Merge pull request #475 from PrincetonUniversity/issue-472

Issue 472 -- Implement templated array reading for multidimensional fortran arrays. Reading ibool, coordinates, partials

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,28 +4,32 @@ about: Create a report to help us improve
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+## Expected behavior
+A clear and concise description of what you expected to happen.
+
+## Actual (buggy) behavior
+A clear and concise description of what is happening instead.
 
-**To Reproduce**
+## Screenshots
+
+If applicable, add screenshots to help explain your problem.
+
+## Setup information:
 
 - Installation instructions:
 ```
-      Please paste the cmake configuration command here
+Please paste the cmake configuration command here
 ```
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+## Machine information:
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+[please complete the following information:]
 
-**Machine information (please complete the following information):**
  - OS: [e.g. Redhat]
  - GPU available: [e.g. Yes (NVIDIA A100)]
 
-**Additional context**
+## Additional context
+
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -7,11 +7,16 @@ assignees: ''
 
 ---
 
-**Is your feature request related to a problem? Please describe.**
+## Is your feature request related to a problem?
 A clear and concise description of what the problem is.
 
-**Describe the solution you'd like**
+## Describe the solution you'd like
+
 A clear and concise description of what you want to happen.
 
-**Additional context**
+## Additional context
+
 Add any other context or screenshots about the feature request here.
+
+If this feature request helps with an existing issue, please link the issue here.
+E.g. #<issue number>

.github/pull_request_template.md

@@ -1,12 +1,12 @@
-# Description
+## Description
 
 Please describe the changes/features in this pull request.
 
-# Issue Number
+## Issue Number
 
 If there is an issue created for these changes, link it here
 
-# Checklist
+## Checklist
 
 Please make sure to check developer documentation on specfem docs.
 

CMakeLists.txt

@@ -28,12 +28,12 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 set(FETCHCONTENT_QUIET TRUE)
 
 if (SPECFEMPP_BINDING_PYTHON)
-    message("-- Adding -fPIC flag for Python binding.")
+    message(STATUS "Adding -fPIC flag for Python binding.")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
             set(CMAKE_CXX_FLAGS "-fp-model=precise -fPIC")
     elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-            message("-- Detected Intel classic compiler which will be deprecated soon.")
-            message("-- It is recommended you use IntelLLVM compiler.")
+            message(STATUS "Detected Intel classic compiler which will be deprecated soon.")
+            message(STATUS "It is recommended you use IntelLLVM compiler.")
             set(CMAKE_CXX_FLAGS "-diag-disable=10441 -fp-model=precise -fPIC")
     else()
             set(CMAKE_CXX_FLAGS "-fPIC")
@@ -42,24 +42,24 @@ else (SPECFEMPP_BINDING_PYTHON)
     if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
             set(CMAKE_CXX_FLAGS "-fp-model=precise")
     elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-            message("-- Detected Intel classic compiler which will be deprecated soon.")
-            message("-- It is recommended you use IntelLLVM compiler.")
+            message(STATUS "Detected Intel classic compiler which will be deprecated soon.")
+            message(STATUS "It is recommended you use IntelLLVM compiler.")
             set(CMAKE_CXX_FLAGS "-diag-disable=10441 -fp-model=precise")
     endif()
 endif (SPECFEMPP_BINDING_PYTHON)
 
 # Check if MacOS
 if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     set(__APPLE__ TRUE)
-    message("-- macOS detected -- setting __APPLE__ TRUE")
+    message(STATUS "macOS detected -- setting __APPLE__ TRUE")
 else(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     set(__APPLE__ FALSE)
-    message("-- macOS not detected -- setting __APPLE__ FALSE")
+    message(STATUS "macOS not detected -- setting __APPLE__ FALSE")
 endif()
 
 if (DEFINED Kokkos_ENABLE_CUDA)
     if (Kokkos_ENABLE_CUDA)
-        # message("Setting CUDA variables")
+        # message(STATUS "Setting CUDA variables")
         set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "Using CUDA Lambda by default")
         set(Kokkos_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE ON CACHE BOOL "Using CUDA Relocatable device by default")
     endif()
@@ -99,7 +99,7 @@ find_package(VTK COMPONENTS
 
