Merge branch 'PhasicFlow:main' into main

src/PostprocessData/fieldsDataBase/fieldFunctions.hpp

@@ -24,7 +24,7 @@ Licence:
 #include "types.hpp"
 #include "span.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename T>

src/PostprocessData/fieldsDataBase/fieldsDataBase.cpp

@@ -26,20 +26,18 @@ Licence:
 #include "fieldFunctions.hpp"
 #include "dictionary.hpp"
 
-namespace pFlow
-{
 
-bool pointFieldGetType(const word& TYPENAME, word& fieldType, word& fieldSpace);
+bool pFlow::postprocessData::fieldsDataBase::loadPointStructureToTime()
-
-}
-
-bool pFlow::fieldsDataBase::loadPointStructureToTime()
 {
     return false;
 }
 
 
-bool pFlow::fieldsDataBase::checkForUpdate(const word &compoundName, bool forceUpdate)
+bool pFlow::postprocessData::fieldsDataBase::checkForUpdate
+(
+    const word &compoundName, 
+    bool forceUpdate
+)
 {
     auto t = currentTime();
     bool shouldUpdate = false;
@@ -58,7 +56,10 @@ bool pFlow::fieldsDataBase::checkForUpdate(const word &compoundName, bool forceU
     return shouldUpdate;
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetRealField(const word &name)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetRealField
+(
+    const word &name
+)
 {
     
     bool shouldUpdate = checkForUpdate(name);
@@ -83,7 +84,10 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetRealField(const word
         field.size());
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetVolume(bool forceUpdate)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetVolume
+(
+    bool forceUpdate
+)
 {
     const word fName = "volume";
     bool shouldUpdate = checkForUpdate(fName, forceUpdate);
@@ -119,7 +123,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetVolume(bool forceUpda
 
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetDensity(bool forceUpdate)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetDensity(bool forceUpdate)
 {
     const word fName = "density";
     
@@ -155,7 +159,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetDensity(bool forceUpd
         field.size());
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetOne(bool forceUpdate)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetOne(bool forceUpdate)
 {
     const word fName = "one";
     
@@ -182,7 +186,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetOne(bool forceUpdate)
         field.size());
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetMass(bool forceUpdate)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetMass(bool forceUpdate)
 {
     const word fName = "mass";
     
@@ -218,7 +222,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetMass(bool forceUpdate
         field.size());
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetI(bool forceUpdate)
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::createOrGetI(bool forceUpdate)
 {
     const word fName = "I";
     
@@ -254,7 +258,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::createOrGetI(bool forceUpdate)
         field.size());
 }
 
-bool pFlow::fieldsDataBase::findFunction(
+bool pFlow::postprocessData::fieldsDataBase::findFunction(
     const word &compoundFieldName,
     word &fieldName,
     fieldsDataBase::Functions &func)
@@ -360,7 +364,7 @@ bool pFlow::fieldsDataBase::findFunction(
     return false; // No match
 }
 
-bool pFlow::fieldsDataBase::inputOutputType
+bool pFlow::postprocessData::fieldsDataBase::inputOutputType
 (
     fieldsDataBase::Functions func, 
     const word &inputType, 
@@ -458,7 +462,7 @@ bool pFlow::fieldsDataBase::inputOutputType
     return false;
 }
 
-pFlow::fieldsDataBase::fieldsDataBase
+pFlow::postprocessData::fieldsDataBase::fieldsDataBase
 (
     systemControl& control,
     const dictionary& postDict,
@@ -488,12 +492,12 @@ pFlow::fieldsDataBase::fieldsDataBase
     }
 }
 
-pFlow::timeValue pFlow::fieldsDataBase::currentTime() const
+pFlow::timeValue pFlow::postprocessData::fieldsDataBase::currentTime() const
 {
     return time_.currentTime();
 }
 
-bool pFlow::fieldsDataBase::getFieldTypeNameFunction
+bool pFlow::postprocessData::fieldsDataBase::getFieldTypeNameFunction
 (
     const word& compoundName,
     word& pointFieldName, 
@@ -543,7 +547,7 @@ bool pFlow::fieldsDataBase::getFieldTypeNameFunction
     return true;
 }
 
-bool pFlow::fieldsDataBase::getFieldType
+bool pFlow::postprocessData::fieldsDataBase::getFieldType
 (
     const word& compoundName,
     word& originalType, 
@@ -559,7 +563,7 @@ bool pFlow::fieldsDataBase::getFieldType
     return true;
 }
 
-bool pFlow::fieldsDataBase::getFieldType
+bool pFlow::postprocessData::fieldsDataBase::getFieldType
 (
     const word &compoundName, 
     word &typeAfterFunction
@@ -575,7 +579,7 @@ bool pFlow::fieldsDataBase::getFieldType
     return true;
 }
 
-pFlow::span<pFlow::realx3> pFlow::fieldsDataBase::updatePoints(bool forceUpdate)
+pFlow::span<pFlow::realx3> pFlow::postprocessData::fieldsDataBase::updatePoints(bool forceUpdate)
 {
     const word fName = "position";
     bool shouldUpdate = checkForUpdate(fName, forceUpdate);
@@ -604,7 +608,7 @@ pFlow::span<pFlow::realx3> pFlow::fieldsDataBase::updatePoints(bool forceUpdate)
 
 }
 
-pFlow::span<pFlow::realx3> pFlow::fieldsDataBase::updateFieldRealx3
+pFlow::span<pFlow::realx3> pFlow::postprocessData::fieldsDataBase::updateFieldRealx3
 (
     const word &compoundName, 
     bool forceUpdate
@@ -640,7 +644,7 @@ pFlow::span<pFlow::realx3> pFlow::fieldsDataBase::updateFieldRealx3
         
 }
 
-pFlow::span<pFlow::realx4> pFlow::fieldsDataBase::updateFieldRealx4
+pFlow::span<pFlow::realx4> pFlow::postprocessData::fieldsDataBase::updateFieldRealx4
 (
     const word &compoundName, 
     bool forceUpdate
@@ -676,7 +680,7 @@ pFlow::span<pFlow::realx4> pFlow::fieldsDataBase::updateFieldRealx4
     
 }
 
-pFlow::span<pFlow::real> pFlow::fieldsDataBase::updateFieldReal
+pFlow::span<pFlow::real> pFlow::postprocessData::fieldsDataBase::updateFieldReal
 (
     const word &compoundName, 
     bool forceUpdate
@@ -843,7 +847,7 @@ pFlow::span<pFlow::real> pFlow::fieldsDataBase::updateFieldReal
     return span<real>(nullptr, 0);
 }
 
-pFlow::span<pFlow::uint32> pFlow::fieldsDataBase::updateFieldUint32
+pFlow::span<pFlow::uint32> pFlow::postprocessData::fieldsDataBase::updateFieldUint32
 (
     const word& name,
     bool forceUpdate
@@ -852,7 +856,7 @@ pFlow::span<pFlow::uint32> pFlow::fieldsDataBase::updateFieldUint32
     return updateField<uint32>(name, forceUpdate);
 }
 
-pFlow::allPointFieldTypes pFlow::fieldsDataBase::updateFieldAll
+pFlow::postprocessData::allPointFieldTypes pFlow::postprocessData::fieldsDataBase::updateFieldAll
 (
     const word &compoundName, 
     bool forceUpdate
@@ -888,10 +892,24 @@ pFlow::allPointFieldTypes pFlow::fieldsDataBase::updateFieldAll
     }
 }
 
+bool pFlow::postprocessData::fieldsDataBase::pointFieldGetType
+(
+    const word& TYPENAME, 
+    word& fieldType, 
+    word& fieldSpace
+)
+{
+	std::regex match("pointField\\<([A-Za-z1-9_]*)\\,([A-Za-z1-9_]*)\\>");
+    std::smatch search;
+	if(!std::regex_match(TYPENAME, search, match)) return false;
+    if(search.size()!= 3) return false;
+    fieldType  = search[1];
+    fieldSpace = search[2];
+	return true;
+}
 
