CPP MOLE 2.0 grid implementation + error handling

.gitignore

@@ -7,6 +7,7 @@
 /src/mole_C++/*.a
 /src/cpp/*.o
 /src/cpp/*.a
+/cpp/build
 
 # CMake generated files
 CMakeCache.txt

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.10)
 project(TopLevelProject VERSION 1.0 LANGUAGES CXX)
 
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
 # Display the detected C++ compiler ID
@@ -147,10 +147,11 @@ set(LINK_LIBS ${ARMADILLO_LIBRARIES}
               ${LAPACK_LIBRARY})
 
 # Add subdirectories
-add_subdirectory(src/cpp)
-add_subdirectory(tests/cpp)
-add_subdirectory(tests/matlab_octave)
-add_subdirectory(examples/cpp)
+#add_subdirectory(src/cpp)
+##add_subdirectory(tests/cpp)
+#add_subdirectory(tests/matlab_octave)
+#add_subdirectory(examples/cpp)
+add_subdirectory(cpp)
 
 # Custom target to build everything
 add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_matlab_octave)

cpp/CMakeLists.txt

@@ -0,0 +1,170 @@
+cmake_minimum_required(VERSION 3.10)
+project(MOLE
+    VERSION 2.0.0
+    DESCRIPTION "Mimetic Operators Library Enhanced (MOLE) - C++ implementation"
+    LANGUAGES CXX
+)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# Display the detected C++ compiler ID
+message(STATUS "Detected CXX Compiler ID: ${CMAKE_CXX_COMPILER_ID}")
+
+# Compiler-specific CXX_FLAGS and linker flags
+if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+    set(CMAKE_CXX_FLAGS "-O3 -Xclang -fopenmp -DARMA_DONT_USE_WRAPPER -DARMA_USE_SUPERLU")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L/usr/local/opt/libomp/lib -L/opt/homebrew/opt/libomp/lib -lomp")
+    message(STATUS "Using AppleClang-specific flags.")
+    include_directories("/usr/local/opt/libomp/include" "/opt/homebrew/opt/libomp/include")
+    message(STATUS "Adding Eigen3 include directory for AppleClang.")
+    set(EIGEN3_INCLUDE_DIR "/opt/homebrew/include/eigen3")
+    include_directories(${EIGEN3_INCLUDE_DIR})
+
+elseif (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+    set(CMAKE_CXX_FLAGS "-O3 -qopenmp -DARMA_DONT_USE_WRAPPER -DARMA_USE_SUPERLU -diag-disable=10430")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}")
+    message(STATUS "Using non-Clang compiler flags.")
+    # Get MKLROOT from environment or fallback to default
+    if(DEFINED ENV{MKLROOT})
+        set(MKLROOT $ENV{MKLROOT})
+    else()
+        set(MKLROOT "/opt/intel/oneapi/mkl/latest")
+    endif()
+    # Automatically set Armadillo to link against MKL
+    set(BLAS_LIBRARIES "${MKLROOT}/lib/intel64/libmkl_rt.so" CACHE STRING "BLAS library path for MKL")
+    set(LAPACK_LIBRARIES "${MKLROOT}/lib/intel64/libmkl_rt.so" CACHE STRING "LAPACK library path for MKL")
+    set(ARMA_USE_WRAPPER OFF CACHE BOOL "Disable Armadillo wrapper to directly use MKL")
+
+    message(STATUS "Using MKL from: ${MKLROOT}")
+
+else()
+    set(CMAKE_CXX_FLAGS "-O3 -fopenmp -DARMA_DONT_USE_WRAPPER -DARMA_USE_SUPERLU")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}")
+    message(STATUS "Using non-Clang compiler flags.")
+endif()
+
+if(UNIX AND NOT APPLE AND NOT MSVC)
+    message(STATUS "Checking for Fortran compiler (gfortran)...")
+    enable_language(Fortran OPTIONAL)
+    if(NOT CMAKE_Fortran_COMPILER)
+        message(FATAL_ERROR "gfortran is required but was not found. Please install it using 'sudo apt install gfortran'.")
+    endif()
+endif()
+
+
+find_package(Eigen3 3.3.7 REQUIRED)
+find_library(OpenBLAS_LIBRARIES NAMES openblas blas PATHS "/usr/lib/x86_64-linux-gnu" "/usr/local/opt/" "usr/local/lib" REQUIRED)
+find_library(LAPACK_LIBRARY lapack REQUIRED PATHS "/usr/lib" "/usr/lib/x86_64-linux-gnu" "/usr/local/lib" "/usr/local/opt/")
+
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 NEW)
+endif()
+
+# Paths for downloading and building libraries
+set(ARMADILLO_VERSION "15.2.2")
+set(SUPERLU_VERSION "7.0.1")
+set(BUILD_DIR "${CMAKE_BINARY_DIR}/third_party_build")
+set(INSTALL_DIR "${CMAKE_BINARY_DIR}/third_party_install")
+
+# SuperLU configuration
+set(SUPERLU_TARBALL_URL "https://github.com/xiaoyeli/superlu/archive/refs/tags/v${SUPERLU_VERSION}.tar.gz")
+set(SUPERLU_SRC_DIR "${BUILD_DIR}/superlu-${SUPERLU_VERSION}")
+set(SUPERLU_BUILD_DIR "${SUPERLU_SRC_DIR}/build")
+set(SUPERLU_INSTALL_DIR "${INSTALL_DIR}/superlu-${SUPERLU_VERSION}")
+
