 @@ Moment Tensor Source Description
 
 **Description** : Mxz moment tensor component.
 
-**Parameter Name** : ``sources.moment_tensor.Dirac`` [optional]
+**Parameter Name** : ``sources.moment-tensor.Dirac`` [optional]
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -147,7 +147,7 @@ Moment Tensor Source Description
 
 **Description** : Definition of Dirac source :ref:`dirac_source_description`
 
-**Parameter Name** : ``sources.moment_tensor.Ricker`` [optional]
+**Parameter Name** : ``sources.moment-tensor.Ricker`` [optional]
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -156,7 +156,7 @@ Moment Tensor Source Description
 
 **Description** : Definition of Ricker source :ref:`ricker_source_description`
 
-**Parameter Name** : ``sources.moment_tensor.External`` [optional]
+**Parameter Name** : ``sources.moment-tensor.External`` [optional]
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **dafault value** : None
@@ -169,7 +169,7 @@ Moment Tensor Source Description
 
     .. code-block:: yaml
 
-        moment_tensor:
+        moment-tensor:
             x: 0.0
             z: 0.0
             Mxx: 1e10

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -3,3 +3,4 @@ cmake_minimum_required(VERSION 3.17.5)
 add_subdirectory(homogeneous-medium-flat-topography)
 add_subdirectory(fluid-solid-interface)
 add_subdirectory(Tromp_2005)
+add_subdirectory(fluid-solid-bathymetry)
diff --git a/examples/Tromp_2005/CMakeFiles/Snakefile.in b/examples/Tromp_2005/CMakeFiles/Snakefile.in
@@ -229,6 +229,10 @@ rule plot_kernels:
     run:
         from plot import plot_kernels
 
+        # Set matplotlib gui off
+        import matplotlib
+        matplotlib.use("Agg")
+
         plot_kernels(input.kernels, output.plot)
 
 

