Merge branch 'develop' into warning

.clang-format

@@ -1,44 +1,44 @@
 ---
-Language:        Cpp
+Language: Cpp
 BasedOnStyle: Microsoft
 
-AlignArrayOfStructures: Left
+AlignArrayOfStructures: Right
 AlwaysBreakTemplateDeclarations: Yes
 
-AllowAllArgumentsOnNextLine: 'false'
-AllowAllParametersOfDeclarationOnNextLine: 'false'
-BinPackArguments: 'false'
-BinPackParameters: 'false'
+AllowAllArgumentsOnNextLine: false
+AllowAllParametersOfDeclarationOnNextLine: false
+BinPackArguments: false
+BinPackParameters: false
 
 BreakBeforeBinaryOperators: All
-BreakBeforeTernaryOperators: 'true'
+BreakBeforeTernaryOperators: true
 
-Cpp11BracedListStyle: 'true'
-FixNamespaceComments: 'true'
+Cpp11BracedListStyle: true
+FixNamespaceComments: true
 
 # About include
-IncludeBlocks:   Regroup
+IncludeBlocks: Regroup
 IncludeCategories:
-  - Regex:           '^<ext/.*\.h>'
-    Priority:        2
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '^<.*'
-    Priority:        2
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '.*'
-    Priority:        3
-    SortPriority:    0
-    CaseSensitive:   false
+  - Regex: '^<ext/.*\.h>'
+    Priority: 2
+    SortPriority: 0
+    CaseSensitive: false
+  - Regex: '^<.*\.h>'
+    Priority: 1
+    SortPriority: 0
+    CaseSensitive: false
+  - Regex: '^<.*'
+    Priority: 2
+    SortPriority: 0
+    CaseSensitive: false
+  - Regex: '.*'
+    Priority: 3
+    SortPriority: 0
+    CaseSensitive: false
 IncludeIsMainRegex: '([-_](test|unittest))?$'
 IncludeIsMainSourceRegex: ''
 
-IndentWidth: '4'
+IndentWidth: 4
 IndentWrappedFunctionNames: true
 
 # About Point
@@ -47,22 +47,22 @@ PointerAlignment: Left
 
 PackConstructorInitializers: NextLine
 
-ReflowComments: 'true'
-SortIncludes: 'true'
-SortUsingDeclarations: 'true'
+ReflowComments: true
+SortIncludes: true
+SortUsingDeclarations: true
 
 # About space
-SpaceAfterCStyleCast: 'false'
-SpaceAfterLogicalNot: 'false'
-SpaceBeforeRangeBasedForLoopColon: 'false'
-SpaceInEmptyParentheses: 'false'
-SpacesInAngles: 'false'
-SpacesInCStyleCastParentheses: 'false'
-SpacesInContainerLiterals: 'false'
-SpacesInParentheses: 'false'
-SpacesInSquareBrackets: 'false'
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceBeforeRangeBasedForLoopColon: false
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
 
-Standard: Cpp11
-TabWidth: '4'
+Standard: c++11
+TabWidth: 4
 UseTab: Never
 ...

.github/pull_request_template.md

@@ -1,11 +1,15 @@
 ### Reminder
 - [ ] Have you linked an issue with this pull request?
+- [ ] Have you added adequate unit tests and/or case tests for your pull request?
 - [ ] Have you noticed possible changes of behavior below or in the linked issue?
 - [ ] Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)
 
 ### Linked Issue
 Fix #...
 
+### Unit Tests and/or Case Tests for my changes
+- A unit test is added for each new feature or bug fix.
+
 ### What's changed?
 - Example: My changes might affect the performance of the application under certain conditions, and I have tested the impact on various scenarios...
 

