Types folder updated

CMakeLists.txt

@@ -72,11 +72,11 @@ include_directories(src/setHelpers src/demComponent "${PROJECT_BINARY_DIR}")
 
 add_subdirectory(src)
 
-add_subdirectory(solvers)
+#add_subdirectory(solvers)
 
-add_subdirectory(utilities)
+#add_subdirectory(utilities)
 
-add_subdirectory(DEMSystems)
+#add_subdirectory(DEMSystems)
 #add_subdirectory(testIO)
 
 install(FILES "${PROJECT_BINARY_DIR}/phasicFlowConfig.H"

src/CMakeLists.txt

@@ -1,15 +1,15 @@
 
 add_subdirectory(phasicFlow)
 
-add_subdirectory(Integration)
+#add_subdirectory(Integration)
 
-add_subdirectory(Property)
+#add_subdirectory(Property)
 
-add_subdirectory(Particles)
+#add_subdirectory(Particles)
 
-add_subdirectory(Interaction)
+#add_subdirectory(Interaction)
 
-add_subdirectory(MotionModel)
+#add_subdirectory(MotionModel)
 
-add_subdirectory(Geometry)
+#add_subdirectory(Geometry)
 

src/phasicFlow/CMakeLists-old.txt

@@ -0,0 +1,87 @@
+
+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/CMakeLists.txt

@@ -4,84 +4,11 @@ types/basicTypes/bTypesFunctions.cpp
 types/basicTypes/Logical.cpp
 types/types.cpp
 
-globals/error.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)
+target_include_directories(phasicFlow PUBLIC ./globals)
 

src/phasicFlow/containers/List/List/List.hpp

@@ -227,9 +227,8 @@ iIstream& operator >>(iIstream& is, List<T>& lst);
 
 using int64List 	= List<int64>;
 using int32List 	= List<int32>;
-using int16List 	= List<int16>;
 using int8List 		= List<int8>;
-using labelList 	= List<label>;
+using uint64List 	= List<uint64>;
 using uint32List 	= List<uint32>;
 
 using realList 		= List<real>;

src/phasicFlow/globals/error.cpp

@@ -21,10 +21,17 @@ Licence:
 #include <iostream>
 #include <stdlib.h>
 
+#ifdef pFlow_Build_MPI
+	#include <mpi.h>
+#endif
+
+#include <Kokkos_Core.hpp>
+
 #include "error.hpp"
 #include "streams.hpp"
 
 
+
 static pFlow::Ostream& errorStream   = pFlow::errReport;
 
 
@@ -93,4 +100,22 @@ pFlow::iOstream& reportAndExit()
 	return errorStream;
 }
 
+int exitPhasicFlow()
+{
+// Kokkos should be finalized first
+Kokkos::finalize();
 
+#ifdef pFlow_Build_MPI
+	int flag=0;
+	MPI_Initialized(&flag)
+	if(flag == 1)
+	{
+		MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
+		MPI_Finalize();
+    }
+    exit(EXIT_FAILURE);
+#else
+    exit(EXIT_FAILURE);
+#endif
+	return EXIT_FAILURE;
+}

src/phasicFlow/globals/error.hpp

@@ -18,7 +18,6 @@ Licence:
 
 -----------------------------------------------------------------------------*/
 
-
 #ifndef __error_hpp__
 #define __error_hpp__
 
@@ -26,36 +25,17 @@ Licence:
 #include "builtinTypes.hpp"
 
 
+//- Forward decleartions 
 namespace pFlow
 {
 	class iOstream;	
 }
 
 
-// reports a fatal error and exit the applicaiton 
+//- Decleartions 
-#define fatalError \
-	fatalErrorMessage(__FILE__, __LINE__)
 
-#define fatalErrorIn( functionName ) \
+/// Take actions to fatal exit phasicFlow
-	fatalErrorInMessage((functionName), __FILE__, __LINE__ )
+int fatalExitPhasicFlow();
-
-#define fatalErrorInFunction fatalErrorIn(FUNCTION_NAME)
-
-#define Not_Implemented(functionName) \
-    notImplementedErrorMessage ((functionName), __FILE__, __LINE__ )
-        
-#define notImplementedFunction Not_Implemented(FUNCTION_NAME);
-
-#define ioErrorInFile( fileName, lineNumber) \
-	ioErrorMessage( fileName, lineNumber, FUNCTION_NAME, __FILE__, __LINE__ )
-
-#define warningIn( functionName ) \
-	warningMessage((functionName), __FILE__, __LINE__ )
-
-#define warningInFunction warningIn(FUNCTION_NAME)
-
-#define fatalExit \
-	reportAndExit()
 
 pFlow::iOstream& fatalErrorMessage(const char* fileName, int linNumber );
 pFlow::iOstream& fatalErrorInMessage(const char* fnName, const char* fileName, int linNumber );
@@ -65,4 +45,38 @@ pFlow::iOstream& ioErrorMessage(const char* fileName, int fileLineNumber, const
 pFlow::iOstream& warningMessage(const char* fnName, const char* fileName, int linNumber );
 pFlow::iOstream& reportAndExit();
 
+
+/// Report a fatal error and exit the applicaiton 
+#define fatalError \
+	fatalErrorMessage(__FILE__, __LINE__)
+
+/// Report a fatal error and supplied function name and exit the application 
+#define fatalErrorIn( functionName ) \
+	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__ )
+
+/// 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__ )
+
+/// Report a warning with supplied function name
+#define warningIn( functionName ) \
+	warningMessage((functionName), __FILE__, __LINE__ )
+
+/// Report a warning
+#define warningInFunction warningIn(FUNCTION_NAME)
+
+/// Fatal exit 
+#define fatalExit \
+	reportAndExit()
+
 #endif

src/phasicFlow/globals/globalSettings.hpp

@@ -25,10 +25,7 @@ Licence:
 
 namespace pFlow
 {
-
+const inline double vectorGrowthFactor__ = 1.2;
-const inline double vectorGrowthFactor__ = 1.1;
-
-
 }
 
 

src/phasicFlow/globals/pFlowMacros.hpp

@@ -70,7 +70,7 @@ Licence:
 
 #define ForAll(i, container) for(auto i=0; i < container.size(); ++i)
 
-#ifdef USE_STD_PARALLEL_ALG
+#ifdef pFlow_STD_Parallel_Alg
 static inline const bool useStdParallel__ = true;
 #else
 static inline const bool useStdParallel__ = false;

src/phasicFlow/streams/Stream/Istream.hpp

@@ -46,128 +46,125 @@ class Istream
     std::istream& is_;
 
 
-    //- Get the next valid character
+    /// Get the next valid character
     char nextValid();
 
-    //- Read a word token
+    /// Read a word token
     void readWordToken(token& t);
 
     
-    //- Read a variable name starting with '$'.
+    /// Read a variable name starting with '$'.
     //  Handles "$var" and "${var}" forms, permits '/' scoping character.
     Istream& readVariable(word& str);
 
-    //- No copy assignment
+    /// No copy assignment
     void operator=(const Istream&) = delete;
 
 
 public:
 
 
-    //- Construct wrapper around std::istream, set stream status
+    /// Construct wrapper around std::istream, set stream status
     Istream( std::istream& is, const word& streamName, writeFormat wf = ASCII);
 
-    //- Destructor
+    /// Destructor
     virtual ~Istream() = default;
 
 
     //// - Methods
 
-    //- Return the name of the stream
+    /// Return the name of the stream
     virtual const word& name() const
     {
         return name_;
     }
 
-    //- Return non-const access to the name of the stream
+    /// Return non-const access to the name of the stream
     virtual word& name()
     {
         return name_;
     }
 
-    //- Return flags of output stream
+    /// Return flags of output stream
     virtual ios_base::fmtflags flags() const;
 
 
     //// Read Functions
 
-    //- Raw, low-level get character function.
+    /// Raw, low-level get character function.
     Istream& get(char& c);
 