diff --git a/examples/fluid-solid-bathymetry/.gitignore b/examples/fluid-solid-bathymetry/.gitignore
@@ -0,0 +1,4 @@
+specfem_config.yaml
+Par_File
+line_sources.yaml
+__pycache__
diff --git a/examples/fluid-solid-bathymetry/CMakeFiles/Par_File.in b/examples/fluid-solid-bathymetry/CMakeFiles/Par_File.in
@@ -0,0 +1,143 @@
+#-----------------------------------------------------------
+#
+# Simulation input parameters
+#
+#-----------------------------------------------------------
+
+# title of job
+title                           = fluid-solid-bathymetry
+
+# parameters concerning partitioning
+NPROC                           = 1              # number of processes
+
+# Output folder to store mesh related files
+OUTPUT_FILES                   = @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES
+
+#-----------------------------------------------------------
+#
+# Mesh
+#
+#-----------------------------------------------------------
+
+# Partitioning algorithm for decompose_mesh
+PARTITIONING_TYPE               = 3              # SCOTCH = 3, ascending order (very bad idea) = 1
+
+# number of control nodes per element (4 or 9)
+NGNOD                           = 9
+
+# location to store the mesh
+database_filename               = @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/database.bin
+
+#-----------------------------------------------------------
+#
+# Receivers
+#
+#-----------------------------------------------------------
+
+# use an existing STATION file found in ./DATA or create a new one from the receiver positions below in this Par_file
+use_existing_STATIONS           = .false.
+
+# number of receiver sets (i.e. number of receiver lines to create below)
+nreceiversets                   = 2
+
+# orientation
+anglerec                        = 0.d0           # angle to rotate components at receivers
+rec_normal_to_surface           = .false.        # base anglerec normal to surface (external mesh and curve file needed)
+
+# first receiver set (repeat these 6 lines and adjust nreceiversets accordingly)
+nrec                            = 1              # number of receivers
+xdeb                            = 1.000d+04      # first receiver x in meters
+zdeb                            = 8.082d+03      # first receiver z in meters
+xfin                            = 1.000d+04      # last receiver x in meters (ignored if only one receiver)
+zfin                            = 8.082d+03      # last receiver z in meters (ignored if only one receiver)
+record_at_surface_same_vertical = .false.        # receivers inside the medium or at the surface
+
+
+# second receiver set (repeat these 6 lines and adjust nreceiversets accordingly)
+nrec                            = 1              # number of receivers
+xdeb                            = 1.000d+04      # first receiver x in meters
+zdeb                            = 5.472d+03      # first receiver z in meters
+xfin                            = 1.000d+04      # last receiver x in meters (ignored if only one receiver)
+zfin                            = 5.472d+03      # last receiver z in meters (ignored if only one receiver)
+record_at_surface_same_vertical = .false.        # receivers inside the medium or at the surface
+
+# filename to store stations file
+stations_filename              = @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/STATIONS
+
+#-----------------------------------------------------------
+#
+# Velocity and density models
+#
+#-----------------------------------------------------------
+
+# number of model materials
+nbmodels                        = 2
+# available material types (see user manual for more information)
+#   acoustic:    model_number 1 rho Vp 0  0 0 QKappa Qmu 0 0 0 0 0 0
+#   elastic:     model_number 1 rho Vp Vs 0 0 QKappa Qmu 0 0 0 0 0 0
+#   anistoropic: model_number 2 rho c11 c13 c15 c33 c35 c55 c12 c23 c25 0 0 0
+#   poroelastic: model_number 3 rhos rhof phi c kxx kxz kzz Ks Kf Kfr etaf mufr Qmu
+#   tomo:        model_number -1 0 9999 9999 A 0 0 9999 9999 0 0 0 0 0
+1 1 2500.d0 3400.d0 1963.d0 0 0 9999 9999 0 0 0 0 0 0
+2 1 1020.d0 1500.d0 0.d0 0 0 9999 9999 0 0 0 0 0 0
+
+# external tomography file
+TOMOGRAPHY_FILE                 = ./DATA/tomo_file.xyz
+
+# use an external mesh created by an external meshing tool or use the internal mesher
+read_external_mesh              = .false.
+
+#-----------------------------------------------------------
+#
+# PARAMETERS FOR EXTERNAL MESHING
+#
+#-----------------------------------------------------------
+
+# data concerning mesh, when generated using third-party app (more info in README)
+# (see also absorbing_conditions above)
+mesh_file                       = ./DATA/Mesh_canyon/canyon_mesh_file   # file containing the mesh
+nodes_coords_file               = ./DATA/Mesh_canyon/canyon_nodes_coords_file   # file containing the nodes coordinates
+materials_file                  = ./DATA/Mesh_canyon/canyon_materials_file   # file containing the material number for each element
+free_surface_file               = ./DATA/Mesh_canyon/canyon_free_surface_file   # file containing the free surface
+axial_elements_file             = ./DATA/axial_elements_file   # file containing the axial elements if AXISYM is true
+absorbing_surface_file          = ./DATA/Mesh_canyon/canyon_absorbing_surface_file   # file containing the absorbing surface
+acoustic_forcing_surface_file   = ./DATA/MSH/Surf_acforcing_Bottom_enforcing_mesh   # file containing the acoustic forcing surface
