Merge pull request #383 from PrincetonUniversity/issue-369

Issue 369 - Adds homework 9 from JT's class
PrincetonUniversity · Jan 15, 2025 · f22674a · f22674a
2 parents 5a91bdc + 0b5d3e3
commit f22674a
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -369,6 +369,7 @@ target_link_libraries(
 add_library(
         source_time_function
         src/source_time_function/dirac.cpp
+        src/source_time_function/dgaussian.cpp
         src/source_time_function/ricker.cpp
         src/source_time_function/external.cpp
 )

diff --git a/docs/source_description/source_discription.rst b/docs/source_description/source_discription.rst
@@ -60,6 +60,16 @@ Force Source Description
 
 **Description** : Definition of Ricker source :ref:`ricker_source_description`
 
+**Parameter Name** : ``sources.force.dGaussian`` [optional]
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : None
+
+**possible values** : [YAML Node]
+
+**Description** : Definition of first derivative of a Gaussian time function :ref:`dgaussian_source_description`
+
+
 **Parameter Name** : ``sources.force.External`` [optional]
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -156,6 +166,15 @@ Moment Tensor Source Description
 
 **Description** : Definition of Ricker source :ref:`ricker_source_description`
 
+**Parameter Name** : ``sources.moment-tensor.dGaussian`` [optional]
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : None
+
+**possible values** : [YAML Node]
+
+**Description** : Definition of first derivative Gaussian time function :ref:`dgaussian_source_description`
+
 **Parameter Name** : ``sources.moment-tensor.External`` [optional]
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/docs/source_description/source_time_function_description.rst b/docs/source_description/source_time_function_description.rst
@@ -93,6 +93,56 @@ Ricker Source Time Function Description
             tshift: 0.0
             f0: 1.0
 
+.. _dgaussian_source_description:
+
+Gaussian Derivative Source Time Function Description
+=======================================
+
+**Parameter Name** : ``dGaussian``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : None
+
+**possible values** : [YAML Node]
+
+**Description** : Definition of first derivative of a Gaussian source time function
+
+**Parameter Name** : ``dGaussian.factor``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : None
+
+**possible values** : [float]
+
+**Description** : Scaling factor for first derivative of a Gaussian time function
+
+**Parameter Name** : ``dGaussian.tshift``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : 0.0
+
+**possible values** : [float]
+
+**Description** : Time shift for first derivative of a Gaussian time function
+
+**Parameter Name** : ``dGaussian.f0``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**dafault value** : None
+
+**possible values** : [float]
+
+**Description** : Central frequency for first derivative of a Gaussian time function
+
+.. admonition:: Example
+
+    .. code-block:: yaml
+
+        dGaussian:
+            factor: 1e10
+            tshift: 0.0
+            f0: 1.0
+
 .. _external_source_description:
 