-
+pFlow::uniquePtr<pFlow::postprocessData::fieldsDataBase> 
-pFlow::uniquePtr<pFlow::fieldsDataBase> 
+    pFlow::postprocessData::fieldsDataBase::create
-    pFlow::fieldsDataBase::create
 (
     systemControl& control, 
     const dictionary& postDict, 
@@ -931,14 +949,5 @@ pFlow::uniquePtr<pFlow::fieldsDataBase>
     return nullptr;
 }
 
-bool pFlow::pointFieldGetType(const word& TYPENAME, word& fieldType, word& fieldSpace)
+
-{
-	std::regex match("pointField\\<([A-Za-z1-9_]*)\\,([A-Za-z1-9_]*)\\>");
-    std::smatch search;
-	if(!std::regex_match(TYPENAME, search, match)) return false;
-    if(search.size()!= 3) return false;
-    fieldType  = search[1];
-    fieldSpace = search[2];
-	return true;
-}
 

src/PostprocessData/fieldsDataBase/fieldsDataBase.hpp

@@ -29,13 +29,15 @@ Licence:
 #include "Map.hpp"
 #include "shape.hpp"
 
-
 namespace pFlow
 {
+    class dictionary;
+    class systemControl;
+    class Time;
+}
 
-class dictionary;
+namespace pFlow::postprocessData
-class systemControl;
+{
-class Time;
 
 
 class fieldsDataBase
@@ -303,6 +305,12 @@ public:
             return -1.0;
         }
     
+    static
+    bool pointFieldGetType(
+        const word& TYPENAME, 
+        word& fieldType, 
+        word& fieldSpace);
+
     static
     uniquePtr<fieldsDataBase> create(
         systemControl& control, 
@@ -311,7 +319,7 @@ public:
         timeValue startTime);
 };
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #include "fieldsDataBaseTemplates.cpp"
 

src/PostprocessData/fieldsDataBase/fieldsDataBaseDclr.hpp

@@ -9,7 +9,7 @@
 #include "types.hpp"
 #include "span.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 

src/PostprocessData/fieldsDataBase/fieldsDataBaseTemplates.cpp

@@ -23,9 +23,9 @@ Licence:
 
 #include "fieldsDataBase.hpp"
 
-template<pFlow::ValidFieldType T>
+template<pFlow::postprocessData::ValidFieldType T>
 inline
-pFlow::span<T> pFlow::fieldsDataBase::updateField(const word& name, bool forceUpdate)
+pFlow::span<T> pFlow::postprocessData::fieldsDataBase::updateField(const word& name, bool forceUpdate)
 {
   
     bool shouldUpdate = checkForUpdate(name, forceUpdate);
@@ -40,8 +40,8 @@ pFlow::span<T> pFlow::fieldsDataBase::updateField(const word& name, bool forceUp
         {
             if( loadPointFieldToTime(name) )
             {
-                const auto& pField = time_.lookupObject<pointField_D<T>>(name);
+                const auto& pField = time_.template lookupObject<pointField_D<T>>(name);
-                allFields_.emplaceBackOrReplace<FieldTypeHost<T>>(
+                allFields_.template emplaceBackOrReplace<FieldTypeHost<T>>(
                 name, 
                 pField.activeValuesHost());
             }
@@ -63,9 +63,9 @@ pFlow::span<T> pFlow::fieldsDataBase::updateField(const word& name, bool forceUp
 }
 
 
-template<pFlow::ValidFieldType T>
+template<pFlow::postprocessData::ValidFieldType T>
 inline
-pFlow::span<T> pFlow::fieldsDataBase::updateReservedField
+pFlow::span<T> pFlow::postprocessData::fieldsDataBase::updateReservedField
 (
     const word& name, 
     bool forceUpdate

src/PostprocessData/fieldsDataBase/simulationFieldsDataBase.cpp

@@ -3,38 +3,38 @@
 #include "dynamicPointStructure.hpp"
 #include "vocabs.hpp"
 
-namespace pFlow
-{
-    bool pointFieldGetType(const word& TYPENAME, word& fieldType, word& fieldSpace);
-}
 
-bool pFlow::simulationFieldsDataBase::pointFieldNameExists(const word &name) const
+
+bool pFlow::postprocessData::simulationFieldsDataBase::pointFieldNameExists(const word &name) const
 {
     return time().lookupObjectName(name);
 }
 
-bool pFlow::simulationFieldsDataBase::loadPointFieldToTime(const word &name)
+bool pFlow::postprocessData::simulationFieldsDataBase::loadPointFieldToTime(const word &name)
 {
     return time().lookupObjectName(name);
 }
 
-bool pFlow::simulationFieldsDataBase::loadPointStructureToTime()
+bool pFlow::postprocessData::simulationFieldsDataBase::loadPointStructureToTime()
 {
     // it is already in the Time object 
     return time().lookupObjectName(pointStructureFile__);
 }
 
 
-const pFlow::shape& pFlow::simulationFieldsDataBase::getShape() const
+const pFlow::shape& pFlow::postprocessData::simulationFieldsDataBase::getShape() const
 {
     return shape_;
 }
 
-pFlow::word pFlow::simulationFieldsDataBase::getPointFieldType(const word &name) const
+pFlow::word pFlow::postprocessData::simulationFieldsDataBase::getPointFieldType
+(
+    const word &name
+) const
 {
     word pfType =  time().lookupObjectTypeName(name);
     word type, space;
-    if(!pointFieldGetType(pfType, type, space))
+    if(!fieldsDataBase::pointFieldGetType(pfType, type, space))
     {
         fatalErrorInFunction
             <<"Error in retriving the type of pointField "
@@ -44,7 +44,7 @@ pFlow::word pFlow::simulationFieldsDataBase::getPointFieldType(const word &name)
     return type;
 }
 
-pFlow::simulationFieldsDataBase::simulationFieldsDataBase
+pFlow::postprocessData::simulationFieldsDataBase::simulationFieldsDataBase
 (
     systemControl &control,
     const dictionary& postDict, 
@@ -60,7 +60,7 @@ pFlow::simulationFieldsDataBase::simulationFieldsDataBase
 {
 }
 
-const pFlow::pointStructure &pFlow::simulationFieldsDataBase::pStruct() const
+const pFlow::pointStructure &pFlow::postprocessData::simulationFieldsDataBase::pStruct() const
 {
     return 
     static_cast<const pointStructure&>

src/PostprocessData/fieldsDataBase/simulationFieldsDataBase.hpp

@@ -23,7 +23,7 @@ Licence:
 
 #include "fieldsDataBase.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 class simulationFieldsDataBase 

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAvMassVelocity.cpp

@@ -1,6 +1,9 @@
 #include "PostprocessOperationAvMassVelocity.hpp"
 
-pFlow::PostprocessOperationAvMassVelocity::PostprocessOperationAvMassVelocity
+namespace pFlow::postprocessData
+{
+
+PostprocessOperationAvMassVelocity::PostprocessOperationAvMassVelocity
 (
     const dictionary &opDict, 
     const regionPoints &regPoints, 
@@ -18,3 +21,5 @@ pFlow::PostprocessOperationAvMassVelocity::PostprocessOperationAvMassVelocity
     )
 {
 }
+
+}

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAvMassVelocity.hpp

@@ -132,7 +132,7 @@ Licence:
 #include "regionField.hpp"
 #include "includeMask.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 
@@ -168,6 +168,6 @@ public:
 }; 
 
 
-}
+} // namespace pFlow::postprocessData
 
 #endif //__PostprocessOperationAvMassVelocity_hpp__

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAverage.cpp

@@ -3,8 +3,11 @@
 #include "fieldsDataBase.hpp"
 #include "operationFunctions.hpp"
 
