Merge branch 'develop' of https://github.com/deepmodeling/abacus-develop into planewave

Author: Qianruipku

.clang-format

@@ -1,166 +1,38 @@
 ---
-Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
+BasedOnStyle: Microsoft
+AccessModifierOffset: '-2'
 AlignAfterOpenBracket: Align
-AlignConsecutiveMacros: None
-AlignConsecutiveAssignments: None
-AlignConsecutiveBitFields: None
-AlignConsecutiveDeclarations: None
-AlignEscapedNewlines: Right
-AlignOperands:   Align
-AlignTrailingComments: true
-AllowAllArgumentsOnNextLine: true
-AllowAllConstructorInitializersOnNextLine: true
-AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortEnumsOnASingleLine: true
-AllowShortBlocksOnASingleLine: Never
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AllowShortLambdasOnASingleLine: All
-AllowShortIfStatementsOnASingleLine: Never
-AllowShortLoopsOnASingleLine: false
-AlwaysBreakAfterDefinitionReturnType: None
-AlwaysBreakAfterReturnType: None
-AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: MultiLine
-AttributeMacros:
-  - __capability
-BinPackArguments: true
-BinPackParameters: true
-BraceWrapping:
-  AfterCaseLabel:  false
-  AfterClass:      false
-  AfterControlStatement: Never
-  AfterEnum:       false
-  AfterFunction:   false
-  AfterNamespace:  false
-  AfterObjCDeclaration: false
-  AfterStruct:     false
-  AfterUnion:      false
-  AfterExternBlock: false
-  BeforeCatch:     false
-  BeforeElse:      false
-  BeforeLambdaBody: false
-  BeforeWhile:     false
-  IndentBraces:    false
-  SplitEmptyFunction: true
-  SplitEmptyRecord: true
-  SplitEmptyNamespace: true
-BreakBeforeBinaryOperators: None
-BreakBeforeConceptDeclarations: true
-BreakBeforeBraces: Attach
-BreakBeforeInheritanceComma: false
-BreakInheritanceList: BeforeColon
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-BreakConstructorInitializers: BeforeColon
-BreakAfterJavaFieldAnnotations: false
-BreakStringLiterals: true
-ColumnLimit:     80
-CommentPragmas:  '^ IWYU pragma:'
-CompactNamespaces: false
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
-ConstructorInitializerIndentWidth: 4
-ContinuationIndentWidth: 4
-Cpp11BracedListStyle: true
-DeriveLineEnding: true
-DerivePointerAlignment: false
-DisableFormat:   false
-EmptyLineBeforeAccessModifier: LogicalBlock
-ExperimentalAutoDetectBinPacking: false
-FixNamespaceComments: true
-ForEachMacros:
-  - foreach
-  - Q_FOREACH
-  - BOOST_FOREACH
-StatementAttributeLikeMacros:
-  - Q_EMIT
-IncludeBlocks:   Preserve
-IncludeCategories:
-  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
-    Priority:        2
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
-    Priority:        3
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '.*'
-    Priority:        1
-    SortPriority:    0
-    CaseSensitive:   false