-    //- Raw, low-level peek function.
+    /// Raw, low-level peek function.
     //  Does not remove the character from the stream.
     //  Returns the next character in the stream or EOF if the
     //  end of file is read.
     int peek();
 
-    //- Raw, low-level getline (until delimiter) into a string.
+    /// Raw, low-level getline (until delimiter) into a string.
     Istream& getLine(word& str, char delim = '\n');
 
-    //- Low-level discard until delimiter
+    /// Low-level discard until delimiter
     //  return the number of characters extracted
     std::streamsize getLine(std::nullptr_t, char delim = '\n');
 
-    //- Raw, low-level putback character function.
+    /// Raw, low-level putback character function.
     Istream& putback(const char c);
 
-    //- Return next token from stream
+    /// Return next token from stream
     virtual iIstream& read(token& t) override;
 
-    //- Read a character
+    /// Read a character
     virtual iIstream& read(char& c) override;
 
-    //- Read a word
+    /// Read a word
     virtual iIstream& read(word& str) override;
 
-    //- Read a string
+    /// Read a string
     virtual iIstream& readString(word& str) override;
 
-    //- Read a int64
+    /// Read a int64
     virtual iIstream& read(int64&) override;
 
-    //- Read a int32
+    /// Read a int32
     virtual iIstream& read(int32&) override;
 
-    //- Read a int16
+    /// Read a int8
-    virtual iIstream& read(int16&) override;
-
-    //- Read a int8
     virtual iIstream& read(int8&) override;
 
-    //- Read a label
+    /// Read a uint64
-    virtual iIstream& read(label&) override;
+    virtual iIstream& read(uint64&) override;
 
-    //- Read a uint32
+    /// Read a uint32
     virtual iIstream& read(uint32&) override;
 
-    //- Read a uint16
+    /// Read a uint8
-    virtual iIstream& read(uint16&) override;
+    virtual iIstream& read(uint8&) override;
 
-    //- Read a float
+    /// Read a float
     virtual iIstream& read(float& val) override;
 
-    //- Read a double
+    /// Read a double
     virtual iIstream& read(double& val) override;
 
     iIstream& read(char* buffer, std::streamsize count) override;
 
     
-    //- Rewind the stream so that it may be read again
+    /// Rewind the stream so that it may be read again
     virtual void rewind();
 
 
-    //- Set stream flags
+    /// Set stream flags
     virtual ios_base::fmtflags flags(const ios_base::fmtflags flags);
 
 
 
-    //- Access to underlying std::istream
+    /// Access to underlying std::istream
     virtual std::istream& stdStream()
     {
         return is_;
     }
 
-    //- Const access to underlying std::istream
+    /// Const access to underlying std::istream
     virtual const std::istream& stdStream() const
     {
         return is_;

src/phasicFlow/streams/Stream/Ostream.hpp

@@ -48,112 +48,115 @@ public:
     
     Ostream ( std::ostream& os, const word& streamName, writeFormat wf = ASCII);
 
-    //- no copy construct 
+    /// no copy construct 
     Ostream(const Ostream&) = delete;
 
-    //- No copy assignment
+    /// No copy assignment
     void operator=(const Ostream&) = delete;
 
 
     //// - Methods
 
-    //- Return the name of the stream
+    /// Return the name of the stream
         virtual const word& name() const
         {
             return name_;
         }
 
-        //- Return non-const access to the name of the stream
+        /// Return non-const access to the name of the stream
         virtual word& name()
         {
             return name_;
         }
 
-        //- Return flags of output stream
+        /// Return flags of output stream
         virtual ios_base::fmtflags flags() const;
 
 
-        //- Write token to stream or otherwise handle it.
+        /// Write token to stream or otherwise handle it.
         //  return false if the token type was not handled by this method
         bool write(const token& tok)override;
 
-        //- Write character
+        /// Write character
         iOstream& write(const char c)override;
 
-        //- Write character string
+        /// Write character string
         iOstream& write(const char* str)override;
 
-        //- Write word
+        /// Write word
         iOstream& write(const word& str)override;
     
-        //- Write std::string surrounded by quotes.
+        /// Write std::string surrounded by quotes.
         //  Optional write without quotes.
         iOstream& writeQuoted ( const word& str, const bool quoted=true ) override;
 
-        //- Write int64
+        /// Write int64
         iOstream& write(const int64 val) override;
 
-        //- Write int32
+        /// Write int32
         iOstream& write(const int32 val) override;
 
-        //- Write label
+        /// Write int32
-        iOstream& write(const label val) override;
+        iOstream& write(const int8 val) override;
 
-        //- Write uint32
+        /// Write uint64
+        iOstream& write(const uint64 val) override;
+
+        /// Write uint32
         iOstream& write(const uint32 val) override;
 
-        //- Write uint16
+        /// Write uint8
-        iOstream& write(const uint16 val) override;
+        iOstream& write(const uint8 val) override;
 
-        //- Write float
+        /// Write float
         iOstream& write(const float val) override;
 
-        //- Write double
+        /// Write double
         iOstream& write(const double val) override;
 
         /// Write a block of binray data 
         iOstream& write(const char* binaryData, std::streamsize count) override;
 
-        //- Add indentation characters
+        /// Add indentation characters
         void indent() override;
 
-        //- Set stream flags
+        /// Set stream flags
         ios_base::fmtflags flags(const ios_base::fmtflags f) override;
 
-        //- Flush stream
+        /// Flush stream
         void flush() override;
 
-        //- Add newline and flush stream
+        /// Add newline and flush stream
         void endl() override;
 
-        //- Get the current padding character
+        /// Get the current padding character
         char fill() const override;
 
-        //- Set padding character for formatted field up to field width
+        /// Set padding character for formatted field up to field width
         //  \return previous padding character
         char fill(const char fillch) override;
 
-        //- Get width of output field
+        /// Get width of output field
         int width() const override;
 
-        //- Set width of output field
+        /// Set width of output field
         //  \return previous width
         int width(const int w) override;
 
-        //- Get precision of output field
+        /// Get precision of output field
         int precision() const override;
 
-        //- Set precision of output field
+        /// Set precision of output field
         //  return old precision
         int precision(const int p) override;
 
-        //- Access to underlying std::ostream
+        /// Access to underlying std::ostream
         virtual std::ostream& stdStream() 
         {
             return os_;
         }
 
-        //- Const access to underlying std::ostream
+        /// Const access to underlying std::ostream
         virtual const std::ostream& stdStream() const
         {
             return os_;

src/phasicFlow/streams/TStream/iTstream.hpp

@@ -46,7 +46,7 @@ public:
 
     //// - Constructors 
 
-        //- construct with a name
+        /// construct with a name
         iTstream(const word& streamName);
 
         // - construct with name and copy
@@ -72,55 +72,52 @@ public:
         // move assignment from tokenList
         void operator=(tokenList&& tList);
 
-        //- Destructor
+        /// Destructor
         virtual ~iTstream() = default;
 
 
     //// Member Functions   
 
-        //- Return the name of the stream
+        /// Return the name of the stream
         virtual const word& name() const;
 
-        //- Return non-const access to the name of the stream
+        /// Return non-const access to the name of the stream
         virtual word& name();
 
-        //- Return next token from stream
+        /// Return next token from stream
         virtual iIstream& read(token& t)override;
 
-        //- Read a character
+        /// Read a character
         virtual iIstream& read(char& c)override;
 
-        //- Read a word
+        /// Read a word
         virtual iIstream& read(word& str)override;
 
-        //- Read a string
+        /// Read a string
         virtual iIstream& readString(word& str)override;
 
-       //- Read a int64
+        /// Read a int64
         virtual iIstream& read(int64&) override;
 
-        //- Read a int32
+        /// Read a int32
         virtual iIstream& read(int32&) override;
         
