Merge branch 'devel' into issue-390

PrincetonUniversity · Feb 5, 2025 · 4de9521 · 4de9521
2 parents 344a434 + ac02df2
commit 4de9521
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Showing 79 changed files with 13,139 additions and 875 deletions.
diff --git a/.jenkins/gnu_compiler_checks.gvy b/.jenkins/gnu_compiler_checks.gvy
@@ -66,7 +66,7 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} with ${GNU_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${GNU_COMPILER_MODULE}
                                         cmake3 -S . -B build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -DBUILD_TESTS=ON -D BUILD_EXAMPLES=OFF
                                         cmake3 --build build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
@@ -78,7 +78,7 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${GNU_COMPILER_MODULE}
                                         cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'

diff --git a/.jenkins/intel_compiler_checks.gvy b/.jenkins/intel_compiler_checks.gvy
@@ -65,7 +65,7 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} with ${INTEL_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${INTEL_MODULE}
                                         export CC=icx
                                         export CXX=icpx
@@ -79,7 +79,7 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${INTEL_MODULE}
                                         cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'

diff --git a/.jenkins/nvidia_compiler_checks.gvy b/.jenkins/nvidia_compiler_checks.gvy
@@ -81,7 +81,7 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} with ${CUDA_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${CUDA_MODULE}
                                         cmake3 -S . -B build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON -D BUILD_EXAMPLES=OFF
                                         cmake3 --build build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
@@ -93,7 +93,7 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${CUDA_MODULE}
                                         cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} ${DEVICE_RUN_FLAGS} bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -69,7 +69,7 @@ endif()
 include(FetchContent)
 FetchContent_Declare(
   kokkos
-  URL https://github.com/kokkos/kokkos/archive/refs/tags/4.3.01.zip
+  URL https://github.com/kokkos/kokkos/archive/refs/tags/4.5.01.zip
   DOWNLOAD_EXTRACT_TIMESTAMP FALSE
 )
 FetchContent_MakeAvailable(kokkos)
@@ -105,7 +105,7 @@ endif()
 
 
 # Try finding boost and if not found install.
-find_package(Boost 1.73.0 COMPONENTS program_options filesystem system)
+find_package(Boost 1.85.0 COMPONENTS program_options filesystem system)
 
 
 if (NOT ${Boost_FOUND})
@@ -435,6 +435,7 @@ add_library(
 
 target_link_libraries(
         compute
+        enumerations
         quadrature
         mesh
         # material_class
@@ -542,30 +543,30 @@ target_link_libraries(
 )
 
 add_library(
-        plotter
-        src/plotter/plot_wavefield.cpp
+        periodic_tasks
+        src/periodic_tasks/plot_wavefield.cpp
 )
 
 if (NOT VTK_CXX_BUILD)
         target_compile_definitions(
-                plotter
+                periodic_tasks
                 PUBLIC -DNO_VTK
         )
 
         target_link_libraries(
-                plotter
+                periodic_tasks
                 compute
         )
 else ()
         target_link_libraries(
-                plotter
+                periodic_tasks
                 compute
                 ${VTK_LIBRARIES}
                 )
 
         # Only define the __APPLE__ compile definition if it is defined
         if (__APPLE__)
-        target_compile_definitions(plotter PRIVATE __APPLE__)
+        target_compile_definitions(periodic_tasks PRIVATE __APPLE__)
         endif(__APPLE__)
 endif()
 
@@ -600,15 +601,13 @@ target_link_libraries(
         ${BOOST_LIBS}
 )
 
-add_executable(
-        specfem2d
-        src/specfem2d.cpp
+add_library(
+        execute
+        src/execute.cpp
 )
 
-
-
 target_link_libraries(
-        specfem2d
+        execute
         specfem_mpi
         Kokkos::kokkos
         mesh
@@ -618,7 +617,7 @@ target_link_libraries(
         parameter_reader
         receiver_class
         writer
-        plotter
+        periodic_tasks
         reader
         medium
         coupled_interface
@@ -627,6 +626,18 @@ target_link_libraries(
         ${BOOST_LIBS}
 )
 
+add_executable(
+        specfem2d
+        src/specfem2d.cpp
+)
+
+
+
+target_link_libraries(
+        specfem2d
+        execute
+)
+
 # Include tests
 if (BUILD_TESTS)
         message("-- Including tests.")
@@ -670,28 +681,13 @@ endif ()
 if (SPECFEMPP_BINDING_PYTHON)
     find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
     find_package(pybind11 CONFIG REQUIRED)
-    python_add_library(_core MODULE src/specfem2d.cpp WITH_SOABI)
+    python_add_library(_core MODULE src/python/core.cpp WITH_SOABI)
     target_link_libraries(
         _core PRIVATE
-        specfem_mpi
-        Kokkos::kokkos
-        mesh
-        quadrature
-        compute
-        source_class
-        parameter_reader
-        receiver_class
-        writer
-        plotter
-        reader
-        medium
-        coupled_interface
-        kokkos_kernels
-        solver
+        execute
         ${BOOST_LIBS}
         pybind11::headers
     )
-    target_compile_definitions(_core PRIVATE SPECFEMPP_BINDING_PYTHON)
     target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
     install(TARGETS _core DESTINATION specfempp_core)
 endif (SPECFEMPP_BINDING_PYTHON)
diff --git a/README.md b/README.md
@@ -16,6 +16,8 @@ SPECFEM++ is a complete re-write of SPECFEM suite of packages (SPECFEM2D, SPECFE
  3. portability that allows the code to run on a variety of architectures (CPU, NVIDIA GPUs, Intel GPUs, AMD GPUs etc.), and
  4. a user-friendly build infrastructure that allows the code to be easily compiled and run on a variety of platforms.
 