-IncludeIsMainRegex: '(Test)?$'
-IncludeIsMainSourceRegex: ''
-IndentCaseLabels: false
-IndentCaseBlocks: false
-IndentGotoLabels: true
-IndentPPDirectives: None
-IndentExternBlock: AfterExternBlock
-IndentRequires:  false
-IndentWidth:     4
-IndentWrappedFunctionNames: false
-InsertTrailingCommas: None
-JavaScriptQuotes: Leave
-JavaScriptWrapImports: true
-KeepEmptyLinesAtTheStartOfBlocks: true
-MacroBlockBegin: ''
-MacroBlockEnd:   ''
-MaxEmptyLinesToKeep: 1
-NamespaceIndentation: None
-ObjCBinPackProtocolList: Auto
-ObjCBlockIndentWidth: 2
-ObjCBreakBeforeNestedBlockParam: true
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
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-PenaltyBreakString: 1000
-PenaltyBreakTemplateDeclaration: 10
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
-PenaltyIndentedWhitespace: 0
+AlignConsecutiveMacros: 'true'
+AlignEscapedNewlines: Left
+AlignOperands: 'true'
+AlignTrailingComments: 'false'
+AllowAllArgumentsOnNextLine: 'false'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+BreakBeforeBinaryOperators: All
+BreakBeforeTernaryOperators: 'true'
+Cpp11BracedListStyle: 'true'
+DerivePointerAlignment: 'true'
+FixNamespaceComments: 'true'
+IncludeBlocks: Regroup
+IndentWidth: '4'
+Language: Cpp
 PointerAlignment: Right
-ReflowComments:  true
-SortIncludes:    true
-SortJavaStaticImport: Before
-SortUsingDeclarations: true
-SpaceAfterCStyleCast: false
-SpaceAfterLogicalNot: false
-SpaceAfterTemplateKeyword: true
-SpaceBeforeAssignmentOperators: true
-SpaceBeforeCaseColon: false
-SpaceBeforeCpp11BracedList: false
-SpaceBeforeCtorInitializerColon: true
-SpaceBeforeInheritanceColon: true
-SpaceBeforeParens: ControlStatements
-SpaceAroundPointerQualifiers: Default
-SpaceBeforeRangeBasedForLoopColon: true
-SpaceInEmptyBlock: false
-SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
-SpacesInAngles:  false
-SpacesInConditionalStatement: false
-SpacesInContainerLiterals: true
-SpacesInCStyleCastParentheses: false
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-SpaceBeforeSquareBrackets: false
-BitFieldColonSpacing: Both
-Standard:        Latest
-StatementMacros:
-  - Q_UNUSED
-  - QT_REQUIRE_VERSION
-TabWidth:        8
-UseCRLF:         false
-UseTab:          Never
-WhitespaceSensitiveMacros:
-  - STRINGIZE
-  - PP_STRINGIZE
-  - BOOST_PP_STRINGIZE
-  - NS_SWIFT_NAME
-  - CF_SWIFT_NAME
-...
+ReflowComments: 'true'
+SortIncludes: 'true'
+SortUsingDeclarations: 'true'
+SpaceAfterCStyleCast: 'false'
+SpaceAfterLogicalNot: 'false'
+SpaceBeforeRangeBasedForLoopColon: 'false'
+SpaceInEmptyParentheses: 'false'
+SpacesInAngles: 'false'
+SpacesInCStyleCastParentheses: 'false'
+SpacesInContainerLiterals: 'false'
+SpacesInParentheses: 'false'
+SpacesInSquareBrackets: 'false'
+Standard: Cpp11
+TabWidth: '4'
+UseTab: ForContinuationAndIndentation
 