-        //- Read a int16
+        /// Read a int8
-        virtual iIstream& read(int16&) override;
-
-        //- Read a int8
         virtual iIstream& read(int8&) override;
 
-        //- Read a label
+        /// Read a uint64
-        virtual iIstream& read(label&) override;
+        virtual iIstream& read(uint64&) override;
 
-        //- Read a uint32
+        /// Read a uint32
         virtual iIstream& read(uint32&) override;
 
-        //- Read a uint16
+        /// Read a uint8
-        virtual iIstream& read(uint16&) override;
+        virtual iIstream& read(uint8&) override;
 
-        //- Read a floatScalar
+        /// Read a floatScalar
         virtual iIstream& read(float&) override;
 
-        //- Read a doubleScalar
+        /// Read a doubleScalar
         virtual iIstream& read(double&) override;
 
         iIstream& read(char* buffer, std::streamsize count) override;
@@ -147,13 +144,13 @@ public:
         // - append token to the end of token and rewind the stream 
         void appendToken(const token& t);
    
-        //- Return flags of output stream
+        /// Return flags of output stream
         ios_base::fmtflags flags() const
         {
             return ios_base::fmtflags(0);
         }
 
-        //- Set flags of stream
+        /// Set flags of stream
         ios_base::fmtflags flags(const ios_base::fmtflags)
         {
             return ios_base::fmtflags(0);        

src/phasicFlow/streams/TStream/oTstream.hpp

@@ -61,45 +61,47 @@ public:
 
     //// - Write
 
-        //- Write token to stream or otherwise handle it.
+        /// Write token to stream or otherwise handle it.
         //  return false if the token type was not handled by this method
         virtual bool write(const token& tok);
 
-        //- Write single character. Whitespace is suppressed.
+        /// Write single character. Whitespace is suppressed.
         virtual iOstream& write(const char c);
 
-        //- Write the word-characters of a character string.
+        /// Write the word-characters of a character string.
         //  Sends as a single char, or as word.
         virtual iOstream& write(const char* str);
 
-        //- Write word
+        /// Write word
         virtual iOstream& write(const word& str);
 
         
-        //- Write std::string surrounded by quotes.
+        /// Write std::string surrounded by quotes.
         //  Optional write without quotes.
         virtual iOstream& writeQuoted(const std::string& str, const bool quoted=true );
 
-        //- Write int64
+        /// Write int64
         virtual iOstream& write(const int64 val) override;
 
-        //- Write int32
+        /// Write int32
         virtual iOstream& write(const int32 val) override;
 
+        /// Write int8
+        virtual iOstream& write(const int8 val) override;
 
-        //- Write label
+        /// Write uint64
-        virtual iOstream& write(const label val) override;
+        virtual iOstream& write(const uint64 val) override;
 
-        //- Write uint32
+        /// Write uint32
         virtual iOstream& write(const uint32 val) override;
 
-        //- Write uint16
+        /// Write uint8
-        virtual iOstream& write(const uint16 val) override;
+        virtual iOstream& write(const uint8 val) override;
 
-        //- Write float
+        /// Write float
         virtual iOstream& write(const float val) override;
 
-        //- Write double
+        /// Write double
         virtual iOstream& write(const double val) override;
 
         /// Write a block of binray data
@@ -107,80 +109,80 @@ public:
             const char* binaryData, 
             std::streamsize count) override;
 
-        // - append token to the stream
+        /// append token to the stream
         virtual void append(const token& tok);
         
-        // - append a list of tokens to the stream
+        /// append a list of tokens to the stream
         virtual void append(const tokenList& tLisk);
         
     
 
     //// - Stream state functions
 
-        //- Reset the output buffer and rewind the stream
+        /// Reset the output buffer and rewind the stream
         void reset();
 
-        //- Rewind the output stream
+        /// Rewind the output stream
         virtual void rewind();
 
-        //- Add indentation characters
+        /// Add indentation characters
         virtual void indent()
         {}
 
-        //- Flush stream
+        /// Flush stream
         virtual void flush()
         {}
 
-        //- Add newline and flush stream
+        /// Add newline and flush stream
         virtual void endl()
         {}
 
-        //- Get the current padding character
+        /// Get the current padding character
         //  \return previous padding character
         virtual char fill() const
         {
             return 0;
         }
 
-        //- Set padding character for formatted field up to field width
+        /// Set padding character for formatted field up to field width
         virtual char fill(const char)
         {
             return 0;
         }
 
-        //- Get width of output field
+        /// Get width of output field
         virtual int width() const
         {
             return 0;
         }
 
-        //- Set width of output field
+        /// Set width of output field
         //  \return previous width
         virtual int width(const int)
         {
              return 0;
         }
 
-        //- Get precision of output field
+        /// Get precision of output field
         virtual int precision() const
         {
              return 0;
         }
 
-        //- Set precision of output field
+        /// Set precision of output field
         //  \return old precision
         virtual int precision(const int)
         {
              return 0;
         }
 
-        //- Return flags of output stream
+        /// Return flags of output stream
         virtual ios_base::fmtflags flags() const
         {
             return ios_base::fmtflags(0);
         }
 
-        //- Set flags of stream
+        /// Set flags of stream
         ios_base::fmtflags flags(const ios_base::fmtflags)
         {
             return ios_base::fmtflags(0);

src/phasicFlow/streams/iStream/iIstream.hpp

@@ -29,7 +29,10 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ *  Interface input stream class 
+ * 
+ */
 class iIstream // interface class for input streams
 :
 	public IOstream
@@ -37,17 +40,17 @@ class iIstream // interface class for input streams
 
 	// Private Data
 
-    //- Has a token been put back on the stream?
+    /// Has a token been put back on the stream?
     bool putBack_;
 
-    //- The last token put back on the stream
+    /// The last token put back on the stream
     token putBackToken_;
 
 public:
 
-    //// - Constructors    
+    ///// Constructors    
 
-    	// - default
+    	/// default
 	    iIstream():
 			IOstream(),
 	        putBack_(false)	
@@ -58,85 +61,82 @@ public:
 	    	putBack_(false)
 	    {}
 
-	    // - Copy construct
+	    /// Copy construct
 	    iIstream(const iIstream&) = default;
 
-	    // - Destructor
+	    /// Destructor
 	    virtual ~iIstream() = default;
 
 
 
     //// member methods
 
-	    //- Put back token
+	    /// Put back token
-	    //  Only a single put back is permitted
+	    ///  Only a single put back is permitted
 	    void putBack(const token& tok);
 
-	    //- Get the put back token if there is one and return true.
+	    /// Get the put back token if there is one and return true.
-	    //  Return false if no put back token is available.
+	    ///  Return false if no put back token is available.
 	    bool getBack(token& tok);
 
-	    //- Peek at the put back token without removing it.
+	    /// Peek at the put back token without removing it.
-	    //  Returns false if no put back token is available and set the
+	    ///  Returns false if no put back token is available and set the
-	    //  token to undefined.
+	    ///  token to undefined.
 	    bool peekBack(token& tok);
 
-	    //- reset the put back token;
+	    /// reset the put back token;
 	    void resetPutBack()
 	    {
 	    	putBackToken_.reset();
 	    	putBack_ = false;
 	    }
 
-	    //- Return next token from stream
+	    /// Return next token from stream
 	    virtual iIstream& read(token&) = 0;
 
-	    //- Read a character
+	    /// Read a character
 	    virtual iIstream& read(char&) = 0;
 
-	    //- Read a string (including enclosing double-quotes)
+	    /// Read a string (including enclosing double-quotes)
 	    virtual iIstream& read(word&) = 0;
 
-	    //- Read a string 
+	    /// Read a string 
 	    virtual iIstream& readString(word&) = 0;    
 
-	    //- Read a int64
+	    /// Read a int64
 	    virtual iIstream& read(int64&) = 0;
 
