Merge branch 'devel' into issue-390

.pre-commit-config.yaml

@@ -11,13 +11,13 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v14.0.5"
+    rev: "v14.0.6"
     hooks:
       - id: clang-format
         types_or: [c++]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.9.1
     hooks:
       # Run the linter.
       - id: ruff

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
 )

docs/cookbooks/dim2/fluid-solid-interface/Par_file

@@ -0,0 +1,134 @@
+#-----------------------------------------------------------
+#
+# 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                   = 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               = 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                            = 11            # number of receivers
+xdeb                            = 1450.d0        # first receiver x in meters
+zdeb                            = 2400   # first receiver z in meters
+xfin                            = 1575.d0        # last receiver x in meters (ignored if only one receiver)
+zfin                            = 3400   # 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              = 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                  = 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                            = 6400.d0        # abscissa of right side of the model
+nx                              = 144            # 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                       = .true.
+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
+1 144 1   54 1
+1 144 55 108 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

docs/cookbooks/dim2/fluid-solid-interface/index.rst

@@ -0,0 +1,153 @@
+Wave propagration through fluid-solid interface
+===============================================
+
+This `example <https://github.com/PrincetonUniversity/SPECFEMPP/tree/main/examples/fluid-solid-interface>`_ simulates the fluid-solid example with flat ocean bottom from `Komatitsch et. al. <https://doi.org/10.1190/1.1444758>`_. This example demonstrates the use of the ``xmeshfem2D`` mesher to generate interface between 2 conforming material systems and the setting up absorbing boundary conditions.
+
+Setting up the workspace
+------------------------
+
+Let's start by creating a workspace from where we can run this example.
+
+.. code-block:: bash
+
+    mkdir -p ~/specfempp-examples/fluid-solid-interface
+    cd ~/specfempp-examples/fluid-solid-interface
+
+We also need to check that the SPECFEM++ build directory is added to the ``PATH``.
+
+.. code:: bash
+
+    which specfem2d
+
+If the above command returns a path to the ``specfem2d`` executable, then the build directory is added to the ``PATH``. If not, you need to add the build directory to the ``PATH`` using the following command.
+
+.. code:: bash
+
+    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY/bin>
+
+.. note::
+
+    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY/bin>`` with the actual path to the SPECFEM++ build directory on your system.
+
+Now let's create the necessary directories to store the input files and output artifacts.
+
+.. code:: bash
+
+    mkdir -p OUTPUT_FILES
+    mkdir -p OUTPUT_FILES/seismograms
+
+    touch specfem_config.yaml
+    touch single_source.yaml
+    touch topography_file.dat
+    touch Par_File
+
+
+Meshing the domain
+------------------
+
+We first start by generating a mesh for our simulation domain using
+``xmeshfem2D``. To do this, we first define our simulation domain and the
+meshing parmeters in a parameter file.
+
+Parameter file
+~~~~~~~~~~~~~~
+
+.. literalinclude:: Par_File
+    :language: bash
+    :emphasize-lines: 65,72-73,113-119
+    :caption: Par_File
+
+- We define the acoustic and elastic velocity models in the `Velocity and
+  density models` section of the parameter file.
+
+  .. literalinclude:: Par_File
+    :language: bash
+    :lineno-match:
+    :linenos:
+    :start-at: nbmodels
+    :end-at: nbmodels
+
+  defines the number of material systems in the simulation domain. We then
+  define the isotropic velocity model for each material system using the
+  following format: ``model_number 1 rho Vp Vs 0 0 QKappa Qmu 0 0 0 0 0 0``.
+  Such model 1 is
+
+  .. literalinclude:: Par_File
+      :language: bash
+      :lineno-match:
+      :linenos:
+      :start-at: 1 1
+      :end-at: 1 1
+
+  and model 2 is
+
+  .. literalinclude:: Par_File
+      :language: bash
+      :lineno-match:
+      :linenos:
+      :start-at: 2 1
+      :end-at: 2 1
+
+- We define stacey absorbing boundary conditions on all the edges of the domain
+  using the ``STACEY_ABSORBING_CONDITIONS``, ``absorbbottom``, ``absorbright``,
+  ``absorbtop`` and ``absorbleft`` parameters.
+
+  .. literalinclude:: Par_File
+      :language: bash
+      :lineno-match:
+      :linenos:
+      :start-at: STACEY_ABSORBING_CONDITIONS
+      :end-at: absorbleft
+
+
+Defining the topography of the domain
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+We define the topography of the domain using the following topography file
+
+.. literalinclude:: topography_file.dat
+    :caption: topography_file.dat
+    :language: bash
+
+
+
+Running ``xmeshfem2D``
+~~~~~~~~~~~~~~~~~~~~~~
+
+To execute the mesher run
+
+.. code:: bash
+
+    xmeshfem2D -p Par_File
+
+.. note::
+
+    Make sure either your are in the build directory of SPECFEM2D kokkos or the
+    ``../path/to/build/bin`` directory is added to your ``PATH``.
+
+Note the path of the database file and a stations file generated after
+successfully running the mesher.
+
+Defining the source
+~~~~~~~~~~~~~~~~~~~
+
+We define the source location and the source time function in the source file.
+
+.. literalinclude:: single_source.yaml
+    :caption: single_source.yaml
+
+
+Running the simulation
+----------------------
+
+To run the solver, we first need to define a configuration file ``specfem_config.yaml``.
+
+.. literalinclude:: specfem_config.yaml
+    :language: yaml
+    :caption: specfem_config.yaml
+
+With the configuration file in place, we can run the solver using the following command
+
+.. code:: bash
+
+    specfem2d -p specfem_config.yaml

docs/cookbooks/dim2/fluid-solid-interface/single_source.yaml

@@ -0,0 +1,13 @@
+number-of-sources: 1
+sources:
+  - force:
+      x : 1575.0
+      z : 2900.0
+      source_surf: false
+      angle : 0.0
+      vx : 0.0
+      vz : 0.0
+      Ricker:
+        factor: 1e9
+        tshift: 0.0
+        f0: 10.0

docs/cookbooks/dim2/fluid-solid-interface/specfem_config.yaml

@@ -0,0 +1,51 @@
+parameters:
+
+header:
+  ## Header information is used for logging. It is good practice to give your simulations explicit names
+  title: Heterogeneous acoustic-elastic medium with 1 acoustic-elastic interface (orientation horizontal)  # 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 : Force source (1)
+    Boundary conditions : Neumann BCs on all edges
+    Debugging comments: This tests checks coupling acoustic-elastic interface implementation.
+                        The orientation of the interface is horizontal with acoustic 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: 0.85e-3
+        nstep: 600
+
+  simulation-mode:
+    forward:
+      writer:
+        seismogram:
+          format: ascii
+          directory: OUTPUT_FILES/seismograms
+
+receivers:
+  stations-file: 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: OUTPUT_FILES/database.bin
+  source-file: single_source.yaml