Refactor: Organize code structure to improve maintainability in pyabacus (#5346)

* fix some typos in `_hsolver.py`

* fix some bugs caused by #5134

* Refactor hsolver module and remove unused code

* refactor the structure of pythonization source code

* fix some bug

* Refactor __getattr__ function in __init__.py to handle attribute errors

* fix some bugs

* Add CONTRIBUTING.md to facilitate contributing to pyabacus project

* fix typos

* Update CONTRIBUTING.md

* Update CONTRIBUTING.md

* update README.md and CONTRIBUTING.md

* update README.md

* update CONTRIBUTING.md

* update CONTRIBUTING.md

* fix a bug caused by tuple in python3.8

* update

Author: a1henu

python/pyabacus/CMakeLists.txt

@@ -1,18 +1,20 @@
 cmake_minimum_required(VERSION 3.15...3.26)
 
+# project settings
 project(
   ${SKBUILD_PROJECT_NAME}
   VERSION ${SKBUILD_PROJECT_VERSION}
   LANGUAGES CXX)
 
+# find python and pybind11
 find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
 find_package(pybind11 CONFIG REQUIRED)
 
+# set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/module_base")
 set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/module_hsolver")
-set(HAMILT_PATH "${ABACUS_SOURCE_DIR}/module_hamilt_general")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
 set(ENABLE_LCAO ON)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/../../cmake")
@@ -63,11 +65,14 @@ else()
   endif()
 endif()
 
-include_directories(${BASE_PATH} 
+# add include directories
+include_directories(
+    ${BASE_PATH} 
     ${ABACUS_SOURCE_DIR}
-    ${ABACUS_SOURCE_DIR}/module_base/module_container)
+    ${ABACUS_SOURCE_DIR}/module_base/module_container
+    )
 
-# add library
+# add basic libraries
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 # add base
 set(BASE_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/base")
@@ -80,83 +85,6 @@ set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
 add_subdirectory(${ABACUS_SOURCE_DIR}/module_basis/module_ao ${ORB_BINARY_DIR})
 # set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
-# add nao shared library  
-list(APPEND _naos
-    ${NAO_PATH}/atomic_radials.cpp
-    ${NAO_PATH}/beta_radials.cpp
-    ${NAO_PATH}/hydrogen_radials.cpp
-    ${NAO_PATH}/numerical_radial.cpp
-    ${NAO_PATH}/pswfc_radials.cpp
-    ${NAO_PATH}/radial_collection.cpp
-    ${NAO_PATH}/radial_set.cpp
-    ${NAO_PATH}/real_gaunt_table.cpp
-    ${NAO_PATH}/sphbes_radials.cpp
-    ${NAO_PATH}/two_center_bundle.cpp
-    ${NAO_PATH}/two_center_integrator.cpp
-    ${NAO_PATH}/two_center_table.cpp
-    ${NAO_PATH}/projgen.cpp
-    # dependency
-    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_op.cpp
-    # ${ABACUS_SOURCE_DIR}/module_psi/kernels/psi_memory_op.cpp
-    ${ABACUS_SOURCE_DIR}/module_base/module_device/memory_op.cpp
-    )
-add_library(naopack SHARED 
-    ${_naos}
-    )
-# add diago shared library
-list(APPEND _diago
-    ${HSOLVER_PATH}/diago_dav_subspace.cpp
-    ${HSOLVER_PATH}/diago_david.cpp
-    ${HSOLVER_PATH}/diag_const_nums.cpp
-    ${HSOLVER_PATH}/diago_iter_assist.cpp
-
-    ${HSOLVER_PATH}/kernels/dngvd_op.cpp
-    ${HSOLVER_PATH}/kernels/math_kernel_op.cpp
-    # dependency
-    ${BASE_PATH}/module_device/device.cpp
-    ${BASE_PATH}/module_device/memory_op.cpp
-
-    ${HAMILT_PATH}/operator.cpp
-    ${PSI_PATH}/psi.cpp
-  )
-add_library(diagopack SHARED 
-    ${_diago}
-    )
-target_link_libraries(diagopack
-    PRIVATE
-    ${OpenBLAS_LIBRARIES} 
-    ${LAPACK_LIBRARIES}
-    )
-# link math_libs
-if(MKLROOT)
-  target_link_libraries(naopack
-    base
-    parameter
-    container
-    orb
-    ${math_libs}
-    MPI::MPI_CXX
-    OpenMP::OpenMP_CXX
-  )
-else()
-  target_link_libraries(naopack
-    base
-    parameter
-    container
-    orb
-    ${math_libs}
-  )
-endif()
-# list(APPEND _sources ${_naos} ${_bases})
-list(APPEND _sources
-    ${PROJECT_SOURCE_DIR}/src/py_abacus.cpp
-    ${PROJECT_SOURCE_DIR}/src/py_base_math.cpp
-    ${PROJECT_SOURCE_DIR}/src/py_m_nao.cpp
-    ${PROJECT_SOURCE_DIR}/src/py_hsolver.cpp
-    )
-pybind11_add_module(_core MODULE ${_sources})
-target_link_libraries(_core PRIVATE pybind11::headers naopack diagopack)
-target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
 # set RPATH
 execute_process(
   COMMAND "${PYTHON_EXECUTABLE}" -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"
@@ -167,9 +95,9 @@ execute_process(
 # set package name to pyabacus
 set(TARGET_PACK pyabacus)
 set(CMAKE_INSTALL_RPATH "${PYTHON_SITE_PACKAGES}/${TARGET_PACK}")
-set_target_properties(_core PROPERTIES INSTALL_RPATH "$ORIGIN")
-set_target_properties(naopack PROPERTIES INSTALL_RPATH "$ORIGIN")
-set_target_properties(diagopack PROPERTIES INSTALL_RPATH "$ORIGIN")
-install(TARGETS _core naopack DESTINATION ${TARGET_PACK})
-install(TARGETS _core diagopack DESTINATION ${TARGET_PACK})
+
+# add subdirectories for submodules
+add_subdirectory(${PROJECT_SOURCE_DIR}/src/hsolver)
+add_subdirectory(${PROJECT_SOURCE_DIR}/src/ModuleBase)
+add_subdirectory(${PROJECT_SOURCE_DIR}/src/ModuleNAO)