+absorbing_cpml_file             = ./DATA/absorbing_cpml_file   # file containing the CPML element numbers
+tangential_detection_curve_file = ./DATA/courbe_eros_nodes  # file containing the curve delimiting the velocity model
+
+#-----------------------------------------------------------
+#
+# PARAMETERS FOR INTERNAL MESHING
+#
+#-----------------------------------------------------------
+
+# file containing interfaces for internal mesh
+interfacesfile                  = @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/topography_file.dat
+
+# geometry of the model (origin lower-left corner = 0,0) and mesh description
+xmin                            = 0.d0             # abscissa of left side of the model
+xmax                            = 2.000d+04        # abscissa of right side of the model
+nx                              = 250              # number of elements along X
+
+STACEY_ABSORBING_CONDITIONS       = .true.        # use Stacey absorbing boundary conditions
+
+# absorbing boundary parameters (see absorbing_conditions above)
+absorbbottom                    = .true.
+absorbright                     = .true.
+absorbtop                       = .false.
+absorbleft                      = .true.
+
+# define the different regions of the model in the (nx,nz) spectral-element mesh
+nbregions                       = 2              # then set below the different regions and model number for each region
+1 250 1   62  1
+1 250 63  120 2
+
+#-----------------------------------------------------------
+#
+# DISPLAY PARAMETERS
+#
+#-----------------------------------------------------------
+
+# meshing output
+output_grid_Gnuplot             = .false.        # generate a GNUPLOT file containing the grid, and a script to plot it
+output_grid_ASCII               = .false.        # dump the grid in an ASCII text file consisting of a set of X,Y,Z points or not
diff --git a/examples/fluid-solid-bathymetry/CMakeFiles/specfem_config.yaml.in b/examples/fluid-solid-bathymetry/CMakeFiles/specfem_config.yaml.in
@@ -0,0 +1,56 @@
+parameters:
+
+  header:
+    ## Header information is used for logging. It is good practice to give your simulations explicit names
+    title: fluid-solid-bathymetry  # name for your simulation
+    # A detailed description for your simulation
+    description: |
+      Material systems : Elastic domain (1), Acoustic domain (1)
+      Interfaces : Acoustic-elastic interface (1) (orientation horizontal with acoustic domain on top)
+      Sources : Moment-tensor (234)
+      Boundary conditions : Neumann BCs on all edges
+
+  simulation-setup:
+    ## quadrature setup
+    quadrature:
+      quadrature-type: GLL4
+
+    ## Solver setup
+    solver:
+      time-marching:
+        type-of-simulation: forward
+        time-scheme:
+          type: Newmark
+          dt: 1.000e-3
+          nstep: 32500
+
+    simulation-mode:
+      forward:
+        writer:
+          seismogram:
+            format: ascii
+            directory: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/results
+
+          display:
+            format: PNG
+            directory: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/display
+            field: displacement
+            simulation-field: forward
+            time-interval: 100
+
+  receivers:
+    stations-file: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/STATIONS
+    angle: 0.0
+    seismogram-type:
+      - pressure
+    nstep_between_samples: 10
+
+  ## Runtime setup
+  run-setup:
+    number-of-processors: 1
+    number-of-runs: 1
+
+  ## databases
+  databases:
+    mesh-database: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/database.bin
+    source-file: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/line_sources.yaml
diff --git a/examples/fluid-solid-bathymetry/CMakeLists.txt b/examples/fluid-solid-bathymetry/CMakeLists.txt
@@ -0,0 +1,5 @@
+
+CMAKE_MINIMUM_REQUIRED(VERSION 3.17.5)
+
+configure_file(CMakeFiles/specfem_config.yaml.in ${CMAKE_SOURCE_DIR}/examples/fluid-solid-bathymetry/specfem_config.yaml)
+configure_file(CMakeFiles/Par_File.in ${CMAKE_SOURCE_DIR}/examples/fluid-solid-bathymetry/Par_File)
diff --git a/examples/fluid-solid-bathymetry/README.md b/examples/fluid-solid-bathymetry/README.md
@@ -0,0 +1,39 @@
+# Wave propagration through fluid-solid interface
+
+This example simulates a tele-seismic plane wave within a fluid-solid domain. This example is contributed by Sirawich Pipatprathanporn and is part of the publication [Pipatprathanporn et al. (2024)](https://doi.org/10.1093/gji/ggae238)
+
+## Running the examples
+
+To run the examples, you first need to install poetry following these [instructions](https://python-poetry.org/docs/#installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
+
+```bash
+# verify poetry is installed
+poetry --version
+
+# install dependencies
+poetry install
+
+```
+
+After installing the dependencies, you can run the examples by running the following command within the example directory you want to run:
+
+```bash
+
+# run the example
+poetry run snakemake -j 1
+
+# or to run the example on a slurm cluster
+poetry run snakemake --executor slurm -j 1
+
+```
+
+## Cleaning up
+
+To clean up the example directory, you can run the following command in the directory of the example you want to clean up:
+
+```bash
+
+# clean up the example
+poetry run snakemake clean
+
+```