.github/workflows/pytest.yml

@@ -0,0 +1,26 @@
+name: Pyabacus Build and Test
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    name: PyTest
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/deepmodeling/abacus-gnu
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+            python-version: 3.8
+      - name: Build Pyabacus
+        run: |
+          cd python/pyabacus
+          python -m pip install -v .[test]
+      - name: Test Pyabacus
+        run: |
+          cd python/pyabacus/tests
+          pytest -v

CMakeLists.txt

@@ -4,7 +4,6 @@ if(POLICY CMP0135) # https://cmake.org/cmake/help/git-stage/policy/CMP0135.html
 endif()
 
 project(ABACUS
-    VERSION 3.0.0
     DESCRIPTION "ABACUS is an electronic structure package based on DFT."
     HOMEPAGE_URL "https://github.com/deepmodeling/abacus-develop"
     LANGUAGES CXX
@@ -394,19 +393,9 @@ if(MKLROOT)
     list(APPEND math_libs -lifcore)
   endif()
 else()
-  # In compatibility to builtin FindLAPACK.cmake before v3.5.4
-  if(DEFINED LAPACK_DIR)
-    string(APPEND CMAKE_PREFIX_PATH ";${LAPACK_DIR}")
-  endif()
-  if(DEFINED LAPACK_LIBRARY)
-    set(LAPACK_LIBRARIES ${LAPACK_LIBRARY})
-  endif()
-  if(DEFINED BLAS_DIR)
-    string(APPEND CMAKE_PREFIX_PATH ";${BLAS_DIR}")
-  endif()
 
   find_package(FFTW3 REQUIRED)
-  find_package(LAPACK REQUIRED)
+  find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
 

Dockerfile.cuda

@@ -17,7 +17,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DUSE_CUDA=ON && \
+    cmake -B build -DUSE_CUDA=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

Dockerfile.gnu

@@ -21,7 +21,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON && \
+    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

Dockerfile.intel

@@ -56,7 +56,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 RUN source /opt/intel/oneapi/setvars.sh && \
     git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON && \
+    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

cmake/FindBlas.cmake

@@ -0,0 +1,15 @@
+if(DEFINED BLAS_DIR)
+    string(APPEND CMAKE_PREFIX_PATH ";${BLAS_DIR}")
+endif()
+if(DEFINED BLAS_LIBRARY)
+    set(BLAS_LIBRARIES ${BLAS_LIBRARY})
+endif()
+
+find_package(BLAS REQUIRED)
+
+if(NOT TARGET BLAS::BLAS)
+    add_library(BLAS::BLAS UNKNOWN IMPORTED)
+    set_target_properties(BLAS::BLAS PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+	IMPORTED_LOCATION "${BLAS_LIBRARIES}")
+endif()

cmake/FindLapack.cmake

@@ -0,0 +1,17 @@
+# In compatibility to builtin FindLAPACK.cmake before v3.5.4
+if(DEFINED LAPACK_DIR)
+  string(APPEND CMAKE_PREFIX_PATH ";${LAPACK_DIR}")
+endif()
+if(DEFINED LAPACK_LIBRARY)
+  set(LAPACK_LIBRARIES ${LAPACK_LIBRARY})
+endif()
+
+find_package(Blas REQUIRED)
+find_package(LAPACK REQUIRED)
+
+if(NOT TARGET LAPACK::LAPACK)
+    add_library(LAPACK::LAPACK UNKNOWN IMPORTED)
+    set_target_properties(LAPACK::LAPACK PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+        IMPORTED_LOCATION "${LAPACK_LIBRARIES}")
+endif()

cmake/FindLibxc.cmake

@@ -11,7 +11,7 @@ endif()
 find_package(PkgConfig)
 if(PKG_CONFIG_FOUND)
   pkg_search_module(Libxc IMPORTED_TARGET GLOBAL libxc)
-  find_package_handle_standard_args(Libxc DEFAULT_MSG Libxc_LINK_LIBRARIES Libxc_INCLUDE_DIRS)
+  find_package_handle_standard_args(Libxc DEFAULT_MSG Libxc_LINK_LIBRARIES Libxc_FOUND)
 endif()
 if(NOT Libxc_FOUND)
   find_package(Libxc REQUIRED HINTS