feat: upgrade build system to CMake, remove hardcoded paths, and add migration documentation

CMakeLists.txt

@@ -0,0 +1,37 @@
+cmake_minimum_required(VERSION 3.18)
+project(MicroSim VERSION 1.0 LANGUAGES C CXX)
+
+# Global options
+option(BUILD_GRAND_POTENTIAL_SERIAL  "Build the Grand-Potential Serial solver"    ON)
+option(BUILD_GRAND_POTENTIAL_MPI     "Build the Grand-Potential MPI solver"       ON)
+option(BUILD_KKS_CUFFT               "Build the KKS cuFFT (CUDA) solver"          ON)
+option(BUILD_KKS_FD_CUDA_MPI         "Build the KKS FD CUDA MPI solver"           ON)
+option(BUILD_KKS_OPENCL              "Build the KKS OpenCL solver"                ON)
+option(BUILD_CAHN_HILLIARD_FFT_2D    "Build the Cahn-Hilliard FFT 2D solver"      ON)
+
+# Append local cmake/ directory to the module search path
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+if(BUILD_GRAND_POTENTIAL_SERIAL)
+    add_subdirectory(Grand_Potential_Serial)
+endif()
+
+if(BUILD_GRAND_POTENTIAL_MPI)
+    add_subdirectory(Grand_Potential_MPI)
+endif()
+
+if(BUILD_KKS_CUFFT)
+    add_subdirectory(KKS_CuFFT)
+endif()
+
+if(BUILD_KKS_FD_CUDA_MPI)
+    add_subdirectory(KKS_FD_CUDA_MPI)
+endif()
+
+if(BUILD_KKS_OPENCL)
+    add_subdirectory(KKS_OpenCl)
+endif()
+
+if(BUILD_CAHN_HILLIARD_FFT_2D)
+    add_subdirectory(Cahn_Hilliard_FFT_2D)
+endif()

Cahn_Hilliard_FFT_2D/CMakeLists.txt

@@ -0,0 +1,27 @@
+cmake_minimum_required(VERSION 3.18)
+project(microsim_ch_fft LANGUAGES C)
+
+# Add the top-level cmake/ directory to the module path so that
+# FindFFTW3.cmake is found whether this is built stand-alone or as part
+# of the top-level project.
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../cmake")
+
+# ── Dependencies ────────────────────────────────────────────────────────────
+find_package(FFTW3 REQUIRED)   # provided by cmake/FindFFTW3.cmake
+
+# ── Main solver target ───────────────────────────────────────────────────────
+add_executable(microsim_ch_fft microsim_ch_fft.c)
+
+target_include_directories(microsim_ch_fft PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/functions
+    ${CMAKE_CURRENT_SOURCE_DIR}/solverloop
+    ${FFTW3_INCLUDE_DIRS}
+)
+
+target_link_libraries(microsim_ch_fft PRIVATE
+    FFTW3::fftw3
+    m
+)
+
+install(TARGETS microsim_ch_fft RUNTIME DESTINATION bin)

Grand_Potential_MPI/CMakeLists.txt

@@ -0,0 +1,56 @@
+cmake_minimum_required(VERSION 3.18)
+project(microsim_gp_mpi LANGUAGES C)
+
+# ── Dependencies ────────────────────────────────────────────────────────────
+find_package(MPI  REQUIRED COMPONENTS C)
+find_package(HDF5 REQUIRED COMPONENTS C HL)
+find_package(GSL  REQUIRED)
+
+# ── Main solver target ───────────────────────────────────────────────────────
+# The build consists of a single .c translation unit; all other files
+# in functions/, solverloop/ and tdbs/ are header-only includes.
+add_executable(microsim_gp microsim_gp.c)
+
+target_include_directories(microsim_gp PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/functions
+    ${CMAKE_CURRENT_SOURCE_DIR}/solverloop
+    ${CMAKE_CURRENT_SOURCE_DIR}/tdbs
+    ${HDF5_INCLUDE_DIRS}
+    ${GSL_INCLUDE_DIRS}
+)
+
+target_compile_definitions(microsim_gp PRIVATE ${HDF5_DEFINITIONS})
+
+target_link_libraries(microsim_gp PRIVATE
+    MPI::MPI_C
+    ${HDF5_C_LIBRARIES}
+    GSL::gsl
+    GSL::gslcblas
+    m
+)
+
+# ── write_xdmf utility ───────────────────────────────────────────────────────
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/write_xdmf.c")
+    add_executable(write_xdmf write_xdmf.c)
+
+    target_include_directories(write_xdmf PRIVATE
+        ${CMAKE_CURRENT_SOURCE_DIR}
+        ${CMAKE_CURRENT_SOURCE_DIR}/functions
+        ${CMAKE_CURRENT_SOURCE_DIR}/solverloop
+        ${HDF5_INCLUDE_DIRS}
+        ${GSL_INCLUDE_DIRS}
+    )
+
+    target_compile_definitions(write_xdmf PRIVATE ${HDF5_DEFINITIONS})
+
+    target_link_libraries(write_xdmf PRIVATE
+        MPI::MPI_C
+        ${HDF5_C_LIBRARIES}
+        GSL::gsl
+        GSL::gslcblas
+        m
+    )
+endif()
+
+install(TARGETS microsim_gp RUNTIME DESTINATION bin)

