some cleanup

src/phasicFlow/CMakeLists-old.txt

@@ -1,87 +0,0 @@
-
-list(APPEND SourceFiles 
-types/basicTypes/bTypesFunctions.cpp
-types/basicTypes/Logical.cpp
-types/types.cpp
-
-globals/error.cpp
-
-streams/token/tokenIO.cpp
-streams/token/token.cpp
-streams/iStream/IOstream.cpp
-streams/iStream/iIstream.cpp
-streams/iStream/iOstream.cpp
-streams/Stream/Istream.cpp
-streams/Stream/Ostream.cpp
-streams/Fstream/iFstream.cpp
-streams/Fstream/oFstream.cpp
-streams/Fstream/fileStream.cpp 
-streams/TStream/iTstream.cpp
-streams/TStream/oTstream.cpp
-streams/streams.cpp 
-
-dictionary/dictionary.cpp
-dictionary/entry/iEntry.cpp
-dictionary/entry/dataEntry.cpp 
-dictionary/twoPartEntry/twoPartEntry.cpp
-
-fileSystem/fileSystem.cpp
-
-commandLine/commandLine.cpp
-
-random/randomReal/randomReal.cpp
-random/randomReal/randomReals.cpp
-
-Timer/Timer.cpp
-Timer/Timers.cpp
-
-repository/Time/Time.cpp
-repository/Time/timeControl.cpp
-repository/systemControl/systemControl.cpp
-repository/systemControl/dynamicLinkLibs.cpp
-repository/repository/repository.cpp
-repository/IOobject/objectFile.cpp
-repository/IOobject/IOobject.cpp
-repository/IOobject/IOfileHeader.cpp
-
-structuredData/box/box.cpp
-structuredData/cells/cells.cpp
-structuredData/cylinder/cylinder.cpp
-structuredData/sphere/sphere.cpp
-structuredData/iBox/iBoxs.cpp
-structuredData/line/line.cpp
-structuredData/zAxis/zAxis.cpp
-structuredData/pointStructure/pointStructure.cpp
-structuredData/pointStructure/mortonIndexing.cpp
-structuredData/pointStructure/selectors/pStructSelector/pStructSelector.cpp
-structuredData/pointStructure/selectors/selectBox/selectBox.cpp
-structuredData/pointStructure/selectors/selectRange/selectRange.cpp 
-structuredData/pointStructure/selectors/selectRandom/selectRandom.cpp
-structuredData/trisurfaceStructure/triSurface.cpp
-structuredData/trisurfaceStructure/multiTriSurface.cpp
-structuredData/trisurfaceStructure/stlFile.cpp
-structuredData/peakableRegion/sphereRegion/sphereRegion.cpp
-structuredData/peakableRegion/cylinderRegion/cylinderRegion.cpp
-structuredData/peakableRegion/boxRegion/boxRegion.cpp
-structuredData/peakableRegion/peakableRegion/peakableRegion.cpp
-structuredData/peakableRegion/peakableRegions.cpp
-
-containers/Vector/Vectors.cpp
-containers/Field/Fields.cpp
-containers/symArrayHD/symArrays.cpp
-containers/triSurfaceField/triSurfaceFields.cpp
-containers/bitsetHD/bitsetHDs.cpp
-containers/indexContainer/indexContainer.cpp
-
-setFieldList/setFieldList.cpp
-setFieldList/setFieldEntry.cpp
-
-eventSubscriber/eventSubscriber.cpp
-eventSubscriber/eventObserver.cpp)
-
-set(link_libs Kokkos::kokkos tbb)
-
-pFlow_add_library_install(phasicFlow SourceFiles link_libs)
-
-target_include_directories(phasicFlow PUBLIC ./Kokkos ./algorithms ./globals)
-

src/phasicFlow/containers/span/span.hpp

@@ -26,11 +26,15 @@ Licence:
 
 namespace pFlow {
 
-
+/// 
+/// @class span
+/// @brief Represents a view into a contiguous sequence of elements.
+/// 
+/// `span` provides a lightweight way to work with arrays and other contiguous 
+/// sequences without the overhead of copying. This will word on both GPU and CPU
 template<typename T>
 class span
 {
-
 public:
     
     using iterator        = T*;
@@ -47,39 +51,40 @@ public:
     
     using constPointer    = const T*;
 