 
 if (NOT VTK_FOUND)
-  message("VTK not found: ${VTK_NOT_FOUND_MESSAGE}")
+  message(STATUS "VTK not found: ${VTK_NOT_FOUND_MESSAGE}")
   set(VTK_CXX_BUILD OFF)
 else ()
   message(STATUS "    VTK:   ${VTK_LIBRARIES}")
@@ -150,31 +150,31 @@ endif()
 find_package(HDF5 COMPONENTS CXX)
 
 if (NOT ${HDF5_FOUND})
-    message("-- HDF5 not found. Building without HDF5.")
+    message(STATUS "HDF5 not found. Building without HDF5.")
     set(HDF5_CXX_BUILD OFF)
 else()
-    message("HDF5 libs/ and incs/:.")
+    message(STATUS "HDF5 libs/ and incs/:.")
     message(STATUS "    LIB:   ${HDF5_LIBRARIES}")
     message(STATUS "    INC:   ${HDF5_INCLUDE_DIRS}")
     message(STATUS "    LIBSO: ${HDF5_CXX_LIBRARIES}")
 endif()
 
 
 if (ENABLE_SIMD)
-    message("-- Enabling SIMD")
+    message(STATUS "Enabling SIMD")
     add_definitions(-DENABLE_SIMD)
 endif()
 
 if (ENABLE_PROFILING)
-    message("-- Enabling profiling")
+    message(STATUS "Enabling profiling")
     add_definitions(-DENABLE_PROFILING)
 endif()
 
 if (ENABLE_DOUBLE_PRECISION)
-    message("-- Enabling double precision")
+    message(STATUS "Enabling double precision")
     set(TYPE_REAL "double")
 else(ENABLE_DOUBLE_PRECISION)
-    message("-- Enabling single precision")
+    message(STATUS "Enabling single precision")
     set(TYPE_REAL "float")
 endif(ENABLE_DOUBLE_PRECISION)
 
@@ -188,9 +188,27 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup/constants.hpp.in
 include_directories(include)
 include_directories(${CMAKE_BINARY_DIR}/include)
 
-# ========== MESHFEM ==============
+# Set loglevel to STATUS if build type is debug
+if (CMAKE_BUILD_TYPE MATCHES Release)
+  set(SUBDIR_LOG_LEVEL NOTICE)
+else()
+  set(SUBDIR_LOG_LEVEL STATUS)
+endif()
+
+# ========== MESHFEM2D ==============
+message(STATUS "Building meshfem2D")
+set(_saved_CMAKE_MESSAGE_LOG_LEVEL ${CMAKE_MESSAGE_LOG_LEVEL})
+set(CMAKE_MESSAGE_LOG_LEVEL ${SUBDIR_LOG_LEVEL})
 add_subdirectory(fortran/meshfem2d)
+set(CMAKE_MESSAGE_LOG_LEVEL ${_saved_CMAKE_MESSAGE_LOG_LEVEL})
+# =================================
+
+# ========== MESHFEM3D ==============
+message(STATUS "Building xmeshfem3D & xgenerate_databases")
+set(_saved_CMAKE_MESSAGE_LOG_LEVEL ${CMAKE_MESSAGE_LOG_LEVEL})
+set(CMAKE_MESSAGE_LOG_LEVEL ${SUBDIR_LOG_LEVEL})
 add_subdirectory(fortran/meshfem3d)
+set(CMAKE_MESSAGE_LOG_LEVEL ${_saved_CMAKE_MESSAGE_LOG_LEVEL})
 # =================================
 
 
@@ -224,8 +242,8 @@ add_library(
         src/IO/mesh/impl/fortran/dim2/read_parameters.cpp
         # Fortran 3D part
         src/IO/mesh/impl/fortran/dim3/read_parameters.cpp
-        src/IO/mesh/impl/fortran/dim3/read_mapping.cpp
         src/IO/mesh/impl/fortran/dim3/read_coordinates.cpp
+        src/IO/mesh/impl/fortran/dim3/read_partial_derivatives.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)
@@ -298,9 +316,9 @@ if (MPI_PARALLEL)
                 specfem_mpi
                 PUBLIC -DMPI_PARALLEL
         )
-        message("-- Compiling SPECFEM with MPI")
+        message(STATUS "Compiling SPECFEM with MPI")
 else()
-        message("-- Compiling SPECFEM without MPI")
+        message(STATUS "Compiling SPECFEM without MPI")
 endif(MPI_PARALLEL)
 