-	    //- Read a int32
+	    /// Read a int32
 	    virtual iIstream& read(int32&) = 0;
 
-	    //- Read a int16
+	    /// Read a int8
-	    virtual iIstream& read(int16&) = 0;
-
-	    //- Read a int8
 	    virtual iIstream& read(int8&) = 0;
 
-	    //- Read a label
+	    /// Read a uint64
-	    virtual iIstream& read(label&) = 0;
+	    virtual iIstream& read(uint64&) = 0;
 
-	    //- Read a uin32
+	    /// Read a uin32
 	    virtual iIstream& read(uint32&) = 0;
 
-	    //- Read a uin16
+	    /// Read a uint8
-	    virtual iIstream& read(uint16&) = 0;
+	    virtual iIstream& read(uint8&) = 0;
 
-	    //- Read a floatScalar
+	    /// Read a floatScalar
 	    virtual iIstream& read(float&) = 0;
 
-	    //- Read a doubleScalar
+	    /// Read a doubleScalar
 	    virtual iIstream& read(double&) = 0;
 
 	    virtual iIstream& read(char* buffer, std::streamsize count) =0;
 
 	    
-	    //- Rewind the stream so that it may be read again
+	    /// Rewind the stream so that it may be read again
 	    virtual void rewind() = 0;
 
 
-    //// - find and lookups
+    ///// find and lookups
 
-        // - search for all tokesn and find the first word token tbat matchs w
+        /// search for all tokesn and find the first word token tbat matchs w
         virtual bool findToken( const word & w );
 
         /// search for all tokesn after the current file position 
@@ -144,69 +144,69 @@ public:
         virtual bool findTokenResume(const word& w);
 
 
-        // - search for all tokesn and find the first word token that matchs 
+        /// search for all tokesn and find the first word token that matchs 
         virtual bool findTokenSilent( const word & w, int32 limitLine = 100 );
 
         /// search for all tokesn after the current file position 
         /// and find the first word token tbat matchs w
         virtual bool findTokenResumeSilent( const word & w, int32 limitLine = 100 );
 
-        // - search for all tokens and find the first word token and also next word token
+        /// search for all tokens and find the first word token and also next word token
-        //   chekck if it is eneded with end statement ;
+        /// chekck if it is eneded with end statement ;
         virtual bool findTokenAndNext( const word& w, word& nextW, bool checkEndStatement = true);
 
 
         virtual bool findTokenAndNextSilent( const word& w, word& nextW, int32 limitLine = 100);
 
-        // - find a pair of keyword and data terminated by ;
+        /// find a pair of keyword and data terminated by ;
-        //   keyword data;
+        ///  keyword data;
-        //   return false if keyword does not exist or reading fails. 
+        ///  return false if keyword does not exist or reading fails. 
         template<typename T>
         bool findKeywordAndVal(const word& keyword, T& val, bool checkEndStatement = true);
 
-        // - lookup for keyword and data;
+        /// lookup for keyword and data;
-        //   fatalExit if fails
+        ///  fatalExit if fails
         template<typename T>
         T lookupData(const word& keyword);
 
-        // - lookup for keyword and data;
+        /// lookup for keyword and data;
-        //   set to setVal if lookup fails. 
+        ///  set to setVal if lookup fails. 
         template<typename T>
         T lookupDataOrSet(const word& keyword, const T& setVal);
         
-        // - read the data next to keword 
+        /// read the data next to keword 
-        //   keyword    data; 
+        /// keyword    data; 
-        //   check the keyword is correct or not 
+        /// check the keyword is correct or not 
         template<typename T>
         bool nextData(const word& keyword, T& data);
 
 	//// Read List punctuation tokens
 
-	    //- Begin read of data chunk, starts with '('.
+	    /// Begin read of data chunk, starts with '('.
-	    //  return true or FatalIOError
+	    /// return true or FatalIOError
 	    bool readBegin(const char* funcName);
 
-	    //- End read of data chunk, ends with ')'
+	    /// End read of data chunk, ends with ')'
-	    //  return true or FatalIOError
+	    /// return true or FatalIOError
 	    bool readEnd(const char* funcName);
 
-	    //- Begin read of data chunk, starts with '('.
+	    /// Begin read of data chunk, starts with '('.
-	    //  return true or FatalIOError
+	    /// return true or FatalIOError
 	    bool readBeginSquare(const char* funcName);
 
-	    //- Begin read of data chunk, starts with '('.
+	    /// Begin read of data chunk, starts with '('.
-	    //  return true or FatalIOError
+	    /// return true or FatalIOError
 	    bool readEndSquare(const char* funcName);
 
-	    //- Begin read of list data, starts with '(' or '{'
+	    /// Begin read of list data, starts with '(' or '{'
-	    //  return starting delimiter or FatalIOError
+	    /// return starting delimiter or FatalIOError
 	    char readBeginList(const char* funcName);
 
-	    //- End read of list data, ends with ')' or '}'
+	    /// End read of list data, ends with ')' or '}'
-	    //  return closing delimiter or FatalIOError
+	    /// return closing delimiter or FatalIOError
 	    char readEndList(const char* funcName);
 
-	    // End statement character ;
+	    /// End statement character ;
 	    char readEndStatement(const char* funcName);
 
     	
@@ -217,13 +217,13 @@ public:
 
 typedef iIstream& (*iIstreamManip)(iIstream&);
 
-//- operator>> handling for manipulators without arguments
+/// operator>> handling for manipulators without arguments
 inline iIstream& operator>>(iIstream& is, iIstreamManip f)
 {
     return f(is);
 }
 
-//- operator>> handling for manipulators without arguments
+/// operator>> handling for manipulators without arguments
 inline iIstream& operator>>(iIstream& is, IOstreamManip f)
 {
     f(is);
@@ -233,22 +233,19 @@ inline iIstream& operator>>(iIstream& is, IOstreamManip f)
 
 // read operation for basic types it gets from the 
 // token stream
-
 inline iIstream& operator>>( iIstream& is, word & w);
 
 inline iIstream& operator>>( iIstream& is, int64& val);
 
 inline iIstream& operator>>( iIstream& is, int32& val);
 
-inline iIstream& operator>>( iIstream& is, int16& val);
-
 inline iIstream& operator>>( iIstream& is, int8& val);
 
+inline iIstream& operator>>( iIstream& is, uint64& val);
+
 inline iIstream& operator>>( iIstream& is, uint32& val);
 
-inline iIstream& operator>>( iIstream& is, uint16& val);
+inline iIstream& operator>>( iIstream& is, uint8& val);
-
-inline iIstream& operator>>( iIstream& is, label& val);
 
 inline iIstream& operator>>( iIstream& is, float& val);
 

src/phasicFlow/streams/iStream/iIstreamI.hpp

@@ -200,13 +200,6 @@ inline pFlow::iIstream& pFlow::operator>>( iIstream& is, int32& val)
     return is;
 }
 
-inline pFlow::iIstream& pFlow::operator>>( iIstream& is, int16& val)
-{
-    int64 lval(0);
-    is>>lval;
-    val = static_cast<int16>(lval);
-    return is;
-}
 
 inline pFlow::iIstream& pFlow::operator>>( iIstream& is, int8& val)
 {
@@ -216,11 +209,11 @@ inline pFlow::iIstream& pFlow::operator>>( iIstream& is, int8& val)
     return is;
 }
 
-inline pFlow::iIstream& pFlow::operator>>( iIstream& is, label& val)
+inline pFlow::iIstream& pFlow::operator>>( iIstream& is, uint64& val)
 {
     int64 lval(0);
     is>>lval;
-    val = static_cast<label>(lval);
+    val = static_cast<uint64>(lval);
     return is;
 }
 
@@ -232,11 +225,11 @@ inline pFlow::iIstream& pFlow::operator>>( iIstream& is, uint32& val)
     return is;
 }
 