 External Source Time Function Description

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -2,5 +2,6 @@ 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)
+add_subdirectory(solid-solid-interface)
+add_subdirectory(Tromp_2005)
diff --git a/examples/solid-solid-interface/CMakeFiles/Par_File.in b/examples/solid-solid-interface/CMakeFiles/Par_File.in
@@ -0,0 +1,139 @@
+#-----------------------------------------------------------
+#
+# Simulation input parameters
+#
+#-----------------------------------------------------------
+
+# title of job
+title                           = Flat fluid/solid interface
+
+# parameters concerning partitioning
+NPROC                           = 1              # number of processes
+
+# Output folder to store mesh related files
+OUTPUT_FILES                   = @CMAKE_SOURCE_DIR@/examples/solid-solid-interface/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/solid-solid-interface/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                   = 1
+
+# 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                            = 150000.d0     # first receiver x in meters
+zdeb                            = 80000.d0      # first receiver z in meters
+xfin                            = 150000.d0     # last receiver x in meters (ignored if only one receiver)
+zfin                            = 3480000.d0    # 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/solid-solid-interface/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
+#
+# The problem values are as follows:
+# top:    rho = 2.60 * 10^3 kg/m3, kappa= 5.2 * 10^10 Pa, mu =2.66 * 10^10 Pa
+# bottom: rho = 3.38 * 10^3 kg/m3, kappa= 1.3 * 10^11 Pa, mu = 6.8 * 10^10 Pa
+# After conversion to VP/VS we have following model values.
+1 1 3380.d0 8079.98d0 4485.35d0 0 0 9999 9999 0 0 0 0 0 0
+2 1 2600.d0 5859.90d0 3199.40d0 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/solid-solid-interface/topography.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                            = 200000.d0     # abscissa of right side of the model
+nx                              = 188           # number of elements along X
+
+STACEY_ABSORBING_CONDITIONS    = .true.
+
+# 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
+1 188 1   38 1
+1 188 39  76 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/solid-solid-interface/CMakeFiles/specfem_config.yaml.in b/examples/solid-solid-interface/CMakeFiles/specfem_config.yaml.in
@@ -0,0 +1,54 @@
+## Coupling interfaces have code flow that is dependent on orientation of the interface.
+## This test is to check the code flow for horizontal acoustic-elastic interface with acoustic domain on top.
+
+parameters:
+
+  header:
+    ## Header information is used for logging. It is good practice to give your simulations explicit names
+    title: Heterogeneous elastic-elastic medium with 1 elastic-elastic interface (orientation horizontal)  # name for your simulation
+    # A detailed description for your simulation
+    description: |
+      Material systems : Elastic domain (1), Elastic domain (1)
+      Interfaces : Elastic-elastic interface (1) (orientation horizontal slower medium on top)
+      Sources : Force source (1)
+      Boundary conditions : Neumann BCs on all edges
+      Debugging comments: This tests checks coupling elastic-elastic interface implementation.
+                          The orientation of the interface is horizontal with elastic domain on top.
+
+  simulation-setup:
+    ## quadrature setup
+    quadrature:
+      quadrature-type: GLL4
+
+    ## Solver setup
+    solver:
+      time-marching:
+        type-of-simulation: forward
+        time-scheme:
+          type: Newmark
+          dt: 5.0e-3
+          nstep: 10000
+
+    simulation-mode:
+      forward:
+        writer:
+          seismogram:
+            format: ascii
+            directory: "@CMAKE_SOURCE_DIR@/examples/solid-solid-interface/OUTPUT_FILES/results"
+
+  receivers:
+    stations-file: "@CMAKE_SOURCE_DIR@/examples/solid-solid-interface/OUTPUT_FILES/STATIONS"
+    angle: 0.0
+    seismogram-type:
+      - displacement
+    nstep_between_samples: 1
+
+  ## Runtime setup
+  run-setup:
+    number-of-processors: 1
+    number-of-runs: 1
+
+  ## databases
+  databases:
+    mesh-database: "@CMAKE_SOURCE_DIR@/examples/solid-solid-interface/OUTPUT_FILES/database.bin"
+    source-file: "@CMAKE_SOURCE_DIR@/examples/solid-solid-interface/sources.yaml"
diff --git a/examples/solid-solid-interface/CMakeLists.txt b/examples/solid-solid-interface/CMakeLists.txt
@@ -0,0 +1,5 @@
+
+CMAKE_MINIMUM_REQUIRED(VERSION 3.17.5)
+
+configure_file(CMakeFiles/specfem_config.yaml.in ${CMAKE_SOURCE_DIR}/examples/solid-solid-interface/specfem_config.yaml)
+configure_file(CMakeFiles/Par_File.in ${CMAKE_SOURCE_DIR}/examples/solid-solid-interface/Par_File)
diff --git a/examples/solid-solid-interface/README.md b/examples/solid-solid-interface/README.md
@@ -0,0 +1,48 @@
+# Wave propagration through solid-solid interface
+
+This example is for a solid-solid simulation that is often used in Jeroen
+Tromp's Computational Seismology course at Princeton University.
+
+For a step-by-step guide on this example, please refer to the
+[documentation](https://specfem2d-kokkos.readthedocs.io/en/latest/cookbooks/dim2/solid-solid-interface/index.html).
+
+## 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
+
+```