 # add_library(
@@ -330,6 +348,7 @@ add_library(
         src/mesh/parameters/parameters.cpp
         src/mesh/mapping/mapping.cpp
         src/mesh/coordinates/coordinates.cpp
+        src/mesh/partial_derivatives/partial_derivatives.cpp
         src/mesh/mesh.cpp
 )
 
@@ -681,12 +700,12 @@ target_link_libraries(
 
 # Include tests
 if (BUILD_TESTS)
-        message("-- Including tests.")
+        message(STATUS "Including tests.")
         add_subdirectory(tests/unit-tests)
 endif()
 
 if (BUILD_EXAMPLES)
-        message("-- Including examples.")
+        message(STATUS "Including examples.")
         add_subdirectory(examples)
 endif()
 
@@ -702,7 +721,7 @@ if (DOXYGEN_FOUND)
 
     # request to configure the file
     configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
-    message("Doxygen build started")
+    message(STATUS "Doxygen build started")
 
     # Note: do not put "ALL" - this builds docs together with application EVERY TIME!
     add_custom_target( docs
@@ -711,7 +730,7 @@ if (DOXYGEN_FOUND)
         COMMENT "Generating API documentation with Doxygen"
         VERBATIM )
 else (DOXYGEN_FOUND)
-  message("Doxygen need to be installed to generate the doxygen documentation")
+  message(STATUS "Doxygen need to be installed to generate the doxygen documentation")
 endif (DOXYGEN_FOUND)
 
 if (SPECFEMPP_USE_SKBUILD AND EXISTS ${SKBUILD_SCRIPTS_DIR})

examples/CMakeLists.txt

@@ -1,8 +1,12 @@
 cmake_minimum_required(VERSION 3.17.5)
 
+# 2D
 add_subdirectory(anisotropic-crystal)
 add_subdirectory(homogeneous-medium-flat-topography)
 add_subdirectory(fluid-solid-interface)
 add_subdirectory(fluid-solid-bathymetry)
 add_subdirectory(solid-solid-interface)
 add_subdirectory(Tromp_2005)
+
+# 3D
+add_subdirectory(dim3/homogeneous_halfspace)

examples/dim3/homogeneous_halfspace/.gitignore

@@ -0,0 +1,6 @@
+build/
+OUTPUT_FILES/
+DATA/meshfem3D_files/Mesh_Par_file
+DATA/meshfem3D_files/interfaces.txt
+Par_File
+specfem_config.yaml

examples/dim3/homogeneous_halfspace/CMakeLists.txt

@@ -0,0 +1,12 @@
+
+CMAKE_MINIMUM_REQUIRED(VERSION 3.17.5)
+
+
+configure_file(config/Mesh_Par_file.in ${CMAKE_CURRENT_SOURCE_DIR}/DATA/meshfem3D_files/Mesh_Par_file)
+configure_file(config/interfaces.txt.in ${CMAKE_CURRENT_SOURCE_DIR}/DATA/meshfem3D_files/interfaces.txt)
+configure_file(config/Par_File.in ${CMAKE_CURRENT_SOURCE_DIR}/Par_File)
+configure_file(config/specfem_config.yaml.in ${CMAKE_CURRENT_SOURCE_DIR}/specfem_config.yaml)
+
+# Mkdir
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/OUTPUT_FILES/DATABASES_MPI)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/OUTPUT_FILES/results)

examples/dim3/homogeneous_halfspace/README.md

@@ -8,6 +8,7 @@ xmeshfem3D -p DATA/meshfem3D_files/Mesh_Par_file
 xgenerate_databases -p Par_File
 ```
 
+## Running the simulation (so far only reading the mesh)
 Then we can run specfem with the following command:
 
 ```bash

examples/dim3/homogeneous_halfspace/DATA/meshfem3D_files/Mesh_Par_file → examples/dim3/homogeneous_halfspace/config/Mesh_Par_file.in

@@ -17,7 +17,7 @@ UTM_PROJECTION_ZONE             = 11
 SUPPRESS_UTM_PROJECTION         = .true.
 