-inline pFlow::iIstream& pFlow::operator>>( iIstream& is, uint16& val)
+inline pFlow::iIstream& pFlow::operator>>( iIstream& is, uint8& val)
 {
     int64 lval(0);
     is>>lval;
-    val = static_cast<uint16>(lval);
+    val = static_cast<uint8>(lval);
     return is;
 }
 

src/phasicFlow/streams/iStream/iOstream.hpp

@@ -118,14 +118,17 @@ public:
         /// Write int32
         virtual iOstream& write(const int32 val) = 0;
 
-        /// Write label
+        /// Write int8
-        virtual iOstream& write(const label val) = 0;
+        virtual iOstream& write(const int8 val) = 0;
+
+        /// Write uint64
+        virtual iOstream& write(const uint64 val) = 0;
 
         /// Write uint32
         virtual iOstream& write(const uint32 val) = 0;
 
-        /// Write uint16
+        /// Write uint8
-        virtual iOstream& write(const uint16 val) = 0;
+        virtual iOstream& write(const uint8 val) = 0;
 
         /// Write float
         virtual iOstream& write(const float val) = 0;
@@ -377,17 +380,13 @@ inline iOstream& operator<<( iOstream& os, const int32& val)
     return os.write(val);
 }
 
-inline iOstream& operator<<( iOstream& os, const int16& val)
-{
-    return os.write(val);
-}
 
 inline iOstream& operator<<( iOstream& os, const int8& val)
 {
     return os.write(val);
 }
 
-inline iOstream& operator<<( iOstream& os, const label& val)
+inline iOstream& operator<<( iOstream& os, const uint64& val)
 {
     return os.write(val);
 }
@@ -397,7 +396,7 @@ inline iOstream& operator<<( iOstream& os, const uint32& val)
     return os.write(val);
 }
 
-inline iOstream& operator<<( iOstream& os, const uint16& val)
+inline iOstream& operator<<( iOstream& os, const uint8& val)
 {
     return os.write(val);
 }

src/phasicFlow/streams/token/token.hpp

@@ -17,28 +17,30 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-// based on OpenFOAM stream, with some modifications/simplifications
-// to be tailored to our needs
-
-
 #ifndef __token_hpp__
 #define __token_hpp__
 
 
 #include "bTypes.hpp"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
 
 namespace pFlow
 {
 
-// Forward Declarations
+//- Forward Declarations
 class token;
 class iIstream;
 class iOstream;
+
 iOstream& operator<<(iOstream& os, const token& tok);
 
 
+/**
+ *  Token class 
+ *  based on OpenFOAM stream, with some modifications/simplifications
+ *  to be tailored to our needs 
+ */
 class token
 {
 public:
@@ -212,8 +214,8 @@ public:
     //- Construct punctuation character token
     inline explicit token(punctuationToken p, int32 lineNumber=0);
 
-    //- Construct label token
+    //- Construct uint64 token
-    inline explicit token(const label val, int32 lineNumber=0);
+    inline explicit token(const uint64 val, int32 lineNumber=0);
 
     //- Construct uint32 token
     inline explicit token(const uint32 val, int32 lineNumber=0);

src/phasicFlow/streams/token/tokenI.hpp

@@ -144,7 +144,7 @@ inline pFlow::token::token(punctuationToken p, int32 lineNumber)
     data_.punctuationVal = p;
 }
 
-inline pFlow::token::token(const label val, int32 lineNumber)
+inline pFlow::token::token(const uint64 val, int32 lineNumber)
 :
     data_(),
     type_(tokenType::INT64),

src/phasicFlow/typeSelection/typeInfo.hpp

@@ -137,18 +137,18 @@ namespace pFlow
 	template<>
 	inline word basicTypeName<int32>(){ return "int32"; }
 
-	template<>
-	inline word basicTypeName<int16>(){ return "int16"; }
-
 		template<>
 	inline word basicTypeName<int8>(){ return "int8"; }
 
 	template<>
-	inline word basicTypeName<label>(){ return "label"; }
+	inline word basicTypeName<uint64>(){ return "uint64"; }
 
 	template<>
 	inline word basicTypeName<uint32>(){ return "uint32"; }
 
+	template<>
+	inline word basicTypeName<uint8>(){ return "uint8"; }
+
 	template<>
 	inline word basicTypeName<real>(){ return "real"; }
 

src/phasicFlow/types/basicTypes/Logical.hpp

@@ -17,7 +17,6 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
 #ifndef __Logical_hpp__
 #define __Logical_hpp__
 
@@ -25,22 +24,32 @@ Licence:
 #include "bTypesFunctions.hpp"
 #include "typeInfo.hpp"
 
+
 namespace pFlow
 {
 
+//- Forward 
 class iIstream;
 class iOstream;
 
-// allias for bool
+/**
+ *  Holds a bool value and converts strings to bool 
+ * 
+ */
 class Logical
 {
 protected:
+
+	/// bool value 
 	bool s_ = false;
 
+	/// Set numbe of of Yes or No
 	int  yesNoSet_ = 0;
 
+	/// Set of Yes or Nos
 	inline static const word YesNo__[4][2] = {{"Yes", "No"},{"on","off"},{"true","false"}, {"Ok","No"}};
 
+	/// Construct from bool and set number 
 	inline explicit Logical(bool s, int yns)
 	:	
 		s_(s),
@@ -49,30 +58,39 @@ protected:
 
 public:
 
+	/// Type info
 	TypeInfoNV("Logical");
 	
+	//// Constructors 
 
+		/// Default constructor 
 		inline Logical(){}
 			
-
+		/// Construct from bool 
 		inline explicit Logical(bool s)
 		:
-	 	s_(s),
+		 	s_(s)
-	 	yesNoSet_(0)
 		{}
 
+		/// Construct from word 
 		Logical(const word& l);
 		
+		/// Construct from char string 
 		Logical(const char* ch);
 
+		/// Copy 
 		Logical(const Logical&) = default;
 
+		/// Move 
 		Logical(Logical&&) = default;
 
+		/// Copy assignment 
 		Logical& operator=(const Logical&) = default;
 
+		/// Move assignment 
 		Logical& operator=(Logical&&) = default;
 
+		/// Assignment with bool
 		inline Logical& operator=(const bool& b)
 		{ 
 			s_ = b;
@@ -80,26 +98,34 @@ public:
 			return *this;
 		}
 	
+	//// Methods 
+	
+		/// () operator, return bool value 
 		inline bool operator()() const
 		{
 			return s_;
 		}
 		
+		/// Return bool value 
 		inline explicit operator bool() const
 		{
 			return s_;
 		}
 
+		/// Not operator 
 		inline Logical operator!()const
 		{
 			return Logical(!s_, yesNoSet_);
 		}
 
 	//// IO operations
+	
 		bool read(iIstream& is);
 
 		bool write(iOstream& os)const; 
 
+	//// Static members 
+
 		bool static evaluteWord(const word& l, bool& b, int& yesNoSet );
 	
 

src/phasicFlow/types/basicTypes/bTypesFunctions.cpp

@@ -41,6 +41,29 @@ pFlow::int32 pFlow::countChar( const char* s, const char c)
     );
 }
 
+pFlow::word pFlow::toUpper(const word & inStr)
+{
+    word oStr(inStr);
+    transform(inStr.begin(), inStr.end(), oStr.begin(), ::toupper);
+    return oStr;
+}
+
+bool pFlow::isYes(const word & str)
+{
+    word s = toUpper(str);
+
+    if( s == "YES" || s=="Y" || s == "OK" || s == "TRUE" || s == "ON" || s=="T") return true;
+    return false;
+}
+
+bool pFlow::isNo(const word & str)
+{
+    word s = toUpper(str);
+
+    if( s == "NO" || s == "N" || "FALSE" || s == "OFF" || s == "F") return true;
+    return false;
+}
+
 pFlow::word pFlow::real2Fixed(const real & v, int32 numPrecision)
 {
     std::stringstream ss;
@@ -104,29 +127,6 @@ pFlow::word pFlow::real2FixedStripZeros(const real & v, int32 numPrecision)
     return removeDecimalZeros(strVal);
 }
 