-protected:
+private:
 
-    T* data_ 		= nullptr;
+    mutable T*     data_ = nullptr;
  
-    uint32 	size_ 	= 0;
+    index          size_ = 0;
 
 public:
     
     TypeInfoTemplateNV11("span", T);
 
-    /// Constructor
+    /// Constructor with no arguments
     INLINE_FUNCTION_HD
     span() = default;
 
 
+    /// Constructor that takes a pointer to the beginning of the data and the size of the span
     INLINE_FUNCTION_HD
     span(T* data, uint32 size)
         : data_(data), size_(size)
     {}
 
-    /// copy
+    /// copy constructor
     INLINE_FUNCTION_HD
     span(const span&) = default;
 
-    /// assignment
+    /// copy assignment operator
     INLINE_FUNCTION_HD
     span& operator=(const span&) = default;
 
-    /// move
+    /// move constructor
     INLINE_FUNCTION_HD
     span(span&&) = default;
 
-    /// assignment
+    /// move assignment operator
     INLINE_FUNCTION_HD
     span& operator=(span&) = default;
 
@@ -90,6 +95,7 @@ public:
         return size_ == 0;
     }
 
+    /// Returns a pointer to the beginning of the data
     INLINE_FUNCTION_HD
     T* data() const
     {
@@ -98,7 +104,7 @@ public:
 
     /// Returns the number of elements in the span
     INLINE_FUNCTION_HD
-    uint32 size() const
+    index size() const
     {
         return size_;
     }
@@ -110,7 +116,7 @@ public:
         return data_;
     }
 
-    /// Returns an iterator to the beginning of the span
+    /// Returns an iterator to the beginning of the span (const version)
     INLINE_FUNCTION_HD
     constIterator cbegin() const
     {
@@ -124,54 +130,34 @@ public:
         return data_ + size_;
     }
 
-    /// Returns an iterator to one past the end of the span
+    /// Returns an iterator to one past the end of the span (const version)
     INLINE_FUNCTION_HD
     constIterator cend() const
     {
         return data_ + size_;
     }
 
+    /// Returns a reference to the element at the specified index
     INLINE_FUNCTION_HD
-    T& operator[](uint32 i)
+    T& operator[](index i)
     {
         return data_[i];
     }
 
+    /// Returns a const reference to the element at the specified index
     INLINE_FUNCTION_HD
-    const T& operator[](uint32 i)const
+    T& operator[](index i)const
-    {
-    	return data_[i];
-    }
-
-    INLINE_FUNCTION_HD
-    T& operator[](int32 i)
-    {
-    	return data_[i];
-    }
-
-    INLINE_FUNCTION_HD
-    const T& operator[](int32 i)const
     {
         return data_[i];
     }
 
 };
 
-/*template<typename T, typename... properties, template<class, class...> class Container>
-size_t makeSpan(Container<T, properties...>& container)
-{
-    return span<T>(container.data(), container.size());
-}
-
-template<typename T, typename... properties, template<class, class...> class Container>
-size_t makeSpan(const Container<T, properties...>& container)
-{
-    return span<T>(
-        const_cast<T*>(container.data()), 
-        container.size());
-}*/
-
 
+/// Creates a span of char from a span of any type.
+/// 
+/// This helper function reinterprets the underlying memory of the given span 
+/// as a span of char.
 template<typename T>
 inline
 span<char> charSpan(span<T> s)
@@ -182,6 +168,10 @@ span<char> charSpan(span<T> s)
 		s.size()*el);
 }
 