+file(DOWNLOAD ${SUPERLU_TARBALL_URL} ${BUILD_DIR}/superlu-${SUPERLU_VERSION}.tar.gz)
+execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf superlu-${SUPERLU_VERSION}.tar.gz WORKING_DIRECTORY ${BUILD_DIR})
+# Detect platform and apply the correct sed command
+if(APPLE)
+    execute_process(
+        COMMAND sed -i "" "s/cmake_minimum_required(VERSION 2.8.12)/cmake_minimum_required(VERSION 3.10)/" CMakeLists.txt
+        WORKING_DIRECTORY ${SUPERLU_SRC_DIR}
+    )
+else()
+    execute_process(
+        COMMAND sed -i "s/cmake_minimum_required(VERSION 2.8.12)/cmake_minimum_required(VERSION 3.10)/" CMakeLists.txt
+        WORKING_DIRECTORY ${SUPERLU_SRC_DIR}
+    )
+endif()
+
+# Confirm the patch
+execute_process(
+    COMMAND grep "cmake_minimum_required" ${SUPERLU_SRC_DIR}/CMakeLists.txt
+    OUTPUT_VARIABLE cmake_version_line
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+message(STATUS "SuperLU CMakeLists.txt after patch: ${cmake_version_line}")
+
+execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${SUPERLU_BUILD_DIR})
+
+execute_process(COMMAND ${CMAKE_COMMAND} ..
+    -DCMAKE_INSTALL_PREFIX=${SUPERLU_INSTALL_DIR}
+    -Denable_internal_blaslib=NO
+    -DTPL_BLAS_LIBRARIES=${OpenBLAS_LIBRARIES}
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+    -DCMAKE_C_FLAGS="-fPIC"
+    -DCMAKE_CXX_FLAGS="-fPIC"
+    WORKING_DIRECTORY ${SUPERLU_BUILD_DIR})
+execute_process(COMMAND make -j4 WORKING_DIRECTORY ${SUPERLU_BUILD_DIR})
+execute_process(COMMAND make install WORKING_DIRECTORY ${SUPERLU_BUILD_DIR})
+
+# Armadillo configuration
+set(ARMADILLO_TARBALL_URL "https://sourceforge.net/projects/arma/files/armadillo-${ARMADILLO_VERSION}.tar.xz")
+set(ARMADILLO_BUILD_DIR "${BUILD_DIR}/armadillo-${ARMADILLO_VERSION}")
+set(ARMADILLO_INSTALL_DIR "${INSTALL_DIR}/armadillo-${ARMADILLO_VERSION}")
+
+file(DOWNLOAD ${ARMADILLO_TARBALL_URL} ${BUILD_DIR}/armadillo-${ARMADILLO_VERSION}.tar.xz)
+execute_process(COMMAND ${CMAKE_COMMAND} -E tar xJf armadillo-${ARMADILLO_VERSION}.tar.xz WORKING_DIRECTORY ${BUILD_DIR})
+execute_process(COMMAND ${CMAKE_COMMAND}
+    -DSuperLU_INCLUDE_DIR=${SUPERLU_INSTALL_DIR}/include
+    -DSuperLU_LIBRARY=${SUPERLU_INSTALL_DIR}/lib/libsuperlu.a
+    -DCMAKE_INSTALL_PREFIX=${ARMADILLO_INSTALL_DIR} .
+    WORKING_DIRECTORY ${ARMADILLO_BUILD_DIR})
+execute_process(COMMAND make -j4 WORKING_DIRECTORY ${ARMADILLO_BUILD_DIR})
+execute_process(COMMAND make install WORKING_DIRECTORY ${ARMADILLO_BUILD_DIR})
+
+# Update paths for Armadillo and SuperLU
+include_directories(${SUPERLU_INSTALL_DIR}/include ${ARMADILLO_INSTALL_DIR}/include)
+link_directories(${SUPERLU_INSTALL_DIR}/lib ${ARMADILLO_INSTALL_DIR}/lib)
+
+# Find required libraries
+set(CMAKE_PREFIX_PATH ${ARMADILLO_INSTALL_DIR} ${CMAKE_PREFIX_PATH})
+set(Armadillo_DIR ${ARMADILLO_INSTALL_DIR}/share/Armadillo)
+
+find_package(Armadillo REQUIRED)
+if(NOT Armadillo_FOUND)
+    message(FATAL_ERROR "Custom Armadillo not found in ${ARMADILLO_INSTALL_DIR}")
+else()
+    message(STATUS "Using Armadillo from ${ARMADILLO_INSTALL_DIR}")
+endif()
+
+find_package(Eigen3 3.3.7 REQUIRED)
+find_library(OpenBLAS_LIBRARIES NAMES openblas blas PATHS "/usr/lib/x86_64-linux-gnu" "/usr/local/opt/" REQUIRED)
+find_library(LAPACK_LIBRARY lapack REQUIRED PATHS "/usr/lib" "/usr/lib/x86_64-linux-gnu" "/usr/local/lib" "/usr/local/opt/")
+
+# Required libraries and link settings
+set(LINK_LIBS ${ARMADILLO_LIBRARIES}
+              ${OpenBLAS_LIBRARIES}
+              ${SUPERLU_INSTALL_DIR}/lib/libsuperlu.a
+              ${LAPACK_LIBRARY})
+
+# Add subdirectories
+add_subdirectory(src)
+add_subdirectory(tests)
+add_subdirectory(examples/grids)
+
+# Custom target to build everything
+add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_matlab_octave)
+# ---------------------------------------------------------------
+# Summary printed at configure time
+# ---------------------------------------------------------------
+message(STATUS "")
+message(STATUS "MOLE ${PROJECT_VERSION} configuration summary:")
+message(STATUS "  Build type:        ${CMAKE_BUILD_TYPE}")
+message(STATUS "  Armadillo version: ${ARMADILLO_VERSION_STRING}")
+message(STATUS "  Build examples:    ${MOLE_BUILD_EXAMPLES}")
+message(STATUS "  Build tests:       ${MOLE_BUILD_TESTS}")
+message(STATUS "")
+