+namespace pFlow::postprocessData
+{
+
 /// Constructs average processor and initializes result field based on input field type
-pFlow::PostprocessOperationAverage::PostprocessOperationAverage
+PostprocessOperationAverage::PostprocessOperationAverage
 (
     const dictionary &opDict, 
     const regionPoints &regPoints, 
@@ -39,7 +42,7 @@ pFlow::PostprocessOperationAverage::PostprocessOperationAverage
     }
 }
 
-pFlow::PostprocessOperationAverage::PostprocessOperationAverage
+PostprocessOperationAverage::PostprocessOperationAverage
 (
     const dictionary &opDict, 
     const word &fieldName, 
@@ -77,8 +80,9 @@ pFlow::PostprocessOperationAverage::PostprocessOperationAverage
     }
 }
 
+
 /// Performs weighted average of field values within each region
-bool pFlow::PostprocessOperationAverage::execute
+bool PostprocessOperationAverage::execute
 (
     const std::vector<span<real>>& weights,
     const regionField<real>& volFactor
@@ -109,7 +113,7 @@ bool pFlow::PostprocessOperationAverage::execute
             allField)
     );
     
-    if(calculateFluctuation2_)
+    if(calculateFluctuation2_())
     {
         auto& processedRegField = processedRegFieldPtr_();
         fluctuation2FieldPtr_ = makeUnique<processedRegFieldType>
@@ -138,3 +142,40 @@ bool pFlow::PostprocessOperationAverage::execute
 
     return true;
 }
+
+bool PostprocessOperationAverage::write(const fileSystem &parDir) const
+{   
+    if(! postprocessOperation::write(parDir))
+    {
+        return false;
+    }
+    if(!calculateFluctuation2_())
+    {
+        return true;
+    }
+    
+    auto ti = time().TimeInfo();
+
+    if(!os2Ptr_)
+    {
+        fileSystem path = parDir+(
+            processedFieldName()+"_prime2" + ".Start_" + ti.timeName());
+        os2Ptr_ = makeUnique<oFstream>(path);
+        
+        regPoints().write(os2Ptr_());
+    }
+
+    
+    std::visit
+    (
+        [&](auto&& arg)->bool
+        {
+            return writeField(os2Ptr_(), ti.t(), arg, threshold());
+        },
+        fluctuation2FieldPtr_()
+    );
+
+    return true;
+}
+
+} // namespace pFlow::postprocessData

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationAverage.hpp

@@ -132,10 +132,9 @@ Licence:
 #include "regionField.hpp"
 #include "includeMask.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
-
 class PostprocessOperationAverage
 :
     public postprocessOperation
@@ -150,6 +149,9 @@ private:
 
     uniquePtr<processedRegFieldType>  fluctuation2FieldPtr_ = nullptr;
 
+    /// Pointer to the output stream for writing fluctuation2 results
+    mutable uniquePtr<oFstream>       os2Ptr_ = nullptr;
+
 public:
 
     TypeInfo("PostprocessOperation<average>");
@@ -190,6 +192,10 @@ public:
         return processedRegFieldPtr_();
     }
 
+    /// write to os stream
+    bool write(const fileSystem &parDir)const override;
+
+
     /// @brief Execute average operation on field values
     /// @param weights Weight factors for particles
     /// @return True if successful
@@ -200,6 +206,6 @@ public:
 }; 
 
 
-}
+} // namespace pFlow::postprocessData
 
 #endif //__PostprocessOperationAverage_hpp__

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationSum.cpp

@@ -3,8 +3,11 @@
 #include "fieldsDataBase.hpp"
 #include "operationFunctions.hpp"
 
+namespace pFlow::postprocessData
+{
+
 /// Constructs sum processor and initializes result field based on input field type
-pFlow::PostprocessOperationSum::PostprocessOperationSum
+PostprocessOperationSum::PostprocessOperationSum
 (
     const dictionary &opDict, 
     const regionPoints &regPoints, 
@@ -39,7 +42,7 @@ pFlow::PostprocessOperationSum::PostprocessOperationSum
 }
 
 /// Performs weighted sum of field values within each region
-bool pFlow::PostprocessOperationSum::execute
+bool PostprocessOperationSum::execute
 (
     const std::vector<span<real>>& weights,
     const regionField<real>& volFactor
@@ -72,3 +75,6 @@ bool pFlow::PostprocessOperationSum::execute
    
     return true;
 }
+
+
+}

src/PostprocessData/operation/PostprocessOperation/PostprocessOperationSum.hpp

@@ -129,7 +129,7 @@ Licence:
 #include "regionField.hpp"
 #include "includeMask.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 
@@ -182,6 +182,6 @@ public:
 }; 
 
 
-}
+} // namespace pFlow::postprocessData
 
 #endif //__PostprocessOperationSum_hpp__

src/PostprocessData/operation/PostprocessOperation/operationFunctions.hpp

@@ -28,7 +28,7 @@ Licence:
 #include "regionField.hpp"
 #include "includeMask.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename T>
@@ -190,6 +190,6 @@ regionField<T> executeFluctuation2Operation
     return processedField;
 }
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #endif //__operationFunctions_hpp__

src/PostprocessData/operation/includeMask/IncludeMask.hpp

@@ -61,7 +61,7 @@ Licence:
 #include "Time.hpp"
 
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename T, typename Operator>
@@ -270,7 +270,7 @@ public:
 };
 
 
-} // pFlow
+} // pFlow::postprocessData
 
 #endif //__IncludeMask_hpp__
 

src/PostprocessData/operation/includeMask/IncludeMasks.cpp

@@ -20,31 +20,34 @@ Licence:
 
 #include "IncludeMask.hpp"
 
+namespace pFlow::postprocessData
+{
+
 // real
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareOne<pFlow::real, pFlow::lessThanOp> >;
+template class IncludeMask<real, compareOne<real, lessThanOp> >;
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareOne<pFlow::real, pFlow::lessThanEqOp> >;
+template class IncludeMask<real, compareOne<real, lessThanEqOp> >;
 
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareOne<pFlow::real, pFlow::greaterThanOp> >;
+template class IncludeMask<real, compareOne<real, greaterThanOp> >;
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareOne<pFlow::real, pFlow::greaterThanEqOp> >;
+template class IncludeMask<real, compareOne<real, greaterThanEqOp> >;
 
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareOne<pFlow::real, pFlow::equalOp> >;
+template class IncludeMask<real, compareOne<real, equalOp> >;
 
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareTwo<pFlow::real, pFlow::betweenOp> >;
+template class IncludeMask<real, compareTwo<real, betweenOp> >;
-template class pFlow::IncludeMask<pFlow::real, pFlow::compareTwo<pFlow::real, pFlow::betweenEqOp> >;
+template class IncludeMask<real, compareTwo<real, betweenEqOp> >;
 
-template class pFlow::IncludeMask<pFlow::real, pFlow::allOp<pFlow::real>>;
+template class IncludeMask<real, allOp<real>>;
 
 // realx3
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareOne<pFlow::realx3, pFlow::lessThanOp> >;
+template class IncludeMask<realx3, compareOne<realx3, lessThanOp> >;
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareOne<pFlow::realx3, pFlow::lessThanEqOp> >;
+template class IncludeMask<realx3, compareOne<realx3, lessThanEqOp> >;
 
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareOne<pFlow::realx3, pFlow::greaterThanOp> >;
+template class IncludeMask<realx3, compareOne<realx3, greaterThanOp> >;
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareOne<pFlow::realx3, pFlow::greaterThanEqOp> >;
+template class IncludeMask<realx3, compareOne<realx3, greaterThanEqOp> >;
 
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareOne<pFlow::realx3, pFlow::equalOp> >;
+template class IncludeMask<realx3, compareOne<realx3, equalOp> >;
 
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareTwo<pFlow::realx3, pFlow::betweenOp> >;
+template class IncludeMask<realx3, compareTwo<realx3, betweenOp> >;
-template class pFlow::IncludeMask<pFlow::realx3, pFlow::compareTwo<pFlow::realx3, pFlow::betweenEqOp> >;
+template class IncludeMask<realx3, compareTwo<realx3, betweenEqOp> >;
 