-pFlow::word pFlow::toUpper(const word & inStr)
-{
-    word oStr(inStr);
-    transform(inStr.begin(), inStr.end(), oStr.begin(), ::toupper);
-    return oStr;
-}
-
-bool pFlow::isYes(const word & str)
-{
-    word s = toUpper(str);
-
-    if( s == "YES" || s == "OK" || s == "TRUE" || s == "ON" || s=="T") return true;
-    return false;
-}
-
-bool pFlow::isNo(const word & str)
-{
-    word s = toUpper(str);
-
-    if( s == "NO" || s == "N" || "FALSE" || s == "OFF" || s == "F") return true;
-    return false;
-}
-
 
 pFlow::word pFlow::angleBracketsNames(const word& w1, const word& w2)
 {
@@ -222,25 +222,6 @@ bool pFlow::validWordWithQuote(const word& w)
     return true;
 }
 
-
-bool pFlow::readLabel( const word& w, label & val)
-{
-    try{
-        val = std::stoull(w);
-    }
-    catch (...)
-    {
-        return false;
-    }
-    return true;
-}
-
-bool pFlow::readLabel( const char* buf, label & val)
-{
-    word w(buf);
-    return readLabel(w, val);
-}
-
 bool pFlow::readUint32( const word& w, uint32 & val)
 {
     try{
@@ -296,42 +277,13 @@ bool pFlow::readInt32( const char* buf, int32 & val)
 }
 
 
-bool pFlow::readInt16( const word& w, int16 & val)
-{
-    try{
-        val = static_cast<int16>(std::stoi(w));
-    }
-    catch (...)
-    {
-        return false;
-    }
-    return true;
-}
-
-bool pFlow::readInt16( const char* buf, int16 & val)
-{
-    word w(buf);
-    return readInt16(w, val);
-}
-
-bool pFlow::readInt8( const word& w, int8 & val)
-{
-    try{
-        val = static_cast<int8>(std::stoi(w));
-    }
-    catch (...)
-    {
-        return false;
-    }
-    return true;
-}
-
 bool pFlow::readInt8( const char* buf, int8 & val)
 {
     word w(buf);
     return readInt8(w, val);
 }
-#include <iostream>
+
+//#include <iostream>
 bool pFlow::readReal( const word& w, real & val)
 {
     try{
@@ -364,7 +316,6 @@ bool pFlow::readReal( const char* buf, real & val )
         return false;
     }
     
-    
     return true;
 }
 

src/phasicFlow/types/basicTypes/bTypesFunctions.hpp

@@ -17,6 +17,10 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
+/*! \file bTypeFunctions.hpp
+   
+    \brief Helper functions for built-in types.  
+ */ 
 
 #ifndef __bTypesFunctions_hpp__
 #define __bTypesFunctions_hpp__
@@ -27,127 +31,132 @@ Licence:
 #include "math.hpp"
 
 
-// helper functions and constants for basic types 
+
 namespace pFlow
 {
 
-
+/// Zero real variable 
 inline const real  zero = 0.0;
+
+/// one real variable 
 inline const real  one  = 1.0;
 
+/// zero int32 variable 
 inline const int32  zero32 = 0;
+
+/// one int32 variable 
 inline const int32  one32  = 1;
 
+/// null/empty word 
 inline const word nullWord;
 
+/// white space 
 inline const word whiteSpace(" \t\n\v\f\r");
 
-
+/// Count numer of chars c in a word
 int32 countChar (const word& s, const char c);
 
+/// Count numer of chars c in a char string
 int32 countChar(const char* s, const char c);
 
+/// convert a word to all caps
 word toUpper(const word & inStr);
 
+/// Check if str equals "Yes", "Y", "True", "Ok", "ON", or "T"
 bool isYes(const word & str);
 
+/// Check if str equals "No", "N", "False", or "Off"
 bool isNo(const word & str);
 
+/// Convert floating point variable to string with fixed number of precisions 
 word real2Fixed(const real & v, int32 numPrecision = 6);
 
+/// Convert floating point variable to string with general format  
 word real2Word(const real & v, int32 numPrecision = 6);
 
-word removeDecimalZeros(const word& str);
+/// Convert int32 to word 
-
-word real2FixedStripZeros(const real & v, int32 numPrecision = 6);
-
 word int322Word(const int32 & v);
 
+/// Remove zeros from decimal part of a string number 
+word removeDecimalZeros(const word& str);
 
+/// Convert to fixed point variable and remove zeros 
+word real2FixedStripZeros(const real & v, int32 numPrecision = 6);
+ 
+/// Output <w1,w2> 
 word angleBracketsNames(const word& w1, const word& w2);
 
- 
+/// Output base<w1,w2>
 word angleBracketsNames2(const word& base, const word& w1, const word& w2);
 
+/// Output base<w1,sw2,w3>
 word angleBracketsNames3(const word& base, const word& w1, const word& w2, const word& w3);
 
+/// Group words and output bw.tw
 word groupNames(const word& bw, const word& tw, char sep = '.');
 
+/// Find the base in a group separated by "." and return it. 
 word baseName(const word& w, char sep = '.');
 
+/// Find tail name in a group separated by "." and return it. 
 word tailName(const word& w, char sep = '.');
 
-
+/// Is the character valid for a word name?
-// is the character valid for a word name  
 bool validWord(char c);
 
+/// Is c a valid character including quote?
 bool validWordWithQuote(char c);
 
-
+/// Is a valid word?
 bool validWord(const word& w);
 
+/// Is a valid word with qoute?
 bool validWordWithQuote(const word& c);
 
-
+/// Convert word to uint32
-bool readLabel( const word& w, label & val);
-
-
-bool readLabel( const char* buf, label & val);
-
-
 bool readUint32( const word& w, uint32 & val);
 
-
+/// Convert char string to uint32
 bool readUint32( const char* buf, uint32 & val);
 
-
+/// Convert word to int64
 bool readInt64( const word& w, int64 & val);
 
-
+/// Convert char string to int64
 bool readInt64( const char* buf, int64 & val);
 
-
+/// Convert word to int32
 bool readInt32( const word& w, int32 & val);
 
-
+/// Convert char string to int32
 bool readInt32( const char* buf, int32 & val);
 
 
-bool readInt16( const word& w, int16 & val);
+/// Convert word to int8
-
-
-bool readInt16( const char* buf, int16 & val);
-
-
 bool readInt8( const word& w, int8 & val);
 
-
+/// Convert char string to int8
 bool readInt8( const char* buf, int8 & val);
 
-
+/// Convert word to real 
 bool readReal( const word& w, real & val);
 
-
+/// Convert char string to real 
 bool readReal( const char* buf, real & val );
 
-
+/// Convert word to bool
 bool readBoolian_Str( const word& w, bool & val);
 
-
+/// Convert char string to bool 
 bool readBoolian_Str( const char* buf, bool & val);
 
+
 inline
 bool readValue(const word& w, real& val)
 {
     return readReal(w,val);
 }
 
-inline
-bool readValue(const word& w, label& val)
-{
-    return readLabel(w,val);
-}
-
 inline
 bool readValue(const word& w, uint32& val)
 {
@@ -166,11 +175,6 @@ bool readValue(const word& w, int32& val)
     return readInt32(w,val);
 }
 
-inline
-bool readValue(const word& w, int16& val)
-{
-    return readInt16(w,val);
-}
 
 inline
 bool readValue(const word& w, int8& val)
@@ -185,53 +189,53 @@ bool readValue(const word& w, bool& val)
 }
 
 
-INLINE_FUNCTION_HD bool equal(const real& s1, const real& s2)
+INLINE_FUNCTION_HD 
+bool equal(const real& s1, const real& s2)
 {
     return abs(s1 - s2) <= smallValue;
 }
 