cpp/README.md

@@ -0,0 +1,52 @@
+<!--
+====================================================================
+=                       MOLE 2.0 - C++                         =
+====================================================================
+ SPDX-License-Identifier: GPL-3.0-or-later
+ Copyright (c) 2008-2024 San Diego State University Research 
+ Foundation (SDSURF).
+ See LICENSE file or https://www.gnu.org/licenses/gpl-3.0.html for details.
+--------------------------------------------------------------------
+File created: 06-24-2026
+====================================================================
+-->
+
+# Top subdirectory for MOLE 2.0 C++ files
+
+Subdirectory and Pathname: **mole/cpp**
+
+## Purpose
+
+Top subdirectory for the MOLE 2.0 C++ implementation.
+It contains the top CMakefile.list.
+
+## MOLE C++ 2.0 Directory structure
+
+```text
+mole/
+├── cpp/
+|   │── cmake/
+|   │── doc/
+|   │── examples
+|   |── src/
+|   │   ├── boundaries
+|   │   └── grids
+|   │   └── include
+|   │   └── operators
+|   │   └── sys
+|   │   └── utils
+|   |── tests
+
+:
+: __Other MOLE 2.0 and v1.2.0 files, including other language__
+: __implementations__
+:
+├── .gitignore
+└── README.md
+```
+
+## Other MOLE 2.0 C++ Files in this directory
+
++ CMakeLists.txt which builds a MOLE 2.0 C++ version of the library
+and all its functional modules
++ README.md (this file)

cpp/cmake/MOLEConfig.cmake.in

@@ -0,0 +1,5 @@
+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/MOLETargets.cmake")
+
+check_required_components(MOLE)