 
-// realx4
+} // postprocessData

src/PostprocessData/operation/includeMask/includeMask.cpp

@@ -24,7 +24,10 @@ Licence:
 #include "fieldsDataBase.hpp"
 
 
-pFlow::includeMask::includeMask
+namespace pFlow::postprocessData
+{
+
+includeMask::includeMask
 (
 	const dictionary& dict, 
 	fieldsDataBase& fieldDB
@@ -33,7 +36,7 @@ pFlow::includeMask::includeMask
 	database_(fieldDB)
 {}
 
-pFlow::includeMask::includeMask
+includeMask::includeMask
 (
 	const word &type, 
 	const dictionary &opDict, 
@@ -44,7 +47,7 @@ pFlow::includeMask::includeMask
 {
 }
 
-pFlow::uniquePtr<pFlow::includeMask> pFlow::includeMask::create
+uniquePtr<includeMask> includeMask::create
 (
     const dictionary& opDict, 
     fieldsDataBase& fieldsDB
@@ -97,8 +100,7 @@ pFlow::uniquePtr<pFlow::includeMask> pFlow::includeMask::create
 	return nullptr;
 }
 
-pFlow::uniquePtr<pFlow::includeMask> 
+uniquePtr<includeMask> includeMask::create
-	pFlow::includeMask::create
 (
 	const word &type, 
 	const dictionary &opDict, 
@@ -150,3 +152,5 @@ pFlow::uniquePtr<pFlow::includeMask>
 	}
 	return nullptr;
 }
+
+}

src/PostprocessData/operation/includeMask/includeMask.hpp

@@ -47,11 +47,15 @@ Licence:
 #include "virtualConstructor.hpp"
 
 namespace pFlow
+{
+	class dictionary;
+}
+
+namespace pFlow::postprocessData
 {
 
 // forward declaration
 class fieldsDataBase;
-class dictionary;
 
 
 class includeMask
@@ -188,7 +192,7 @@ public:
 
 
 
-} // pFlow
+} // pFlow::postprocessData
 
 #endif //__IncludeMask_hpp__
 

src/PostprocessData/operation/includeMask/maskOperations.hpp

@@ -24,7 +24,7 @@ Licence:
 #include "types.hpp"
 #include "dictionary.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename T>
@@ -176,6 +176,6 @@ public:
 	}
 };
 
-}
+} // namespace pFlow::postprocessData
 
 #endif //__maskOperation_hpp__

src/PostprocessData/operation/postprocessOperation/postprocessOperation.cpp

@@ -23,66 +23,11 @@ Licence:
 #include "regionPoints.hpp"
 #include "fieldsDataBase.hpp"
 
-namespace pFlow
+
+namespace pFlow::postprocessData
 {
 
-template<typename T>
+postprocessOperation::postprocessOperation
-inline
-bool writeField
-(
-    iOstream&             os,
-    timeValue             t,
-    const regionField<T>  field,
-    uint32                threshold,
-    const T&              defValue=T{}    
-)
-{
-    const auto& regPoints = field.regPoints();
-    const uint32 n = field.size();
-    os<<t<<tab;
-    for(uint32 i=0; i<n; i++)
-    {
-        auto numPar = regPoints.indices(i).size();
-        if(numPar >= threshold)
-        {
-            if constexpr(std::is_same_v<T,realx3>)
-            {
-                os<<field[i].x()<<' '<<field[i].y()<<' '<<field[i].z()<<tab;
-            }
-            else if constexpr( std::is_same_v<T,realx4>)
-            {
-                os << field[i].x() << ' ' << field[i].y() << ' ' << field[i].z() << ' ' << field[i].w() << tab;
-            }
-            else
-            {
-                os<<field[i]<<tab;
-            }
-            
-        }
-        else
-        {
-            if constexpr(std::is_same_v<T,realx3>)
-            {
-                os<<defValue.x()<<' '<<defValue.y()<<' '<<defValue.z()<<tab;
-            }
-            else if constexpr( std::is_same_v<T,realx4>)
-            {
-                os << defValue.x() << ' ' << defValue.y() << ' ' << defValue.z() << ' ' << defValue.w() << tab;
-            }
-            else
-            {
-                os<<defValue<<tab;
-            }
-        }
-
-    }
-    os<<endl;
-    return true;
-}
-
-}
-
-pFlow::postprocessOperation::postprocessOperation
 (
     const dictionary &opDict, 
     const regionPoints& regPoints,
@@ -100,7 +45,7 @@ pFlow::postprocessOperation::postprocessOperation
     )
 {}
 
-pFlow::postprocessOperation::postprocessOperation
+postprocessOperation::postprocessOperation
 (
     const dictionary &opDict, 
     const word &fieldName, 
@@ -147,12 +92,12 @@ pFlow::postprocessOperation::postprocessOperation
         fatalExit;
     }
 }
-const pFlow::Time& pFlow::postprocessOperation::time() const
+const Time& postprocessOperation::time() const
 {
     return database_.time();
 }
 
-bool pFlow::postprocessOperation::write(const fileSystem &parDir) const
+bool postprocessOperation::write(const fileSystem &parDir) const
 {   
     auto ti = time().TimeInfo();
 
@@ -179,11 +124,12 @@ bool pFlow::postprocessOperation::write(const fileSystem &parDir) const
     return true;
 }
 
-pFlow::uniquePtr<pFlow::postprocessOperation>
+uniquePtr<postprocessOperation> postprocessOperation::create
-pFlow::postprocessOperation::create(
+(
     const dictionary &opDict,
     const regionPoints &regPoints,
-    fieldsDataBase &fieldsDB)
+    fieldsDataBase &fieldsDB
+)
 {
     word func = opDict.getVal<word>("function");
     word method = angleBracketsNames("PostprocessOperation", func);
@@ -209,3 +155,5 @@ pFlow::postprocessOperation::create(
         return nullptr;
     }
 }
+
+}

src/PostprocessData/operation/postprocessOperation/postprocessOperation.hpp

@@ -76,23 +76,19 @@ Licence:
 #include "oFstream.hpp"
 #include "regionField.hpp"
 #include "includeMask.hpp"
+#include "postprocessOperationFunctions.hpp"
 
 namespace pFlow
 {
+    class Time;
+} 
 
-/// Type alias for processed region field types.
+namespace pFlow::postprocessData
-/// Only regionField<real>, regionField<realx3>, and regionField<realx4> are supported
+{
-/// in the postprocessOperation class.
-using processedRegFieldType = std::variant
-    <
-        regionField<real>,
-        regionField<realx3>,
-        regionField<realx4>
-    >;
 
 /// - forward declaration
 class fieldsDataBase;
-class Time;
+
 
 class postprocessOperation
 {
@@ -103,7 +99,7 @@ public:
 private:
 
     /// Dictionary containing operation-specific parameters.
-    dictionary              operationDict_;
+    pFlow::dictionary              operationDict_;
 
     /// This Threshold is used to exclude the regions which contain
     /// fewer than this value. 
@@ -273,6 +269,6 @@ public:
     
 };
 
-}
+} // namespace pFlow::postprocessData
 
 #endif //__postprocessOperation_hpp__

src/PostprocessData/operation/postprocessOperation/postprocessOperationFunctions.hpp

