Feature/codecleanup icrar

.clang-format

@@ -0,0 +1,192 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Right
+AlignOperands:   Align
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: 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:     120
+CommentPragmas:  '^ IWYU pragma:'
+QualifierAlignment: Leave
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+PackConstructorInitializers: BinPack
+BasedOnStyle:    ''
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+AllowAllConstructorInitializersOnNextLine: true
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IfMacros:
+  - KJ_IF_MAYBE
+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: ''
+IndentAccessModifiers: false
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+IndentRequires:  false
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+LambdaBodyIndentation: Signature
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 4
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Right
+PPIndentWidth:   -1
+ReferenceAlignment: Pointer
+ReflowComments:  true
+RemoveBracesLLVM: false
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+SortIncludes:    CaseSensitive
+SortJavaStaticImport: Before
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDefinitionName: false
+  AfterFunctionDeclarationName: false
+  AfterIfMacros:   true
+  AfterOverloadedOperator: false
+  BeforeNonEmptyParentheses: false
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  Never
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        Latest
+StatementAttributeLikeMacros:
+  - Q_EMIT
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        4
+UseCRLF:         false
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - STRINGIZE
+  - PP_STRINGIZE
+  - BOOST_PP_STRINGIZE
+  - NS_SWIFT_NAME
+  - CF_SWIFT_NAME
+...
+

CMakeLists.txt

@@ -10,6 +10,7 @@
 # This file is part of VELOCIraptor.
 
 cmake_minimum_required(VERSION 3.13)
+set(CMAKE_CXX_STANDARD 14)
 
 # We have the version here
 file(STRINGS ${CMAKE_CURRENT_SOURCE_DIR}/VERSION VR_VERSION)
@@ -37,6 +38,14 @@ include (VRCMakeUtils)
 # complation summary
 include(VRCompilationMessages)
 
+include(CTest)
+enable_testing()
+
+# Let the *_ROOT variables indicate where to find packages (cmake >= 3.12)
+if (POLICY CMP0074)
+	cmake_policy(SET CMP0074 NEW)
+endif()
+
 #
 # Options users can give on the command line via -D
 #
@@ -75,6 +84,9 @@ vr_option(GADGET_SPH_INFO   "Support for extra SPH information in Gadget" OFF)
 vr_option(GADGET_STAR_INFO  "Support for extra star information in Gadget" OFF)
 vr_option(GADGET_BH_INFO    "Support for extra black hole information in Gadget" OFF)
 
+# Input data perodic wrapping
+vr_option(PARTICLES_OUTSIDE_PERIOD_LIMIT  "If particles are outside the periodic limit, wrap the positions before determining mpi domain" OFF)
+
 # Particle data options
 vr_option(USE_STAR      "Use star particles" OFF)
 vr_option(USE_GAS       "Use gas particles" OFF)
@@ -91,6 +103,7 @@ vr_option(STRUCTURE_DEN "Calculate local density dist. only for particles in fie
 vr_option(HALO_DEN      "Like STRUCTURE_DEN, but se particles inside field objects" OFF)
 vr_option(ZOOM_SIM      "Used to run against simulations with a high resolution region" OFF)
 vr_option(USE_SWIFT_INTERFACE "Used to compile the code with hooks for being called from the SWIFT Hydro nbody code" OFF)
+vr_option(LOG_SOURCE_LOCATION "Append source code location to all logging statements" ON)
 
 
 # Let's true to our word
@@ -173,6 +186,8 @@ vr_option_defines(GADGET_SPH_INFO           EXTRASPHINFO)
 vr_option_defines(GADGET_STAR_INFO          EXTRASTARINFO)
 vr_option_defines(GADGET_BH_INFO            EXTRABHINFO)
 
+vr_option_defines(PARTICLES_OUTSIDE_PERIOD_LIMIT            PERIODWRAPINPUT)
+
 vr_option_defines(USE_GAS                   GASON)
 vr_option_defines(USE_STAR                  STARON)
 vr_option_defines(USE_BH                    BHON)
@@ -187,6 +202,7 @@ vr_option_defines(ZOOM_SIM                  HIGHRES)
 vr_option_defines(USE_LARGE_KDTREE          LARGETREE)
 
 vr_option_defines(USE_SWIFT_INTERFACE       SWIFTINTERFACE)
+vr_option_defines(LOG_SOURCE_LOCATION       VR_LOG_SOURCE_LOCATION)
 
 if (VR_USE_SWIFT_INTERFACE)
         list(APPEND VR_INCLUDE_DIRS ${SWIFT_INCLUDE_DIR})
@@ -218,6 +234,14 @@ vr_nbodylib()
 # compilation state
 vr_compilation_summary()
 
+#
+# Store compilation flags for future reference
+#
+set(compilation_info_cxx "${CMAKE_CURRENT_BINARY_DIR}/compilation_info.cxx")
+configure_file("src/compilation_info.cxx.in" ${compilation_info_cxx} @ONLY)
+
+
+
 # Are we part of an outside build (i.e., of a treefrog build)?
 # If so, we want to let the caller know what to include
 set(_export OFF)

src/CMakeLists.txt

@@ -13,15 +13,19 @@ set(VR_SOURCES
     allvars.cxx
     bgfield.cxx
     buildandsortarrays.cxx
+    "${compilation_info_cxx}"
     endianutils.cxx
     fofalgo.cxx
     gadgetio.cxx
     "${git_revision_cxx}"
     haloproperties.cxx
     hdfio.cxx
+    h5_output_file.cxx
+    h5_utils.cxx
     io.cxx
     localbgcomp.cxx
     localfield.cxx
+    logging.cxx
     mpigadgetio.cxx
     mpihdfio.cxx
     mpinchiladaio.cxx
@@ -39,29 +43,29 @@ set(VR_SOURCES
     ui.cxx
     unbind.cxx
     utilities.cxx
+    vr_exceptions.cxx
 )
 
 add_library(velociraptor STATIC ${VR_SOURCES})
-target_compile_definitions(velociraptor PRIVATE ${VR_DEFINES})
+target_compile_definitions(velociraptor PUBLIC ${VR_DEFINES})
 if (VR_CXX_FLAGS)
-	set_target_properties(velociraptor PROPERTIES COMPILE_FLAGS ${VR_CXX_FLAGS})
+	target_compile_options(velociraptor PUBLIC ${VR_CXX_FLAGS})
 endif()
 set_target_properties(velociraptor PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 
 # Bringing NBodyLib objects into the velociraptor library
-target_link_libraries(velociraptor nbodylib_iface)
+target_link_libraries(velociraptor PUBLIC nbodylib_iface)
 
 add_executable(stf main.cxx)
 target_link_libraries(stf velociraptor ${VR_LIBS})
 
-target_compile_definitions(stf PRIVATE ${VR_DEFINES})
-if (VR_CXX_FLAGS)
-	set_target_properties(stf PROPERTIES COMPILE_FLAGS ${VR_CXX_FLAGS})
-endif()
 if (VR_LINK_FLAGS)
 	set_target_properties(stf PROPERTIES LINK_FLAGS ${VR_LINK_FLAGS})
 endif()
 set_target_properties(stf PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 sanitizer_options(velociraptor)
 
+if (BUILD_TESTING)
+	add_subdirectory(tests)
+endif()