-INLINE_FUNCTION_HD bool equal(const int64& s1, const int64& s2)
+INLINE_FUNCTION_HD 
+bool equal(const int64& s1, const int64& s2)
 {
     return s1 == s2;
 }
 
-INLINE_FUNCTION_HD bool equal(const int32& s1, const int32& s2)
+INLINE_FUNCTION_HD 
+bool equal(const int32& s1, const int32& s2)
 {
 	return s1 == s2;
 }
 
-INLINE_FUNCTION_HD bool equal(const int16& s1, const int16& s2)
+INLINE_FUNCTION_HD 
+bool equal(const int8& s1, const int8& s2)
 {
     return s1 == s2;
 }
 
-INLINE_FUNCTION_HD bool equal(const int8& s1, const int8& s2)
+INLINE_FUNCTION_HD 
+bool equal(const uint32& s1, const uint32& s2)
 {
     return s1 == s2;
 }
 
-INLINE_FUNCTION_HD bool equal(const uint32& s1, const uint32& s2)
+/// Are two words equal (host only)?
+INLINE_FUNCTION 
+bool equal(const word& s1, const word& s2)
 {
 	return s1==s2;
 }
 
-INLINE_FUNCTION_HD bool equal(const label& s1, const label& s2)
+/// Convert degree to radians
-{
+INLINE_FUNCTION_HD 
-    return s1 == s2;
+real degree2Radian(const real &theta)
-}
-
-// host only
-INLINE_FUNCTION bool equal(const word& s1, const word& s2)
-{
-	return s1==s2;
-}
-
-INLINE_FUNCTION_HD real degree2Radian(const real &theta)
 {
     return theta / 180.0 * Pi;
 }
 
-INLINE_FUNCTION_HD real radian2Degree(const real &phi)
+/// Convert radians to degree
+INLINE_FUNCTION_HD 
+real radian2Degree(const real &phi)
 {
     return phi / Pi * 180.0;
 }

src/phasicFlow/types/basicTypes/builtinTypes.hpp

@@ -48,22 +48,22 @@ inline const bool usingDouble__ = false;
 
 using int8    = signed char;
 
-using int16   = short int;
-
 using int32   = int;
 
 using int64   = long long int;
 
-using uint16  = unsigned short int  ;
+using uint8  = unsigned char  ;
 
 using uint32  = unsigned int;
 
-using label   = std::size_t;
+using uint64  = unsigned long long int;
+
+using size_t  = std::size_t;
 
 using word    = std::string;
 
 inline 
-auto floatingPointDescription()
+word floatingPointDescription()
 {
   return word("In this build, ") + word(floatingPointType__) +
          word(" is used for floating point operations.");

src/phasicFlow/types/basicTypes/math.hpp

@@ -88,12 +88,12 @@ INLINE_FUNCTION_HD int32 mod(int32 x, int32 y)
 	return x%y;
 }
 
-INLINE_FUNCTION_HD int64 mod(label x, label y)
+INLINE_FUNCTION_HD int64 mod(uint64 x, uint64 y)
 {
 	return x%y;
 }
 
-INLINE_FUNCTION_HD int32 mod(uint32 x, uint32 y)
+INLINE_FUNCTION_HD auto mod(uint32 x, uint32 y)
 {
 	return x%y;
 }
@@ -319,7 +319,7 @@ INLINE_FUNCTION_HD int64 min(int64 x, int64 y)
 #endif
 }
 
-INLINE_FUNCTION_HD label min(label x, label y)
+INLINE_FUNCTION_HD uint64 min(uint64 x, uint64 y)
 {
 #ifdef __CUDACC__
 	return ::min(x, y);
@@ -338,14 +338,7 @@ INLINE_FUNCTION_HD uint32 min(uint32 x, uint32 y)
 #endif
 }
 
-INLINE_FUNCTION_HD uint32 min(uint16 x, uint16 y)
+
-{
-#ifdef __CUDACC__
-	return ::min(x, y);
-#else
-	return std::min(x, y);
-#endif
-}
 
 INLINE_FUNCTION_HD real max(real x, real y)
 {
@@ -374,7 +367,7 @@ INLINE_FUNCTION_HD int32 max(int32 x, int32 y)
 #endif
 }
 
-INLINE_FUNCTION_HD label max(label x, label y)
+INLINE_FUNCTION_HD uint64 max(uint64 x, uint64 y)
 {
 #ifdef __CUDACC__
 	return ::max(x, y);
@@ -393,15 +386,6 @@ INLINE_FUNCTION_HD uint32 max(uint32 x, uint32 y)
 #endif
 }
 
-INLINE_FUNCTION_HD uint32 max(uint16 x, uint16 y)
-{
-#ifdef __CUDACC__
-	return ::max(x, y);
-#else
-	return std::max(x, y);
-#endif
-
-}
 
 } // pFlow
 

src/phasicFlow/types/triple/triple.hpp

@@ -17,7 +17,6 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
 #ifndef __triple_hpp__
 #define __triple_hpp__
 
@@ -33,42 +32,51 @@ Licence:
 namespace pFlow
 {
 
-
+/// - Forward
 template<typename T> class triple;
 
 
 #include "tripleFwd.hpp"
 
-
+/**
-// for 3D vectors
+ * A set of 3 variables that can be used for vector variables.
-// it should be used only for numeric types, real, unit 
+ * The template parameter should be numeric type only.
+ *  
+ */
 template <typename T>
 struct triple
 {
-	// data members
+	/// data members
 	T x_;
 	T y_;
 	T z_;
 
-	// initilizes to zero
+	//// Constructors
-	INLINE_FUNCTION_HD triple():
+
+		/// Initilize to zero
+		INLINE_FUNCTION_HD 
+		triple():
 		x_(0),
 		y_(0),
 		z_(0)
 		{}
 
-	// Constructors
+		
-	INLINE_FUNCTION_HD triple(const T &x, const T &y, const T &z):
+		/// Construct from x, y, z
+		INLINE_FUNCTION_HD 
+		triple(const T &x, const T &y, const T &z):
 		x_(x),
 		y_(y),
 		z_(z)
 		{}
 
-	INLINE_FUNCTION_HD triple(const T &v):
+		/// Construct from v
+		INLINE_FUNCTION_HD 
+		triple(const T &v):
 		triple(v, v, v)
 		{}
 
-	// type conversion trough assignment  
+		/// Type conversion trough assignment  
 		template <typename T2>
 		INLINE_FUNCTION_HD triple<T> & operator = (const triple<T2> & rhs)
 		{
@@ -78,48 +86,34 @@ struct triple
 			return *this;
 		}
 
-	// type casting through copy constructor 
+		/// Type casting through copy constructor 
 		template<typename T2>
-	INLINE_FUNCTION_HD triple(const triple<T2> &src):
+		INLINE_FUNCTION_HD triple(const triple<T2> &src)
+		:
 			x_(static_cast<T>(src.x_)),
 			y_(static_cast<T>(src.y_)),
 			z_(static_cast<T>(src.z_))
-	{
+		{}
-	}
 	
-	// copy construct
+		/// Copy construct
 		INLINE_FUNCTION_HD
 		triple(const triple<T>& src) = default;
 
-	// volatile copy construct
-	/*INLINE_FUNCTION_HD
-	triple(volatile triple<T>& src):
-		x_(src.x_),
-		y_(src.y_),
-		z_(src.z_)
-	{}*/
 	
-	/*INLINE_FUNCTION_HD
-	triple& operator=(volatile triple<T>& src)	
-	{
-		x_ = src.x_;
-		y_ = src.y_;
-		z_ = src.z_;
-	}*/
 
-	// move construct
+		/// Move construct
 		INLINE_FUNCTION_HD
 		triple(triple<T>&& src) = default;
 