@@ -0,0 +1,100 @@
+/*------------------------------- phasicFlow ---------------------------------
+      O        C enter of
+     O O       E ngineering and
+    O   O      M ultiscale modeling of
+   OOOOOOO     F luid flow
+------------------------------------------------------------------------------
+  Copyright (C): www.cemf.ir
+  email: hamid.r.norouzi AT gmail.com
+------------------------------------------------------------------------------
+Licence:
+  This file is part of phasicFlow code. It is a free software for simulating
+  granular and multiphase flows. You can redistribute it and/or modify it under
+  the terms of GNU General Public License v3 or any other later versions.
+
+  phasicFlow is distributed to help others in their research in the field of
+  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
+  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+-----------------------------------------------------------------------------*/
+
+#ifndef __postprocessOperationFunctions_hpp__
+#define __postprocessOperationFunctions_hpp__
+
+#include <variant>
+
+#include "types.hpp"
+#include "iOstream.hpp"
+#include "regionField.hpp"
+
+namespace pFlow::postprocessData
+{
+
+/// Type alias for processed region field types.
+/// Only regionField<real>, regionField<realx3>, and regionField<realx4> are supported
+/// in the postprocessOperation class.
+using processedRegFieldType = std::variant
+<
+    regionField<real>,
+    regionField<realx3>,
+    regionField<realx4>
+>;
+
+
+template<typename T>
+inline
+bool writeField
+(
+    iOstream&             os,
+    timeValue             t,
+    const regionField<T>  field,
+    uint32                threshold,
+    const T&              defValue=T{}    
+)
+{
+    const auto& regPoints = field.regPoints();
+    const uint32 n = field.size();
+    os<<t<<tab;
+    for(uint32 i=0; i<n; i++)
+    {
+        auto numPar = regPoints.indices(i).size();
+        if(numPar >= threshold)
+        {
+            if constexpr(std::is_same_v<T,realx3>)
+            {
+                os<<field[i].x()<<' '<<field[i].y()<<' '<<field[i].z()<<tab;
+            }
+            else if constexpr( std::is_same_v<T,realx4>)
+            {
+                os << field[i].x() << ' ' << field[i].y() << ' ' << field[i].z() << ' ' << field[i].w() << tab;
+            }
+            else
+            {
+                os<<field[i]<<tab;
+            }
+            
+        }
+        else
+        {
+            if constexpr(std::is_same_v<T,realx3>)
+            {
+                os<<defValue.x()<<' '<<defValue.y()<<' '<<defValue.z()<<tab;
+            }
+            else if constexpr( std::is_same_v<T,realx4>)
+            {
+                os << defValue.x() << ' ' << defValue.y() << ' ' << defValue.z() << ' ' << defValue.w() << tab;
+            }
+            else
+            {
+                os<<defValue<<tab;
+            }
+        }
+
+    }
+    os<<endl;
+    return true;
+}
+
+} // namespace pFlow::postprocessData
+
+#endif //__postprocessOperationFunctions_hpp__

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponent.cpp

@@ -20,7 +20,7 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 template<typename RegionType, typename ProcessMethodType>
-pFlow::PostprocessComponent<RegionType,ProcessMethodType>::PostprocessComponent
+pFlow::postprocessData::PostprocessComponent<RegionType,ProcessMethodType>::PostprocessComponent
 (
     const dictionary& dict,
     fieldsDataBase& fieldsDB,
@@ -61,7 +61,7 @@ pFlow::PostprocessComponent<RegionType,ProcessMethodType>::PostprocessComponent
 
 
 template <typename RegionType, typename ProcessMethodType>
-bool pFlow::PostprocessComponent<RegionType, ProcessMethodType>::execute
+bool pFlow::postprocessData::PostprocessComponent<RegionType, ProcessMethodType>::execute
 (
     const timeInfo &ti, 
     bool forceUpdate
@@ -129,7 +129,7 @@ bool pFlow::PostprocessComponent<RegionType, ProcessMethodType>::execute
 
 template <typename RegionType, typename ProcessMethodType>
 inline 
-bool pFlow::PostprocessComponent<RegionType, ProcessMethodType>::write
+bool pFlow::postprocessData::PostprocessComponent<RegionType, ProcessMethodType>::write
 (
     const fileSystem &parDir
 ) const

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponent.hpp

@@ -32,7 +32,7 @@ Licence:
 #include "regionPoints.hpp"
 #include "regionField.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename RegionType, typename ProcessMethodType>

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponentArithmetic.hpp

@@ -24,7 +24,7 @@ Licence:
 #include "PostprocessComponent.hpp"
 #include "arithmetic.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename RegionType>

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponentGaussian.hpp

@@ -25,7 +25,7 @@ Licence:
 #include "GaussianDistribution.hpp"
 #include "numericConstants.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename RegionType>

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponentUniform.hpp

@@ -24,7 +24,7 @@ Licence:
 #include "PostprocessComponent.hpp"
 #include "uniformDistribution.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename RegionType>

src/PostprocessData/postprocessComponent/PostprocessComponent/PostprocessComponents.cpp

@@ -27,16 +27,18 @@ Licence:
 #include "lineRegionPoints.hpp"
 #include "multipleSpheresRegionPoints.hpp"
 
+namespace pFlow::postprocessData
+{
+template class PostprocessComponentGaussian<sphereRegionPoints>;
+template class PostprocessComponentUniform<sphereRegionPoints>;
+template class PostprocessComponentArithmetic<sphereRegionPoints>;
 
-template class pFlow::PostprocessComponentGaussian<pFlow::sphereRegionPoints>;
+template class PostprocessComponentGaussian<multipleSpheresRegionPoints>;
-template class pFlow::PostprocessComponentUniform<pFlow::sphereRegionPoints>;
+template class PostprocessComponentUniform<multipleSpheresRegionPoints>;
-template class pFlow::PostprocessComponentArithmetic<pFlow::sphereRegionPoints>;
+template class PostprocessComponentArithmetic<multipleSpheresRegionPoints>;
 
-template class pFlow::PostprocessComponentGaussian<pFlow::multipleSpheresRegionPoints>;
+template class PostprocessComponentGaussian<lineRegionPoints>;
-template class pFlow::PostprocessComponentUniform<pFlow::multipleSpheresRegionPoints>;
+template class PostprocessComponentUniform<lineRegionPoints>;
-template class pFlow::PostprocessComponentArithmetic<pFlow::multipleSpheresRegionPoints>;
+template class PostprocessComponentArithmetic<lineRegionPoints>;
-
-template class pFlow::PostprocessComponentGaussian<pFlow::lineRegionPoints>;
-template class pFlow::PostprocessComponentUniform<pFlow::lineRegionPoints>;
-template class pFlow::PostprocessComponentArithmetic<pFlow::lineRegionPoints>;
 
+}

src/PostprocessData/postprocessComponent/particleProbePostprocessComponent/particleProbePostprocessComponent.cpp

@@ -1,7 +1,27 @@
+/*------------------------------- phasicFlow ---------------------------------
+      O        C enter of
+     O O       E ngineering and
+    O   O      M ultiscale modeling of
+   OOOOOOO     F luid flow
+------------------------------------------------------------------------------
+  Copyright (C): www.cemf.ir
+  email: hamid.r.norouzi AT gmail.com
+------------------------------------------------------------------------------
+Licence:
+  This file is part of phasicFlow code. It is a free software for simulating
+  granular and multiphase flows. You can redistribute it and/or modify it under
+  the terms of GNU General Public License v3 or any other later versions.
+
+  phasicFlow is distributed to help others in their research in the field of
+  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
+  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+-----------------------------------------------------------------------------*/
+
 #include "particleProbePostprocessComponent.hpp"
 #include "Time.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
     
 template<typename T>
@@ -62,7 +82,7 @@ inline bool writeField
 
 }
 
-pFlow::particleProbePostprocessComponent::particleProbePostprocessComponent
+pFlow::postprocessData::particleProbePostprocessComponent::particleProbePostprocessComponent
 (
     const dictionary &dict, 
     fieldsDataBase &fieldsDB, 
@@ -81,7 +101,7 @@ pFlow::particleProbePostprocessComponent::particleProbePostprocessComponent
     name_(dict.name())
 {}
 
-bool pFlow::particleProbePostprocessComponent::execute
+bool pFlow::postprocessData::particleProbePostprocessComponent::execute
 (
     const timeInfo &ti, 
     bool forceExecute
@@ -126,7 +146,7 @@ bool pFlow::particleProbePostprocessComponent::execute
 }
 