Grand_Potential_MPI/Makefile

@@ -2,12 +2,12 @@ FDIR=functions
 SDIR=solverloop
 TDIR=tdbs
 CC=h5pcc #-O3
-# CFLAGS=-I.
-#LDIR=$(GSL_ROOT_DIR)/lib
-#IDIR=$(GSL_ROOT_DIR)/include
 
-LDIR=/share/apps/gsl/lib
-IDIR=/share/apps/gsl/include
+# GSL paths: set GSL_ROOT_DIR to your GSL installation prefix.
+# If unset, the build tries to locate GSL via gsl-config.
+GSL_ROOT_DIR ?= $(shell gsl-config --prefix 2>/dev/null)
+LDIR=$(GSL_ROOT_DIR)/lib
+IDIR=$(GSL_ROOT_DIR)/include
 CFLAGS=-I $(IDIR)
 
 _FUNCTION_DEPS = global_vars.h functions.h matrix.h utility_functions.h functionH.h functionF_01.h functionF_02.h functionF_03.h functionF_04.h functionF_05.h  functionF_06.h functionQ.h \

Grand_Potential_Serial/CMakeLists.txt

@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 3.18)
+project(microsim_gp_serial LANGUAGES C)
+
+# Source files – the solver is a single translation unit; all other files
+# are header-only and referenced via include paths.
+add_executable(microsim_gp microsim_gp.c)
+
+target_include_directories(microsim_gp PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/functions
+    ${CMAKE_CURRENT_SOURCE_DIR}/solverloop
+)
+
+target_link_libraries(microsim_gp PRIVATE m)
+
+install(TARGETS microsim_gp RUNTIME DESTINATION bin)

KKS_CuFFT/CMakeLists.txt

@@ -0,0 +1,36 @@
+cmake_minimum_required(VERSION 3.18)
+project(microsim_kks_cufft LANGUAGES CUDA)
+
+# ── Dependencies ────────────────────────────────────────────────────────────
+find_package(CUDAToolkit REQUIRED)
+
+# ── Target ───────────────────────────────────────────────────────────────────
+add_executable(microsim_kks_cufft KKS_cuFFT.cu)
+
+# Optimisation flags passed through to ptxas (matches -Xptxas -O3 in Makefile)
+target_compile_options(microsim_kks_cufft PRIVATE
+    $<$<COMPILE_LANGUAGE:CUDA>:-Xptxas -O3>
+)
+
+# GPU architecture – default sm_70; override via -DCUDA_ARCH=<arch>
+if(NOT DEFINED CUDA_ARCH)
+    set(CUDA_ARCH "70")
+endif()
+set_target_properties(microsim_kks_cufft PROPERTIES
+    CUDA_ARCHITECTURES ${CUDA_ARCH}
+)
+
+target_include_directories(microsim_kks_cufft PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/functions
+)
+
+target_link_libraries(microsim_kks_cufft PRIVATE
+    CUDA::cufft
+    CUDA::cuda_driver
+    CUDA::cudart
+)
+
+# Create DATA output directory expected by the solver at run-time
+file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/DATA")
+
+install(TARGETS microsim_kks_cufft RUNTIME DESTINATION bin)