+[specfempp-py](https://github.com/PrincetonUniversity/SPECFEMPP-py) is the official Python package for configuring and running SPECFEM++ with Python.
+
 ## Documentation
 
 

diff --git a/docs/api/assembly/receivers/receiver.rst → docs/api/assembly/receivers/receivers.rst b/docs/api/assembly/receivers/receiver.rst → docs/api/assembly/receivers/receivers.rst
diff --git a/docs/api/assembly/sources/source.rst → docs/api/assembly/sources/sources.rst b/docs/api/assembly/sources/source.rst → docs/api/assembly/sources/sources.rst
diff --git a/docs/api/mesh/boundaries/index.rst b/docs/api/mesh/boundaries/index.rst
@@ -6,3 +6,9 @@ Boundaries
 
 .. doxygenstruct:: specfem::mesh::boundaries
     :members:
+
+.. toctree::
+    :maxdepth: 1
+
+    absorbing_boundaries
+    acoustic_free_surface
diff --git a/docs/api/mesh/index.rst b/docs/api/mesh/index.rst
@@ -6,3 +6,13 @@ SPECFEM++ Mesh
 
 .. doxygenstruct:: specfem::mesh::mesh
     :members:
+
+
+.. toctree::
+    :maxdepth: 1
+
+    boundaries/index
+    control_nodes/index
+    coupled_interfaces/index
+    materials/index
+    tags/index
diff --git a/docs/cookbooks/dim2/anisotropic-crystal/index.rst b/docs/cookbooks/dim2/anisotropic-crystal/index.rst
@@ -1,4 +1,4 @@
-Wave propagration through anistoropic zinc crystal
+Wave propagration through anisotropic zinc crystal
 ==================================================
 
 In this `example

diff --git a/docs/cookbooks/dim2/anisotropic-crystal/plot.py b/docs/cookbooks/dim2/anisotropic-crystal/plot.py
@@ -2,9 +2,6 @@
 import os
 import numpy as np
 import obspy
-import matplotlib
-
-matplotlib.use("agg")
 
 
 def get_traces(directory):
@@ -16,19 +13,15 @@ def get_traces(directory):
         "S0040",
         "S0050",
     ]
-    files = [
-        glob.glob(directory + f"/{stationname}*.sem*")[0]
-        for stationname in station_name
-    ]
+    files = []
+    for station in station_name:
+        files += glob.glob(directory + f"/??.{station}.S2.BX?.semd")
 
     ## iterate over all seismograms
     for filename in files:
         station_id = os.path.splitext(filename)[0]
         station_id = station_id.split("/")[-1]
-        network = station_id[5:7]
-        station = station_id[0:5]
-        location = "00"
-        component = station_id[7:10]
+        network, station, location, channel = station_id.split(".")[:4]
         trace = np.loadtxt(filename, delimiter=" ")
         starttime = trace[0, 0]
         dt = trace[1, 0] - trace[0, 0]
@@ -39,7 +32,7 @@ def get_traces(directory):
                     "network": network,
                     "station": station,
                     "location": location,
-                    "channel": component,
+                    "channel": channel,
                     "starttime": starttime,
                     "delta": dt,
                 },
@@ -52,4 +45,5 @@ def get_traces(directory):
 
 
 stream = get_traces("OUTPUT_FILES/results")
-stream.plot(size=(800, 1000))
+stream.select(component="X").plot(size=(1000, 750))
+stream.select(component="Z").plot(size=(1000, 750))
diff --git a/docs/cookbooks/dim2/fluid-solid-interface/index.rst b/docs/cookbooks/dim2/fluid-solid-interface/index.rst
@@ -151,3 +151,31 @@ With the configuration file in place, we can run the solver using the following
 .. code:: bash
 
     specfem2d -p specfem_config.yaml
+
+
+Visualizing the results
+-----------------------
+
+The simulation generates seismograms at the stations defined in the
+``specfem_config.yaml`` file. You can visualize the seismograms using the
+following python script.
+
+.. literalinclude:: plot.py
+    :language: python
+    :caption: plot.py
+
+
+.. figure:: seismograms_X.svg
+   :alt: X-component seismograms
+   :width: 800
+   :align: center
+
+   X-component seismograms
+
+
+.. figure:: seismograms_Z.svg
+    :alt: Z-component seismograms
+    :width: 800
+    :align: center
+
+    Z-component seismograms
diff --git a/docs/cookbooks/dim2/fluid-solid-interface/plot.py b/docs/cookbooks/dim2/fluid-solid-interface/plot.py
@@ -0,0 +1,42 @@
+import glob
+import os
+import numpy as np
+import obspy
+
+
+def get_traces(directory):
+    traces = []
+
+    files = glob.glob(directory + "/AA.S00??.S2.BX?.semd")
+    files.sort()
+
+    ## iterate over all seismograms
+    for filename in files:
+        station_id = os.path.splitext(filename)[0]
+        station_id = station_id.split("/")[-1]
+        network, station, location, channel = station_id.split(".")[:4]
+        trace = np.loadtxt(filename, delimiter=" ")
+        starttime = trace[0, 0]
+        dt = trace[1, 0] - trace[0, 0]
+        traces.append(
+            obspy.Trace(
+                trace[:, 1],
+                {
+                    "network": network,
+                    "station": station,
+                    "location": location,
+                    "channel": channel,
+                    "starttime": starttime,
+                    "delta": dt,
+                },
+            )
+        )
+
+    stream = obspy.Stream(traces)
+
+    return stream
+
+
+stream = get_traces("OUTPUT_FILES/seismograms")
+stream.select(component="X").plot(size=(1000, 750))
+stream.select(component="Z").plot(size=(1000, 750))