Merge pull request #93 from PrincetonUniversity/integrate-meshfem

Integrate meshfem
PrincetonUniversity · Oct 31, 2023 · 46cad7e · 46cad7e
2 parents fafedef + 076a387
commit 46cad7e
Show file tree

Hide file tree

Showing 78 changed files with 20,447 additions and 407 deletions.
diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,9 @@ examples/*/*_config.yaml
 tests/regression-tests/*.yaml
 tests/regression-tests/*/cpu/*.yaml
 tests/regression-tests/*/gpu/*.yaml
+*.mod
+*.o
+*/OUTPUT_FILES/*
+*.gnu
+examples/*/Par_File
+*OUTPUT_FILES*
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,6 +5,7 @@ project(specfem2d_kokkos VERSION 0.1.0)
 set(CMAKE_CXX_STANDARD 17)
 option(MPI_PARALLEL "MPI enabled" OFF)
 option(BUILD_TESTS "Tests included" OFF)
+option(BUILD_EXAMPLES "Examples included" OFF)
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
         set(CMAKE_CXX_FLAGS "-fp-model=precise")
@@ -54,6 +55,8 @@ configure_file(constants.hpp.in constants.hpp)
 include_directories(include)
 include_directories(${CMAKE_BINARY_DIR})
 
+add_subdirectory(meshfem2d)
+
 # Build specfem2d libraries
 add_library(
         quadrature
@@ -295,6 +298,10 @@ if (BUILD_TESTS)
         message("-- Including tests.")
         add_subdirectory(tests/unit-tests)
         add_subdirectory(tests/regression-tests)
+endif()
+
+if (BUILD_EXAMPLES)
+        message("-- Including examples.")
         add_subdirectory(examples)
 endif()
 

diff --git a/docs/api/compute/index.rst b/docs/api/compute/index.rst
@@ -7,6 +7,7 @@ The interfaces provided here stores data required to compute mass and stiffness
 
 .. toctree::
     :maxdepth: 1
+
     compute
     compute_partial_derivatives
     compute_properties

diff --git a/docs/api/domain/kernels/index.rst b/docs/api/domain/kernels/index.rst
@@ -7,17 +7,78 @@ The ``kernels`` namespace is used to store Kokkos kernel implementations. The ke
 Kernels storage class
 ---------------------
 
-.. toctree::
-    :maxdepth: 1
+Interface
+~~~~~~~~~
 
-    kernels
+.. code-block::
+
+  template <class medium, class quadrature_points_type>
+  class specfem::domain::impl::kernels::kernels
+
+Parameters
+~~~~~~~~~~
+
+.. _dim2: ../enumerations/element/dim2.html
+
+.. |dim2| replace:: dim2()
+
+.. _dim3: ../enumerations/element/dim3.html
+
+.. |dim3| replace:: dim3()
+
+.. _elastic: ../enumerations/element/elastic.html
+
+.. |elastic| replace:: elastic()
+
+.. _acoustic: ../enumerations/element/acoustic.html
+
+.. |acoustic| replace:: acoustic()
+
+.. _static_quadrature_points: ../enumerations/element/static_quadrature_points.html
+
+.. |static_quadrature_points| replace:: static_quadrature_points< NGLL >()
+
+.. _isotropic: ../enumerations/element/isotropic.html
+
+.. |isotropic| replace:: isotropic()
+
+* ``medium``:
+
+  The medium of the element.
+
+  - |elastic|_: An elastic element.
+  - |acoustic|_: An acoustic element.
+
+* ``quadrature_points_type``:
+
+  The quadrature points of the element.
+
+  - |static_quadrature_points|_: A static quadrature point set.
+
+Class Description
+~~~~~~~~~~~~~~~~~
+
+.. _kernels: kernels.html
+
+.. |kernels| replace:: kernels()
+
+- |kernels|_
 
 Kernel implementations
 ----------------------
 
-.. toctree::
-    :maxdepth: 1
+.. _elemental_kernels: elemental_kernels.html
+
+.. |elemental_kernels| replace:: elemental_kernels()
+
+.. _source_kernels: source_kernel.html
+
+.. |source_kernels| replace:: source_kernels()
+
+.. _receiver_kernels: receiver_kernels.html
+
+.. |receiver_kernels| replace:: receiver_kernels()
 
-    elemental_kernels
-    source_kernels
-    receiver_kernels
+- |elemental_kernels|_
+- |source_kernels|_
+- |receiver_kernels|_