+...

.devcontainer/devcontainer.json

@@ -1,5 +1,10 @@
-// For format details, see https://aka.ms/devcontainer.json.
+// To develop inside a pre-configured container, see https://code.visualstudio.com/docs/remote/containers .
+// For format details, see https://aka.ms/devcontainer.json .
 {
 	"image":"ghcr.io/deepmodeling/abacus-development-kit:gnu",
-	"extensions": ["ms-vscode.cpptools-extension-pack"]
-}
+	"extensions": [
+		"ms-vscode.cpptools-extension-pack",
+		"xaver.clang-format",
+		"cschlosser.doxdocgen"
+	]
+}

.editorconfig

@@ -1,7 +1,7 @@
 root = true
 
 [*]
-indent_style = space
+indent_style = tab
 indent_size = 4
 charset = utf-8
 end_of_line = lf

.github/workflows/test.yml

@@ -4,9 +4,10 @@ on:
   pull_request_target:
     branches:
       - develop
-      - reconstruction
-      - newelpa
-
+      - update_MD
+      - ABACUS_2.2.0_beta
+      - deepks
+      - planewave
 jobs:
 
   start-runner:

.gitpod.yml

@@ -0,0 +1,2 @@
+# https://www.gitpod.io/docs/configure
+image: "ghcr.io/deepmodeling/abacus-development-kit:gnu"

.readthedocs.yaml

@@ -7,7 +7,8 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: ABACUS.develop/source/module_orbital/1_Documents/sphinx/source/conf.py
+   configuration: source/module_deepks/sphinx/source/conf.py
+#   configuration: source/module_orbital/1_Documents/sphinx/source/conf.py
 
 # Optionally build your docs in additional formats such as PDF
 formats:
@@ -17,4 +18,4 @@ formats:
 python:
    version: 3.7
    install:
-   - requirements: ABACUS.develop/source/module_orbital/1_Documents/sphinx/requirements.txt
+   - requirements: source/module_orbital/1_Documents/sphinx/requirements.txt

CMakeLists.txt

@@ -47,7 +47,7 @@ if(USE_OPENMP)
   find_package(OpenMP REQUIRED)
   target_link_libraries(${ABACUS_BIN_NAME} OpenMP::OpenMP_CXX)
   add_compile_options(${OpenMP_CXX_FLAGS})
-  add_compile_definitions(__OPENMP)
+  #add_compile_definitions(_OPENMP)
 endif()
 
 set(CMAKE_CXX_STANDARD 11)
@@ -114,10 +114,20 @@ if(MKLROOT)
   find_package(IntelMKL REQUIRED)
   add_definitions(-D__MKL -DMKL_ILP64)
   include_directories(${MKL_INCLUDE_DIRS} ${MKL_INCLUDE_DIRS}/fftw)
-  target_link_libraries(${ABACUS_BIN_NAME}
-    -lifcore
-    IntelMKL::MKL
-  )
+  
+  # Since libtorch will find its own MKL, the fftw part conflicts with the original one.
+  # When enable deepks, mkl will be linked within ${TORCH_LIBRARIES}.
+  if(ENABLE_DEEPKS)
+    target_link_libraries(${ABACUS_BIN_NAME}
+      -lifcore
+      # IntelMKL::MKL
+    )
+  else()
+    target_link_libraries(${ABACUS_BIN_NAME}
+      -lifcore
+      IntelMKL::MKL
+    )
+  endif()
 else()
   find_package(FFTW3 REQUIRED)
   find_package(LAPACK REQUIRED)
@@ -135,7 +145,7 @@ if(ENABLE_DEEPKS)
   find_package(Torch REQUIRED)
   include_directories(${TORCH_INCLUDE_DIRS})
   target_link_libraries(${ABACUS_BIN_NAME} ${TORCH_LIBRARIES})
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
+  add_compile_options(${TORCH_CXX_FLAGS})
 
   find_path(libnpy_SOURCE_DIR
     npy.hpp
@@ -149,7 +159,7 @@ if(ENABLE_DEEPKS)
     )
     FetchContent_MakeAvailable(libnpy)
   endif()
-  include_directories(${libnpy_SOURCE_DIR})
+  include_directories(${libnpy_SOURCE_DIR}/include)
   add_compile_definitions(__DEEPKS)
 endif()
 

Dockerfile.gnu

@@ -39,8 +39,8 @@ RUN cd /tmp \
     && cd /tmp && rm -rf fftw-3.3.9 && rm fftw-3.3.9.tar.gz
 
 RUN cd /tmp \
-    && wget https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-1.9.0%2Bcpu.zip --no-check-certificate --quiet \
-    && unzip libtorch-shared-with-deps-1.9.0+cpu.zip \
+    && wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.9.1%2Bcpu.zip --no-check-certificate --quiet \
+    && unzip libtorch-cxx11-abi-shared-with-deps-1.9.1+cpu.zip \
     && cp -r libtorch/include /usr/local \
     && cp -r libtorch/lib /usr/local \
     && cp -r libtorch/share /usr/local \