 
-bool pFlow::particleProbePostprocessComponent::write(const fileSystem& parDir)const
+bool pFlow::postprocessData::particleProbePostprocessComponent::write(const fileSystem& parDir)const
 {
     if(! executed_ ) return true;
     

src/PostprocessData/postprocessComponent/particleProbePostprocessComponent/particleProbePostprocessComponent.hpp

@@ -27,7 +27,7 @@ Licence:
 #include "regionField.hpp"
 #include "oFstream.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 

src/PostprocessData/postprocessComponent/postprocessComponent/postprocessComponent.cpp

@@ -1,9 +1,29 @@
+/*------------------------------- phasicFlow ---------------------------------
+      O        C enter of
+     O O       E ngineering and
+    O   O      M ultiscale modeling of
+   OOOOOOO     F luid flow
+------------------------------------------------------------------------------
+  Copyright (C): www.cemf.ir
+  email: hamid.r.norouzi AT gmail.com
+------------------------------------------------------------------------------
+Licence:
+  This file is part of phasicFlow code. It is a free software for simulating
+  granular and multiphase flows. You can redistribute it and/or modify it under
+  the terms of GNU General Public License v3 or any other later versions.
+
+  phasicFlow is distributed to help others in their research in the field of
+  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
+  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+-----------------------------------------------------------------------------*/
+
 #include "postprocessComponent.hpp"
 #include "fieldsDataBase.hpp"
 #include "Time.hpp"
 
 
-pFlow::postprocessComponent::postprocessComponent
+pFlow::postprocessData::postprocessComponent::postprocessComponent
 ( 
     const dictionary &dict,
     fieldsDataBase &fieldsDB, 
@@ -23,7 +43,7 @@ pFlow::postprocessComponent::postprocessComponent
 }
 
 
-pFlow::uniquePtr<pFlow::postprocessComponent> pFlow::postprocessComponent::create
+pFlow::uniquePtr<pFlow::postprocessData::postprocessComponent> pFlow::postprocessData::postprocessComponent::create
 (
     const dictionary& dict,
     fieldsDataBase& fieldsDB,

src/PostprocessData/postprocessComponent/postprocessComponent/postprocessComponent.hpp

@@ -25,12 +25,17 @@ Licence:
 #include "dictionary.hpp"
 #include "virtualConstructor.hpp"
 
-namespace pFlow
+namespace
+{
+    class dictionary;
+}
+
+namespace pFlow::postprocessData
 {
 
-class fieldsDataBase;
+
 class regionPoints;
-class dictionary;
+class fieldsDataBase;
 
 class postprocessComponent
 {
@@ -112,6 +117,6 @@ public:
 
 };
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #endif // __postprocessComponent_hpp__

src/PostprocessData/postprocessData/postprocessData.cpp

@@ -1,4 +1,3 @@
-
 /*------------------------------- phasicFlow ---------------------------------
       O        C enter of
      O O       E ngineering and
@@ -25,7 +24,7 @@ Licence:
 #include "postprocessGlobals.hpp"
 #include "postprocessComponent.hpp"
 
-pFlow::postprocessData::postprocessData
+pFlow::postprocessData::postprocessData::postprocessData
 (
     const systemControl &control,
     timeValue startTime
@@ -45,7 +44,7 @@ pFlow::postprocessData::postprocessData
         )
     )
 {
-    postProcessGlobals::defaultDir__ = CWD()/pFlow::postProcessGlobals::defaultRelDir__;
+    defaultDir__ = CWD()/defaultRelDir__;
     
     // if dictionary is not provided, no extra action is required. 
     if( !dict_.fileExist() || !dict_.headerOk() )
@@ -98,8 +97,10 @@ pFlow::postprocessData::postprocessData
 
 }
 
-bool pFlow::postprocessData::execute() 
+bool pFlow::postprocessData::postprocessData::execute() 
 {
+    if( inSimulation_ && !activeInSimulation_() ) return true; 
+
     const auto& ti = time_.TimeInfo();
 
     for(auto& component:postprocesses_)
@@ -116,8 +117,10 @@ bool pFlow::postprocessData::execute()
     return true;
 }
 
-bool pFlow::postprocessData::write() const
+bool pFlow::postprocessData::postprocessData::write() const
 {
+    if( inSimulation_ && !activeInSimulation_() ) return true; 
+    
     for(auto& component:postprocesses_)
     {   
         if(!component->executed())
@@ -125,7 +128,7 @@ bool pFlow::postprocessData::write() const
             continue;
         }
 
-        if(!component->write(postProcessGlobals::defaultDir__/component->name()))
+        if(!component->write(defaultDir__/component->name()))
         {
             fatalErrorInFunction
                 <<"Error occured in writing postprocess component: "
@@ -136,7 +139,7 @@ bool pFlow::postprocessData::write() const
     return true;
 }
 
-void pFlow::postprocessData::setOutputDirectory(const fileSystem &path) const
+void pFlow::postprocessData::postprocessData::setOutputDirectory(const fileSystem &path) const
 {
-    postProcessGlobals::defaultDir__ = path;
+    defaultDir__ = path;
 }

src/PostprocessData/postprocessData/postprocessData.hpp

@@ -28,7 +28,6 @@ Licence:
 #include "fieldsDataBase.hpp"
 #include "postprocessComponent.hpp"
 
-
 namespace pFlow
 {
 
@@ -36,6 +35,11 @@ class systemControl;
 class Time;
 class timeInfo;
 
+}
+
+namespace pFlow::postprocessData 
+{
+
 
 /**
  * @class postprocessData
@@ -109,6 +113,6 @@ public:
     void setOutputDirectory(const fileSystem& path)const;
 };
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #endif // __postprocessData_hpp__

src/PostprocessData/postprocessData/postprocessGlobals.hpp

@@ -23,7 +23,7 @@ Licence:
 
 #include "fileSystem.hpp"
 
-namespace pFlow::postProcessGlobals
+namespace pFlow::postprocessData
 {
 
 static fileSystem defaultDir__;

src/PostprocessData/postprocessData/postprocessTimeControl.hpp

@@ -22,9 +22,11 @@ Licence:
 #define __postprocessTimeControl_hpp__
 
 #include "baseTimeControl.hpp"  
+#include "dictionary.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
+
 class postprocessTimeControl 
 : 
     public baseTimeControl
@@ -60,6 +62,6 @@ postprocessTimeControl(
     // Additional methods and members can be added here
 };
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #endif // __postprocessTimeControl_hpp__

src/PostprocessData/processMethod/GaussianDistribution.hpp

@@ -28,7 +28,7 @@ Licence:
 #include "span.hpp"
 #include "numericConstants.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 class GaussianDistribution

src/PostprocessData/processMethod/arithmetic.hpp

@@ -32,6 +32,9 @@ namespace pFlow
 
 class dictionary;
 
+namespace postprocessData
+{
+
 class arithmetic
 {
 private:
@@ -86,6 +89,8 @@ public:
 
 };
 
-}
+} // namespace postprocessData
+
+} // namespace pFlow
 
 #endif //__arithmetic_hpp__

src/PostprocessData/processMethod/uniformDistribution.hpp

@@ -32,6 +32,9 @@ namespace pFlow
 
 class dictionary;
 
+namespace postprocessData
+{
+
 class uniformDistribution
 {
 private:
@@ -86,6 +89,8 @@ public:
 
 };
 