 # file that contains the interfaces of the model / mesh
-INTERFACES_FILE                 = DATA/meshfem3D_files/interfaces.txt
+INTERFACES_FILE                 = @CMAKE_CURRENT_SOURCE_DIR@/DATA/meshfem3D_files/interfaces.txt
 
 # file that contains the cavity
 CAVITY_FILE                     = no_cavity.dat
@@ -67,7 +67,7 @@ CREATE_VTK_FILES                = .true.
 SAVE_MESH_AS_CUBIT              = .false.
 
 # path to store the databases files
-LOCAL_PATH                      = ./OUTPUT_FILES/DATABASES_MPI
+LOCAL_PATH                      = @CMAKE_CURRENT_SOURCE_DIR@/OUTPUT_FILES/DATABASES_MPI
 
 #-----------------------------------------------------------
 #

examples/dim3/homogeneous_halfspace/Par_File → examples/dim3/homogeneous_halfspace/config/Par_File.in

@@ -66,12 +66,12 @@ NGNOD                           = 8
 MODEL                           = default
 
 # path for external model files (if MODEL = coupled)
-COUPLED_MODEL_DIRECTORY         = DATA/coupled_model/
+COUPLED_MODEL_DIRECTORY         = @CMAKE_CURRENT_SOURCE_DIR@/DATA/coupled_model/
 
 # path for external tomographic models files
-TOMOGRAPHY_PATH                 = DATA/tomo_files/
+TOMOGRAPHY_PATH                 = @CMAKE_CURRENT_SOURCE_DIR@/DATA/tomo_files/
 # if you are using a SEP model (oil-industry format)
-SEP_MODEL_DIRECTORY             = DATA/my_SEP_model/
+SEP_MODEL_DIRECTORY             = @CMAKE_CURRENT_SOURCE_DIR@/DATA/my_SEP_model/
 
 #-----------------------------------------------------------
 
@@ -166,7 +166,7 @@ HDUR_MOVIE                      = 0.0
 SAVE_MESH_FILES                 = .false.
 
 # path to store the local database file on each node
-LOCAL_PATH                      = OUTPUT_FILES/DATABASES_MPI
+LOCAL_PATH                      = @CMAKE_CURRENT_SOURCE_DIR@/OUTPUT_FILES/DATABASES_MPI
 
 # interval at which we output time step info and max of norm of displacement
 NTSTEP_BETWEEN_OUTPUT_INFO      = 500
@@ -194,7 +194,7 @@ USE_SOURCES_RECEIVERS_Z         = .false.
 # its norm is ignored and the norm of the force used is the factor force source times the source time function.
 USE_FORCE_POINT_SOURCE          = .false.
 
-SOURCE_FILENAME                    = DATA/CMTSOLUTION
+SOURCE_FILENAME                    = @CMAKE_CURRENT_SOURCE_DIR@/DATA/CMTSOLUTION
 
 # set to true to use a Ricker source time function instead of the source time functions set by default
 # to represent a (tilted) FORCESOLUTION force point source or a CMTSOLUTION moment-tensor source.
@@ -347,7 +347,7 @@ SAVE_MOHO_MESH                  = .false.
 COUPLE_WITH_INJECTION_TECHNIQUE = .false.
 INJECTION_TECHNIQUE_TYPE        = 3   # 1 = DSM, 2 = AxiSEM, 3 = FK
 MESH_A_CHUNK_OF_THE_EARTH       = .false.
-TRACTION_PATH                   = DATA/AxiSEM_tractions/3/
+TRACTION_PATH                   = @CMAKE_CURRENT_SOURCE_DIR@/DATA/AxiSEM_tractions/3/
 FKMODEL_FILE                    = FKmodel
 RECIPROCITY_AND_KH_INTEGRAL     = .false.   # does not work yet
 

examples/dim3/homogeneous_halfspace/DATA/meshfem3D_files/interfaces.txt → examples/dim3/homogeneous_halfspace/config/interfaces.txt.in

@@ -8,7 +8,7 @@
 #
 # interface number 1 (topography, top of the mesh)
  .true. 2 2 0.0 0.0 1000.0 1000.0
- DATA/meshfem3D_files/interface1.txt
+ @CMAKE_CURRENT_SOURCE_DIR@/DATA/meshfem3D_files/interface1.txt
 #
 # for each layer, we give the number of spectral elements in the vertical direction
 #