+/// Creates a span of const char from a span of const any type.
+/// 
+/// This helper function reinterprets the underlying memory of the given span 
+/// as a span of const char.
 template<typename T>
 inline
 span<const char> charSpan(span<const T> s)
@@ -192,24 +182,6 @@ span<const char> charSpan(span<const T> s)
 		s.size()*el);
 }
 
-/*template<typename T, template<class> class Container>
-span<T> makeSpan(Container<T>& container)
-{
-    return span<T>(container.data(), container.size());
-}
-
-template<typename T, template<class> class Container>
-span<T> makeSpan(const Container<T>& container)
-{
-    return span<T>(
-        const_cast<T*>(container.data()), 
-        container.size());
-}*/
-
-
-
-
-
 
 } // pFlow
 

src/phasicFlow/globals/error.cpp

@@ -32,41 +32,35 @@ Licence:
 static pFlow::Ostream& errorStream = pFlow::pOutput;
 
 pFlow::iOstream&
-fatalErrorMessage(const char* fileName, int linNumber)
+pFlow::fatalErrorMessage(const char* fileName, int lineNumber)
 {
-	errorStream << "\n>>> Fatal error in phasicFlow\n"
+	errorStream << "\nError occured in file ("<<lineNumber<<"):" <<Red_Text(fileName)<<'\n';
-	            << "Error occured in source file " << Red_Text(fileName)
-	            << " at line " << Red_Text(linNumber) << '\n';
 	return errorStream;
 }
 
 pFlow::iOstream&
-fatalErrorInMessage(const char* fnName, const char* fileName, int linNumber)
+pFlow::fatalErrorInMessage(const char* fnName, const char* fileName, int lineNumber)
 {
-	errorStream << "\n>>> Fatal error in phasicFlow\n"
+	errorStream << "\nError occured in file ("<<lineNumber<<"):" <<Red_Text(fileName)<<'\n'<<
-	            << " Error is issued in function " << Red_Text(fnName)
+	"Function: "<<Red_Text(fnName)<<'\n';
-	            << ", located in file " << Red_Text(fileName) << " at line "
-	            << Red_Text(linNumber) << '\n';
 	return errorStream;
 }
 
 pFlow::iOstream&
-notImplementedErrorMessage(
+pFlow::notImplementedErrorMessage(
   const char* fnName,
   const char* fileName,
   int         lineNumber
 )
 {
-	errorStream << "\n>>> Fatal error in phasicFlow\n";
+	errorStream << "\n Function " << Yellow_Text(fnName)
-	errorStream << " Function " << Red_Text(fnName)
 	            << " has not been implemented yet!\n"
-	            << " File " << Yellow_Text(fileName) << " at line "
+	            << " Look into file  ("<<lineNumber<<"):" <<fileName<<'\n';
-	            << Yellow_Text(lineNumber) << '\n';
 	return errorStream;
 }
 
 pFlow::iOstream&
-ioErrorMessage(
+pFlow::ioErrorMessage(
   const char* fileName,
   int         fileLineNumber,
   const char* fnName,
@@ -84,7 +78,7 @@ ioErrorMessage(
 }
 
 pFlow::iOstream&
-ioErrorMessage(
+pFlow::ioErrorMessage(
   const pFlow::word& fileName,
   int                fileLineNumber,
   const char*        fnName,
@@ -98,7 +92,7 @@ ioErrorMessage(
 }
 
 pFlow::iOstream&
-warningMessage(const char* fnName, const char* fileName, int linNumber)
+pFlow::warningMessage(const char* fnName, const char* fileName, int linNumber)
 {
 	errorStream << "\n>>> Warning in phasicFlow\n"
 	            << " Warning is issued in function " << Yellow_Text(fnName)
@@ -108,7 +102,7 @@ warningMessage(const char* fnName, const char* fileName, int linNumber)
 }
 