-}
+} // namespace postprocessData
+
+} // namespace pFlow
 
 #endif //__uniformDistribution_hpp__

src/PostprocessData/readme.md

@@ -0,0 +1,569 @@
+# PostprocessData Module in phasicFlow
+
+The `PostprocessData` module in phasicFlow provides powerful tools for analyzing particle-based simulations both during runtime (in-simulation) and after simulation completion (post-simulation). This document explains how to configure and use the postprocessing features through the dictionary-based input system.
+
+- in-simulation: this is postprocessing that is active during simulation. When running a solver, it allows for real-time data analysis and adjustments based on the simulation's current state. See below to see how you can activate in-simulation postprocessing.
+- post-simulation: this is postprocessing that is done after the simulation is completed. It allows for detailed analysis of the simulation results, including data extraction and visualization based on the results that are stored in time-folders. If you want to use post-simulation, you need to run utility `postprocessPhasicFlow` in terminal (in the simulation case setup folder) to run the postprocessing. This utility reads the `postprocessDataDict` file and performs the specified operations on the simulation data.
+
+## 1. Overview
+
+Postprocessing in phasicFlow allows you to:
+
+- Extract information about particles in specific regions of the domain
+- Calculate statistical properties such as averages and sums of particle attributes
+- Track specific particles throughout the simulation
+- Apply different weighing methods when calculating statistics
+- Perform postprocessing at specific time intervals
+
+## Table of Contents
+
+- [1. Overview](#1-overview)
+- [2. Setting Up Postprocessing](#2-setting-up-postprocessing)
+  - [2.1. Basic Configuration](#21-basic-configuration)
+- [3. Time Control Options](#3-time-control-options)
+- [4. Processing Methods](#4-processing-methods)
+- [5. Region Types](#5-region-types)
+- [6. Processing Operations](#6-processing-operations)
+  - [6.1. Available Functions in average](#61-available-functions-in-average)
+  - [6.2. About fluctuation2 in average function](#62-about-fluctuation2-in-average-function)
+  - [6.3. Derived Functions](#63-derived-functions)
+  - [6.4. Available Fields](#64-available-fields)
+  - [6.5. Optional Parameters](#65-optional-parameters)
+- [7. Examples](#7-examples)
+  - [7.1. Example 1: Probing Individual Particles](#71-example-1-probing-individual-particles)
+  - [7.2. Example 2: Processing in a Spherical Region](#72-example-2-processing-in-a-spherical-region)
+  - [7.3. Example 3: Processing Along a Line](#73-example-3-processing-along-a-line)
+- [8. Advanced Features](#8-advanced-features)
+  - [8.1. Special functions applied on fields](#81-special-functions-applied-on-fields)
+  - [8.2. Particle Filtering with includeMask](#82-particle-filtering-with-includemask)
+  - [8.3. Implementation Notes](#83-implementation-notes)
+- [9. Mathematical Formulations](#9-mathematical-formulations)
+- [10. A complete dictionary file (postprocessDataDict)](#10-a-complete-dictionary-file-postprocessdatadict)
+
+## 2. Setting Up Postprocessing
+
+Postprocessing is configured through a dictionary file named `postprocessDataDict` which should be placed in the `settings` directory. Below is a detailed explanation of the configuration options.
+
+### 2.1. Basic Configuration
+
+The input dictionary, **settings/postprocessDataDict**, may look like this:
+
+```cpp
+// PostprocessData dictionary
+
+
+// Enable/disable postprocessing during simulation
+runTimeActive yes;  // Options: yes, no
+
+// Shape type - only needed when doing post-simulation processing
+shapeType sphere;   // Options depend on the simulation type: sphere, grain, etc.
+
+// Default time control for postprocessing components
+defaultTimeControl
+{
+    timeControl         timeStep;  // Options: timeStep, simulationTime, settings
+    startTime           0;         // Start time for postprocessing
+    endTime             1000;      // End time for postprocessing
+    executionInterval   150;       // How frequently to run postprocessing
+}
+
+// List of postprocessing components
+components
+(
+    // Component definitions here...
+);
+```
+
+
+If you want to activate in-simulation postprocessing, you need to add these lines to the `settings/settingsDict` file:
+
+```cpp
+libs   ("libPostprocessData.so");
+
+auxFunctions    postprocessData;
+```
+
+This will link the postprocessing library to your simulation, allowing you to use its features. Note that, anytime you want to deactivate the in-simulation postprocessing, you can simply change the `runTimeActive` option to `no` in `postprocessDataDict` file.
+
+## 3. Time Control Options
+
+Each postprocessing component can either use the default time control settings or define its own. There are three main options for time control:
+
+| Option | Description | Required Parameters |
+|--------|-------------|---------------------|
+| `timeStep` | Controls execution based on simulation time steps | `startTime`, `endTime`, `executionInterval` |
+| `simulationTime` | Controls execution based on simulation time | `startTime`, `endTime`, `executionInterval` |
+| `settings` | Uses parameters from settingsDict file | None (defined elsewhere) |
+| `default` | Uses the default time control settings (uses `defaultTimeControl` settings)| None (uses default) |
+
+If no time control is specified, the `default` option is used automatically.
+
+## 4. Processing Methods
+
+The postprocessing module provides several methods for processing particle data. They are categorized into two main groups: bulk and individual methods.
+
+- **Bulk Methods**: Operate on all particles that are located in a specified locations/regions (cells, spheres, etc.).
+- **Individual Methods**: Operate on specific particles, allowing for targeted particle property extraction.
+
+| Method | Property type | Description | Formula |
+|--------|------------------|-------------|---------|
+| `arithmetic` | bulk | Simple arithmetic mean/sum with equal weights | Each particle contributes equally |
+| `uniformDistribution` | bulk | Each particle contributes inversely proportional to the total number of particles | $w_i = 1/n$ where $n$ is the number of particles |
+| `GaussianDistribution` | bulk | Weight contribution based on distance from center with Gaussian falloff | $w_i = \exp(-\|x_i - c\|^2/(2\sigma^2))/\sqrt{2\pi\sigma^2}$ |
+| `particleProbe` | individual | Extracts values from specific particles | Direct access to particle properties |
+
+## 5. Region Types
+
+Regions define where in the domain the postprocessing operations are applied:
+
+| Region Type | Description | Required Parameters | Compatible with |
+|-------------|-------------|---------------------|-----------------|
+| `sphere` | A spherical region | `radius`, `center` | bulk |
+| `multipleSpheres` | Multiple spherical regions | `centers`, `radii` | bulk |
+| `line` | Spheres along a line with specified radius | `p1`, `p2`, `nSpheres`, `radius` | bulk |
+| `centerPoints` | Specific particles selected by ID | `ids` | individual |
+
+## 6. Processing Operations
+
+Within each processing region of type `bulk`, you can define multiple operations to be performed:
+
+### 6.1. Available Functions in average
+
+| Function | Property type | Description | Formula | Required Parameters |
+|----------|---------------|-------------|---------|---------------------|
+| `average` | bulk | Weighted average of particle field values | see Equation 1 | `field`, `phi` (optional), `threshold` (optional), `includeMask` (optional), `divideByVolume` (optional), `fluctuation2` (optional) |
+| `sum` | bulk | Weighted sum of particle field values | see Equation 2 | `field`, `phi` (optional),`threshold` (optional), `includeMask` (optional), `divideByVolume` (optional) |
+
+Equation 1:
+
+$$\text{mean} = \frac{\sum_j w_j \cdot \phi_j \cdot \text{field}_j}{\sum_i w_i \cdot \phi_i}$$
+
+Equation 2:
+
+$$\text{sum} = \sum_j w_j \cdot \phi_j \cdot \text{field}_j$$
+
+where:
+
+- $j$ is the index of the particle in the region that also satisfies the `includeMask`
+- $i$ is the index of the particle in the region
+- $w_j$ is the weight of particle $j$ based on the selected processing method
+- $\phi_j$ is the value of the `phi` field for particle $j$ (default is 1)
+- $field_j$ is the value of the specified field for particle $j$
+
+### 6.2. About fluctuation2 in average function
+
+Fluctuation2 is an optional parameter that can be used to account for fluctuations in the particle field values with respect to mean value of the field.