-	// copy assignment
+		/// copy assignment
 		INLINE_FUNCTION_HD
 		triple<T>& operator=(const triple<T>& src) = default;
 
-	// move assignment
+		/// move assignment
 		INLINE_FUNCTION_HD
 		triple<T>& operator=(triple<T>&& src) = default;
 
-	// clone 
+		/// clone 
 		INLINE_FUNCTION 
 		uniquePtr<triple<T>> clone() const
 		{
@@ -132,53 +126,64 @@ struct triple
 			return new triple<T>(*this);
 		}
 
-	//// member methods
+	////// member methods
 
-	// access
+		/// access component
 		INLINE_FUNCTION_HD T & x(){ return x_; }
+
+		/// access component
 		INLINE_FUNCTION_HD const T & x()const { return x_; }
 		
+		/// access component
 		INLINE_FUNCTION_HD T & y(){ return y_; }
+		
+		/// access component
 		INLINE_FUNCTION_HD const T & y()const { return y_; }
 
+		/// access component
 		INLINE_FUNCTION_HD T & z(){ return z_; }
+		
+		/// access component
 		INLINE_FUNCTION_HD const T & z()const { return z_; }
 
-	// methods
+	//// methods
+
+		/// Dot product of two vectors
 		friend FUNCTION_HD T dot <T> (const triple<T> & oprnd1, const triple<T> & oprnd2);
 		
+		/// Cross product of two vectors
 		friend FUNCTION_HD triple<T> cross <T>(const triple<T> & v1, const triple<T> & v2);
 		
+		/// Length of the vector 
 		INLINE_FUNCTION_HD T length() const; 
 
+		/// Normalize the vector 
 		INLINE_FUNCTION_HD void normalize(); 
 
-
-
 	//// operators 
 	
-	// + operator
+		/// + operator
 		friend FUNCTION_HD triple<T> operator+ <T> (const triple<T> & oprnd1, const triple<T> & oprnd2);
 
 		friend FUNCTION_HD triple<T> operator+ <T> (const triple<T> & oprnd1, const T & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator+ <T> (const T & oprnd1, const triple<T> & oprnd2);	
 		
-	// - operator 
+		/// - operator 
 		friend FUNCTION_HD triple<T> operator - <T> (const triple<T> & oprnd1, const triple<T> & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator - <T> (const triple<T> & oprnd1, const T & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator - <T> (const T & oprnd1, const triple<T> & oprnd2);
 		
-	// * operators
+		/// * operators
 		friend FUNCTION_HD triple<T> operator * <T> (const triple<T> & oprnd1, const triple<T> & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator * <T> (const triple<T> & oprnd1, const T & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator * <T> (const T & oprnd1, const triple<T> & oprnd2);
 
-	// / operators
+		/// / operators
 		friend FUNCTION_HD triple<T> operator / <T> (const triple<T> & oprnd1, const triple<T> & oprnd2);
 		
 		friend FUNCTION_HD triple<T> operator / <T> (const triple<T> & oprnd1, const T & oprnd2);
@@ -195,10 +200,10 @@ struct triple
 		INLINE_FUNCTION_HD void operator/= (const triple & oprnd2);
 	
 	
-	// unary negate operator 
+		/// unary negate operator 
 		INLINE_FUNCTION_HD triple operator- ()const;
 		
-	// unary plus operator 
+		/// unary plus operator 
 		INLINE_FUNCTION_HD triple operator+ ()const;
 		
 
@@ -212,13 +217,15 @@ struct triple
 
 		friend FUNCTION_HD bool operator <= <T> (const triple<T> &opr1, const triple<T> &opr2);
 	
-	// << operator 	
+	//// IO operators
+
+		/// << operator 	
 		friend iOstream& operator<< <T> (iOstream& str, const triple<T> & ov);
 		
-	// >> operator 
+		/// >> operator 
 		friend iIstream& operator >> <T> (iIstream & str, triple<T> & iv);
 
-	// same as >> operator, but faster, good for mass read
+		/// same as >> operator, but faster, good for mass read
 		friend void readIstream <T>( iIstream& str, triple<T> &iv);
 
 };
@@ -227,7 +234,7 @@ template<typename T>
 bool INLINE_FUNCTION_HD equal( const triple<T>& opr1, const triple<T>& opr2 );
 
 
-} // end of pFlow
+} /// end of pFlow
 
 #include "tripleI.hpp"
 #include "tripleMath.hpp"

src/phasicFlow/types/types.cpp

@@ -25,15 +25,11 @@ namespace pFlow
 		
 	const realx3 zero3(0.0);
 	const realx3 one3(1.0);
-	const uint32x3 zeroU3(0);
-	const uint32x3 oneU3(1);
 	
 	const realx3x3   zero33(zero3);
 	const realx3x3   one33(one3);
-	const uint32x3x3 zeroU33(zeroU3);
-	const uint32x3x3 oneU33(oneU3);
 	
-	const real4 zero4(zero);
+	const realx4 zero4(zero);
 	
 
 } // pFlow

src/phasicFlow/types/types.hpp

@@ -37,31 +37,23 @@ namespace pFlow
 {
 
 using int8x3 	= triple<int8>;
-using int16x3 	= triple<int16>;
 using int32x3 	= triple<int32>;
 using int64x3	= triple<int64>;
-using uint16x3 	= triple<uint16>;
+using uint8x3   = triple<uint8>;
 using uint32x3 	= triple<uint32>;
-using int32x3 	= triple<int32>;
+using uint64x3 	= triple<uint64>;
-using int64x3 	= triple<int64>;
-using labelx3 	= triple<label>;
 using realx3 	= triple<real>;
 
-using uint16x3x3= triple<uint16x3>;
-using uint32x3x3= triple<uint32x3>;
 using int32x3x3 = triple<int32x3>;
-using labelx3x3 = triple<labelx3>;
+using uint32x3x3= triple<uint32x3>;
 using realx3x3 	= triple<realx3>;
 
-using real4 	= quadruple<real>;
+using realx4 	= quadruple<real>;
 
 
 template<>
 inline word basicTypeName<int8x3>(){	return "int8x3"; }
 
-template<>
-inline word basicTypeName<int16x3>(){	return "int16x3"; }
-
 template<>
 inline word basicTypeName<int32x3>(){	return "int32x3"; }
 
@@ -69,19 +61,19 @@ template<>
 inline word basicTypeName<int64x3>(){	return "int64x3"; }
 
 template<>
-inline word basicTypeName<uint16x3>(){	return "uint16x3"; }
+inline word basicTypeName<uint8x3>(){	return "uint8x3"; }
 
 template<>
 inline word basicTypeName<uint32x3>(){	return "uint32x3"; }
 
 template<>
-inline word basicTypeName<labelx3>(){	return "labelx3"; }
+inline word basicTypeName<uint64x3>(){	return "unit64x3"; }
 
 template<>
 inline word basicTypeName<realx3>(){	return "realx3";	}
 
 template<>
-inline word basicTypeName<uint16x3x3>(){ return "uint16x3x3"; }
+inline word basicTypeName<int32x3x3>(){ return "int32x3x3"; }
 
 template<>
 inline word basicTypeName<uint32x3x3>(){ return "uint32x3x3"; }
@@ -91,20 +83,17 @@ inline word basicTypeName<realx3x3>(){ return "realx3x3"; }
 
 
 template<>
-inline word basicTypeName<real4>(){	return "real4";	}
+inline word basicTypeName<realx4>(){	return "realx4";	}
 
 
 extern const realx3 zero3;
 extern const realx3 one3;
-extern const uint32x3 zeroU3;
+
-extern const uint32x3 oneU3;
 
 extern const realx3x3 zero33;
 extern const realx3x3 one33;
-extern const uint32x3x3 zeroU33;
-extern const uint32x3x3 oneU33;
-
 
+extern const realx4 zero4; 
 
 } // pFlow