KKS_FD_CUDA_MPI/CMakeLists.txt

@@ -0,0 +1,183 @@
+cmake_minimum_required(VERSION 3.18)
+project(microsim_kks_fd_cuda_mpi LANGUAGES C CXX CUDA)
+
+# ── Dependencies ────────────────────────────────────────────────────────────
+find_package(MPI         REQUIRED COMPONENTS C CXX)
+find_package(HDF5        REQUIRED COMPONENTS C HL)
+find_package(GSL         REQUIRED)
+find_package(CUDAToolkit REQUIRED)
+
+# ── Build options ─────────────────────────────────────────────────────────────
+option(ENABLE_HDF5    "Enable HDF5 output"        ON)
+option(ENABLE_CUFFTMP "Enable multi-GPU cuFFTMp"  OFF)
+
+# GPU architecture – default sm_70; override via -DCUDA_ARCH=<arch>
+if(NOT DEFINED CUDA_ARCH)
+    set(CUDA_ARCH "70")
+endif()
+
+# ── Helper: convenience path variables ───────────────────────────────────────
+set(FUNCTIONS  ${CMAKE_CURRENT_SOURCE_DIR}/functions)
+set(SOLVERLOOP ${CMAKE_CURRENT_SOURCE_DIR}/solverloop)
+set(TDBS       ${CMAKE_CURRENT_SOURCE_DIR}/tdbs)
+
+# ── Sources ──────────────────────────────────────────────────────────────────
+set(HOST_SOURCES
+    microsim_kks_fd_cuda_mpi.c
+    ${SOLVERLOOP}/fileWriter.c
+    ${FUNCTIONS}/utilityFunctions.c
+    ${FUNCTIONS}/initialize_variables.c
+    ${FUNCTIONS}/filling.c
+    ${FUNCTIONS}/reading_input_parameters.c
+    ${FUNCTIONS}/fill_domain.c
+    ${FUNCTIONS}/read_boundary_conditions.c
+    ${FUNCTIONS}/calc_bn.c
+    ${FUNCTIONS}/box_iterator.cpp
+    ${FUNCTIONS}/error_checks.cpp
+)
+
+set(DEVICE_SOURCES
+    ${TDBS}/Thermo.cu
+    ${FUNCTIONS}/functionF.cu
+    ${FUNCTIONS}/functionH.cu
+    ${FUNCTIONS}/functionTau.cu
+    ${FUNCTIONS}/functionW_02.cu
+    ${FUNCTIONS}/anisotropy_01.cu
+    ${FUNCTIONS}/functionA_01.cu
+    ${FUNCTIONS}/functionA_02.cu
+    ${FUNCTIONS}/matrix.cu
+    ${SOLVERLOOP}/utilityKernels.cu
+    ${SOLVERLOOP}/boundary.cu
+    ${SOLVERLOOP}/calcPhaseComp.cu
+    ${SOLVERLOOP}/smooth.cu
+    ${SOLVERLOOP}/computeDrivingForce.cu
+    ${SOLVERLOOP}/computeElastic.cu
+    ${SOLVERLOOP}/updateComposition.cu
+    ${SOLVERLOOP}/updatePhi.cu
+)
+
+# ── Target ───────────────────────────────────────────────────────────────────
+add_executable(microsim_kks_fd_cuda_mpi
+    ${HOST_SOURCES}
+    ${DEVICE_SOURCES}
+)
+
+# CUDA separable compilation handles the -dc / device-link steps automatically.
+set_target_properties(microsim_kks_fd_cuda_mpi PROPERTIES
+    CUDA_SEPARABLE_COMPILATION ON
+    CUDA_ARCHITECTURES         ${CUDA_ARCH}
+)
+
+# computeElastic requires C++17
+set_source_files_properties(${SOLVERLOOP}/computeElastic.cu
+    PROPERTIES COMPILE_OPTIONS "$<$<COMPILE_LANGUAGE:CUDA>:-std=c++17>"
+)
+
+# ── Include directories ──────────────────────────────────────────────────────
+target_include_directories(microsim_kks_fd_cuda_mpi PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    ${FUNCTIONS}
+    ${SOLVERLOOP}
+    ${TDBS}
+    ${HDF5_INCLUDE_DIRS}
+    ${GSL_INCLUDE_DIRS}
+    ${CUDAToolkit_INCLUDE_DIRS}
+)
+
+if(ENABLE_CUFFTMP)
+    # cuFFTMp headers are shipped with the HPC SDK; users can override the path.