 pFlow::iOstream&
-reportAndExit(int errorCode)
+pFlow::reportAndExit(int errorCode)
 {
 	errorStream << "\n>>> phasicFlow is exiting . . ." << pFlow::endl;
 	fatalExitPhasicFlow(errorCode);
@@ -116,7 +110,7 @@ reportAndExit(int errorCode)
 }
 
 int
-fatalExitPhasicFlow(int errorCode)
+pFlow::fatalExitPhasicFlow(int errorCode)
 {
 	// Kokkos should be finalized first
 	Kokkos::finalize();

src/phasicFlow/globals/error.hpp

@@ -27,7 +27,7 @@ Licence:
 namespace pFlow
 {
 class iOstream;
-}
+
 
 //- Decleartions
 
@@ -66,35 +66,37 @@ warningMessage(const char* fnName, const char* fileName, int linNumber);
 pFlow::iOstream&
 reportAndExit(int errorCode = EXIT_FAILURE);
 
+}
+
 /// Report a fatal error and exit the applicaiton
-#define fatalError fatalErrorMessage(__FILE__, __LINE__)
+#define fatalError pFlow::fatalErrorMessage(__FILE__, __LINE__)
 
 /// Report a fatal error and supplied function name and exit the application
 #define fatalErrorIn(functionName)                                             \
-	fatalErrorInMessage((functionName), __FILE__, __LINE__)
+	pFlow::fatalErrorInMessage((functionName), __FILE__, __LINE__)
 
 /// Report a fatal error and function name and exit the application
 #define fatalErrorInFunction fatalErrorIn(FUNCTION_NAME)
 
 /// Report that a function is yet not implemented with supplied function name.
 #define Not_Implemented(functionName)                                          \
-	notImplementedErrorMessage((functionName), __FILE__, __LINE__)
+	pFlow::notImplementedErrorMessage((functionName), __FILE__, __LINE__)
 
 /// Report that a function is yet not implemented.
 #define notImplementedFunction Not_Implemented(FUNCTION_NAME)
 
 /// Report an error in file operation with supplied fileName and lineNumber.
 #define ioErrorInFile(fileName, lineNumber)                                    \
-	ioErrorMessage(fileName, lineNumber, FUNCTION_NAME, __FILE__, __LINE__)
+	pFlow::ioErrorMessage(fileName, lineNumber, FUNCTION_NAME, __FILE__, __LINE__)
 
 /// Report a warning with supplied function name
 #define warningIn(functionName)                                                \
-	warningMessage((functionName), __FILE__, __LINE__)
+	pFlow::warningMessage((functionName), __FILE__, __LINE__)
 
 /// Report a warning
 #define warningInFunction warningIn(FUNCTION_NAME)
 
 /// Fatal exit
-#define fatalExit reportAndExit()
+#define fatalExit pFlow::reportAndExit()
 
 #endif

src/phasicFlow/repository/IOobject/objectFile.hpp

@@ -60,7 +60,7 @@ private:
 	fileSystem localPath_ = "";
 
 	/// Number of bytes used for writing/reading real variable (used for binray)
-	int 		numBytesForReal_ = numBytesForReal__;
+	int 		numBytesForReal_ = sizeof(real);
 	
 	/// Does the objectFile read & write the header?
 	bool        readWriteHeader_ = true;

src/phasicFlow/types/basicTypes/bTypesFunctions.hpp

@@ -277,7 +277,7 @@ equal(const uint32& s1, const uint32& s2)
 }
 
 /// Are two words equal (host only)?
-INLINE_FUNCTION
+inline
 bool
 equal(const word& s1, const word& s2)
 {

src/phasicFlow/types/basicTypes/builtinTypes.hpp

@@ -29,20 +29,22 @@ namespace pFlow
 {
 
 #ifdef pFlow_Build_Double
-#define useDouble 1
+	#define UseDouble 1
-inline const char* floatingPointType__ = "double";
+	inline const char* floatingPointType__ = "double";
-inline const bool  usingDouble__       = true;
+	inline const bool  usingDouble__       = true;
 #else
-#define useDouble 0
+	#define UseDouble 0
-inline const char* floatingPointType__ = "float";
+	inline const char* floatingPointType__ = "float";
-inline const bool  usingDouble__       = false;
+	inline const bool  usingDouble__       = false;
 #endif
 