cpp/examples/README.md

@@ -0,0 +1,45 @@
+<!--
+====================================================================
+=                           MOLE 2.0 - C++                         =
+====================================================================
+ SPDX-License-Identifier: GPL-3.0-or-later
+ Copyright (c) 2008-2024 San Diego State University Research 
+ Foundation (SDSURF).
+ See LICENSE file or https://www.gnu.org/licenses/gpl-3.0.html for 
+ details.
+--------------------------------------------------------------------
+File created: 06-24-2026
+====================================================================
+ -->
+
+# Subdirectory of Use Cases/Examples for the MOLE 2.0 Implementation
+
+Subdirectory and Pathname: **mole/cpp/examples**
+
+## Purpose
+
+This is the top subdirectory for the MOLE 2.0 C++ example
+implementations. Examples are organized by the different modules
+contained in the MOLE Library
+
+## Structure of the MOLE C++ 2.0 Subdirectory of Examples
+
+```text
+mole/
+├── cpp/
+|   │── examples
+|   │   ├── boundaries
+|   │   └── grids
+|   │   └── operators
+|   │   └── sys
+|   |   └── time_integrators
+|   │   └── utils
+```
+
+## MOLE 2.0 C++ Files and Subdirectories in this subdirectory
+
++ subdirectory **grids**: contains examples on how to declare and
+ construct MOLE grids
++ subdirectory **sys**: contains examples on how to use MOLE v2.0
+ error handling mechanisms
++ file **README.md** this file

cpp/examples/grids/CMakeLists.txt

@@ -0,0 +1,35 @@
+cmake_minimum_required(VERSION 3.14)
+
+# ---------------------------------------------------------------
+# The files in the CMakeLists.txt file are all examples of the
+# the use of the MOLE Library
+# ---------------------------------------------------------------
+set(MOLE_EXAMPLE_SOURCES
+    grid1D_basic.cpp                # basic 1D grid generation
+    grid2D_basic.cpp                # basic 2D grid generation
+    err_grid2D_basic.cpp            # basic 2D grid generation
+    gridBuilder1D_basic.cpp         # 1D grid through gridBuilder
+    gridBuilder2D_basic.cpp         # 2D grid with periodicity
+    gridBuilder_arg_order.cpp       # attribute order independence
+    gridBuilder_error_handling.cpp  # parse-time error reporting
+)
+
+# Builds all the examples listed in MOLE_EXAMPLE_SOURCES
+add_custom_target(mole_examples)
+
+foreach(_mole_example_src IN LISTS MOLE_EXAMPLE_SOURCES)
+    if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_mole_example_src}")
+        message(FATAL_ERROR
+            "MOLE example source listed in examples/CMakeLists.txt "
+            "is missing: ${_mole_example_src}")
+    endif()
+    get_filename_component(_mole_example_name
+                            ${_mole_example_src} NAME_WE)
+    add_executable(${_mole_example_name} ${_mole_example_src})
+    target_link_libraries(${_mole_example_name} PRIVATE MOLE::mole)
+    target_compile_options(${_mole_example_name} PRIVATE -Wall -Wextra)
+    # Group all example binaries under a single "examples" target so
+    # `cmake --build . --target examples` builds just these, without
+    # also building the (potentially much larger) test suite.
+    add_dependencies(mole_examples ${_mole_example_name})
+endforeach()

cpp/examples/grids/README.md

@@ -0,0 +1,34 @@
+<!--
+====================================================================
+=                          MOLE 2.0 - C++                          =
+====================================================================
+ SPDX-License-Identifier: GPL-3.0-or-later
+ Copyright (c) 2008-2024 San Diego State University Research 
+ Foundation (SDSURF).
+ See LICENSE file or https://www.gnu.org/licenses/gpl-3.0.html for 
+ details.
+--------------------------------------------------------------------
+File created: 06-24-2026
+====================================================================
+ -->
+
+# Subdirectory for MOLE 2.0 C++ grid examples
+
+Subdirectory and Pathname: **mole/cpp/examples/grids/**
+
+## Purpose
+
+Subdirectory containing examples of MOLE grid declarations and
+generation using MOLE grid classes and the MOLE gridBuilder
+
+## List of Files in This Subdirectory
+
++ **CMakeLists.txt**: support the building of MOLE 2.0 C++ examples of
+MOLE grids
++ **err_grid2D_basic.cpp**: a C++ example of how the MOLE error log
+mechanisms works in the context of grids
++ **grid1D_basic.cpp**: a C++ example of a 1D grid declaration and
+instantiation (checking for errors)
++ **grid2D_basic.cpp**:a C++ example of a 1D grid declaration and
+instantiation (checking for errors)
++ **README.md**: (this file)