+    if(NOT DEFINED CUFFTMP_INCLUDE_DIR)
+        message(WARNING "ENABLE_CUFFTMP=ON but CUFFTMP_INCLUDE_DIR is not set. "
+                        "Provide -DCUFFTMP_INCLUDE_DIR=<path> to the cuFFTMp headers.")
+    else()
+        target_include_directories(microsim_kks_fd_cuda_mpi PRIVATE ${CUFFTMP_INCLUDE_DIR})
+    endif()
+endif()
+
+# ── Compile definitions ───────────────────────────────────────────────────────
+target_compile_definitions(microsim_kks_fd_cuda_mpi PRIVATE
+    ENABLE_HDF5=$<BOOL:${ENABLE_HDF5}>
+    ENABLE_CUFFTMP=$<BOOL:${ENABLE_CUFFTMP}>
+    ${HDF5_DEFINITIONS}
+)
+
+# Suppress common NVHPC/nvcc diagnostic noise
+target_compile_options(microsim_kks_fd_cuda_mpi PRIVATE
+    $<$<COMPILE_LANGUAGE:CXX>:
+        --diag_suppress=declared_but_not_referenced
+        --diag_suppress=set_but_not_used>
+    $<$<COMPILE_LANGUAGE:C>:
+        --diag_suppress=declared_but_not_referenced
+        --diag_suppress=set_but_not_used>
+)
+
+# ── Link libraries ────────────────────────────────────────────────────────────
+target_link_libraries(microsim_kks_fd_cuda_mpi PRIVATE
+    MPI::MPI_CXX
+    GSL::gsl
+    GSL::gslcblas
+    CUDA::cudart
+    m
+)
+
+if(ENABLE_HDF5)
+    target_link_libraries(microsim_kks_fd_cuda_mpi PRIVATE ${HDF5_C_LIBRARIES})
+endif()
+
+if(ENABLE_CUFFTMP)
+    # cuFFTMp – library location can be overridden with -DCUFFTMP_LIB_DIR=<path>
+    if(DEFINED CUFFTMP_LIB_DIR)
+        target_link_directories(microsim_kks_fd_cuda_mpi PRIVATE ${CUFFTMP_LIB_DIR})
+    endif()
+    target_link_libraries(microsim_kks_fd_cuda_mpi PRIVATE cufftMp)
+else()
+    target_link_libraries(microsim_kks_fd_cuda_mpi PRIVATE CUDA::cufft)
+endif()
+
+# ── Utility: write_xdmf ──────────────────────────────────────────────────────
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/write_xdmf.c")
+    add_executable(write_xdmf_kks write_xdmf.c)
+
+    target_include_directories(write_xdmf_kks PRIVATE
+        ${CMAKE_CURRENT_SOURCE_DIR}
+        ${FUNCTIONS}
+        ${SOLVERLOOP}
+        ${HDF5_INCLUDE_DIRS}
+        ${CUDAToolkit_INCLUDE_DIRS}
+    )
+
+    target_compile_definitions(write_xdmf_kks PRIVATE
+        THERMO=0
+        ENABLE_HDF5=$<BOOL:${ENABLE_HDF5}>
+        ${HDF5_DEFINITIONS}
+    )
+
+    target_link_libraries(write_xdmf_kks PRIVATE
+        MPI::MPI_CXX
+        ${HDF5_C_LIBRARIES}
+        CUDA::cudart
+        m
+    )
+endif()
+
+# ── Utility: reconstruct ──────────────────────────────────────────────────────
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/reconstruct.c")
+    add_executable(reconstruct_kks reconstruct.c)
+
+    target_include_directories(reconstruct_kks PRIVATE
+        ${CMAKE_CURRENT_SOURCE_DIR}
+        ${FUNCTIONS}
+        ${SOLVERLOOP}
+        ${CUDAToolkit_INCLUDE_DIRS}
+    )
+
+    target_compile_definitions(reconstruct_kks PRIVATE THERMO=0)
+
+    target_link_libraries(reconstruct_kks PRIVATE
+        MPI::MPI_CXX
+        CUDA::cudart
+        m
+    )
+endif()
+
+install(TARGETS microsim_kks_fd_cuda_mpi RUNTIME DESTINATION bin)