+
+
 // scalars
-#if useDouble
+#if UseDouble
-using real = double;
+	using real = double;
 #else
-using real = float;
+	using real = float;
 #endif
 
 using int8 = signed char;
@@ -57,21 +59,27 @@ using uint32 = unsigned int;
 
 using uint64 = unsigned long long int;
 
-using id_t = uint32;
-
-using size_t = std::size_t;
-
 using word = std::string;
 
 using timeValue = double;
 
-inline const int numBytesForReal__ = sizeof(real);
+#ifdef pFlow_Build_Index64
+	#define Index64 1
+	using index = std::size_t;
+	inline const char* IndexType__ = "std::size_t";
+#else
+	#define Index64 0
+	using index = uint32;
+	inline const char* IndexType__ = "uint32";
+#endif
+
 
 inline word
 floatingPointDescription()
 {
 	return word("In this build, ") + word(floatingPointType__) +
-	       word(" is used for floating point operations.");
+	       word(" is used for floating point operations and ") +
+		   IndexType__ + "for indexing.";
 }
 
 } // end of pFlow

src/phasicFlow/types/triple/triple.hpp

@@ -114,13 +114,13 @@ struct triple
 	triple<T>& operator=(triple<T>&& src) = default;
 
 	/// clone
-	INLINE_FUNCTION
+	inline
 	uniquePtr<triple<T>> clone() const
 	{
 		return makeUnique<triple<T>>(*this);
 	}
 
-	INLINE_FUNCTION
+	inline
 	triple<T>* clonePtr() const
 	{
 		return new triple<T>(*this);

src/phasicFlow/types/triple/tripleFwd.hpp

@@ -103,13 +103,13 @@ INLINE_FUNCTION_HD bool
 operator>=(const triple<T>& opr1, const triple<T>& opr2);
 
 template<typename T>
-INLINE_FUNCTION iOstream&
+inline iOstream&
 operator<<(iOstream& str, const triple<T>& ov);
 
 template<typename T>
-INLINE_FUNCTION iIstream&
+inline iIstream&
 operator>>(iIstream& str, triple<T>& iv);
 
 template<typename T>
-INLINE_FUNCTION void
+inline void
 readIstream(iIstream& str, triple<T>& iv);

src/phasicFlow/types/triple/tripleI.hpp

@@ -287,7 +287,7 @@ pFlow::operator>=(const triple<T>& opr1, const triple<T>& opr2)
 }
 
 template<typename T>
-INLINE_FUNCTION pFlow::iOstream&
+inline pFlow::iOstream&
     pFlow::operator<<(iOstream& str, const triple<T>& ov)
 {
 	str << token::BEGIN_LIST << ov.x_ << token::SPACE << ov.y_ << token::SPACE
@@ -299,7 +299,7 @@ INLINE_FUNCTION pFlow::iOstream&
 }
 
 template<typename T>
-INLINE_FUNCTION pFlow::iIstream&
+inline pFlow::iIstream&
     pFlow::operator>>(iIstream& str, triple<T>& iv)
 {
 	str.readBegin("triple<T>");
@@ -316,7 +316,7 @@ INLINE_FUNCTION pFlow::iIstream&
 }
 
 template<typename T>
-INLINE_FUNCTION void
+inline void
 pFlow::readIstream(iIstream& str, triple<T>& iv)
 {
 	str.readBegin("triple<T>");