+It is used in the `average` function to calculate the fluctuation of the field values around the mean. The formula for fluctuation2 is:
+
+$$\text{fluctuation}^2 = \frac{\sum_j w_j \cdot \phi_j \cdot (\text{field}_j - \text{mean})^2}{\sum_i w_i \cdot \phi_i}$$
+
+where:
+
+- `mean`: is the average value of the field in the region.
+- `field`: The field to be processed (e.g., `velocity`, `mass`, etc.)
+- `fluctuation2`: Optional parameter to account for fluctuations in the particle field values.
+
+### 6.3. Derived Functions
+
+In addition to the above basic functions, some derived functions are available for specific calculations:
+
+| Function | Property type | Description | Formula | Required Parameters |
+|----------|---------------|-------------|---------|---------------------|
+|`avMassVelocity` | bulk | Average velocity weighted by mass | $\frac{\sum_{i \in \text{region}} w_i \cdot m_i \cdot v_i}{\sum_{i \in \text{region}} w_i \cdot m_i}$ | - |
+
+### 6.4. Available Fields
+
+All the pointFields in the simulation database (for in-simulation processing), or the ones stored in the time folders (for post-simulation processing) can be referenced in the operations. In addition to them, some extra fields are available for use in the operations. The following fields are available for use in the operations:
+
+1. Extra fileds to be used in post-processing operations:
+
+| Field | Field Type | Description | Default Value |
+|-------|------------|-------------|---------------|
+| `position` | `realx3` | Particle positions | - |
+| `one` | `real` | Value 1 for each particle | 1 |
+| `mass` | `real` | Particle mass | - |
+| `density` | `real` | Particle density | - |
+| `volume` | `real` | Particle volume | - |
+| `diameter` | `real` | Particle diameter | - |
+| `I` | `real` | Moment of inertia | - |
+
+2. Common fields which are available in the simulation database/time folders:
+
+| Field | Field Type | Description |
+|-------|------------|-------------|
+| `velocity` | `realx3` | Particle velocity |
+| `rVelocity` | `realx3` | Particle rotational velocity |
+| `acceleration` | `realx3` | Particle acceleration |
+| `rAcceleration` | `realx3` | Particle rotational acceleration |
+| `contactForce` | `realx3` | Particle contact force |
+| `contactTorque` | `realx3` | Particle contact torque |
+| `id` | `integer` | Particle ID |
+| `shapeIndex` | `integer` | Particle shape index |
+
+The above fields may vary from one type of simulation to other. Pleas note that this is only a tentative list.
+
+### 6.5. Optional Parameters
+
+| Parameter | Description | Default | Options |
+|-----------|-------------|---------|---------|
+| `divideByVolume` | Divide result by region volume | `no` | `yes` or `no` |
+| `threshold` | Exclude regions with fewer particles | 1 | Integer value |
+| `includeMask` | Filter particles based on a field value | `all` | `all`, `lessThan`, `greaterThan`, `between`, `lessThanOrEq`, `greaterThanOrEq`, `betweenEq` |
+|`fluctuation2` (in average only)| Calculate fluctuation of field values | `no` | `yes` or `no` |
+| `phi` | Field to be used for weighted averaging | `one` | Any valid field name |
+
+## 7. Examples
+
+### 7.1. Example 1: Probing Individual Particles
+
+```cpp
+velocityProb
+{
+    processMethod    particleProbe;
+    processRegion    centerPoints;
+    selector         id;
+    field            component(position,y);
+    ids              (0 10 100);
+    timeControl      default;
+}
+```
+
+This example extracts the y-component of the position for particles with IDs 0, 10, and 100.
+
+### 7.2. Example 2: Processing in a Spherical Region
+
+```cpp
+on_single_sphere
+{
+    processMethod    arithmetic;
+    processRegion    sphere;
+    
+    sphereInfo
+    {
+        radius  0.01;
+        center  (-0.08 -0.08 0.015);
+    }
+    
+    timeControl default;
+    
+    operations
+    (
+        averageVel
+        {
+            function        average;
+            field           mag(velocity);
+            divideByVolume  no;
+            fluctuation2    yes;
+            threshold       3;
+            includeMask     all;
+        }
+        
+        par1Fraction
+        {
+            function        average;
+            field           one;
+            phi             one;
+            divideByVolume  no;
+            includeMask     lessThan;
+            
+            lessThanInfo
+            {
+                field       diameter;
+                value       0.0031;
+            }
+        }
+        
+        numberDensity
+        {
+            function        sum;
+            field           one;
+            phi             one;
+            divideByVolume  yes;
+        }
+    );
+}
+```
+
+This example defines a sphere region and performs three operations:
+
+1. Calculate the average of velocity magnitude of particles
+2. Calculate the fraction of particles with diameter less than 0.0031
+3. Calculate the number density by summing and dividing by volume
+
+### 7.3. Example 3: Processing Along a Line
+
+In this example, a line region is defined. The `lineInfo` section specifies the start and end points of the line, the number of spheres to create along the line, and the radius of each point. Bulk properties are calculated in each sphere, based on the properties of particles contained in each sphere.
+
+```cpp
+along_a_line
+{
+      processMethod    arithmetic;
+      processRegion    line;
+      
+      timeControl simulationTime;
+      startTime   1.0;
+      endTime     3.0;
+      executionInterval 0.1;
+      
+      lineInfo
+      {
+        p1   (0 0 0);
+        p2   (0 0.15 0.15);
+        nSpheres    10;
+        radius    0.01;
+      }
+      
+      operations
+      (
+          bulkDensity
+          {
+              function       sum;
+              field          mass;
+              phi            one;
+              divideByVolume yes;
+          }
+          
+          volumeDensity
+          {
+            function         sum;
+            field            volume;
+            divideByVolume   yes;
+          }
+     );
+}
+```
+
+This example creates 10 spherical regions along a line from (0,0,0) to (0,0.15,0.15) and calculates the bulk density and volume density in each region.
+
+## 8. Advanced Features
+
+### 8.1. Special functions applied on fields
+
+You can access specific components of vector fields (`realx3`) using the `component` function:
+
+```cpp
+field  component(position,y);  // Access the y-component of position
+```
+
+Here is a complete list of these special functions: 
+
+| Function Name | Valid field Type | Example |
+|-----------------|------------|---------|
+| `component` | `realx3` | `component(velocity,x)` |
+| `abs` | `real` | `abs(s)` |
+| `square` | `real` | `square(I)` |
+| `cube` | `real` | `cube(diameter)` |
+| `squre root` | `real` | `sqrt(mass)` |
+| `magnitude` | `realx3` | `mag(contactForce)` |
+| `magnitude square` | `realx3` | `magSquare(velocity)` |
+| `magnitude cube` | `realx3` | `magCube(velocity)` |
+| `magnitude square root` | `realx3` | `magSqrt(acceleration)` |
+
+### 8.2. Particle Filtering with includeMask
+
+The `includeMask` parameter allows you to filter particles based on field values:
+
+```cpp
+includeMask  lessThan;
+lessThanInfo
+{
+    field   diameter;
+    value   0.0031;
+}
+```
+
+Supported masks:
+
+- `all`: Include all particles (default)
+- `lessThan`: Include particles where field < value
+- `greaterThan`: Include particles where field > value
+- `between`: Include particles where value1 < field < value2
+- `lessThanOrEq`: Include particles where field ≤ value
+- `greaterThanOrEq`: Include particles where field ≥ value
+- `betweenEq`: Include particles where value1 ≤ field ≤ value2
+
+### 8.3. Implementation Notes
+
+- The postprocessing system can work both during simulation (`runTimeActive yes`) or after simulation completion.
+- When using post-simulation mode, you must specify the correct `shapeType` to properly initialize the shape objects.
+- Results are written to output files in the case directory with timestamps.
+- The `threshold` parameter helps eliminate statistical noise in regions with few particles.
+- Setting `divideByVolume` to `yes` normalizes results by the volume of the region, useful for calculating densities.
+
+## 9. Mathematical Formulations
+
+For weighted `bulk` properties calculation, we have these two general formulations:
+
+- For weighted averaging:
+
+$$ \text{average} = \frac{\sum_j w_j \cdot \phi_j \cdot \text{field}_j}{\sum_i w_i \cdot \phi_i} $$
+
+- For weighted summing:
+
+$$ \text{sum} = \sum_j w_j \cdot \phi_j \cdot \text{field}_j $$
+
+If `divideByVolume` is set to `yes`, the result is divided by the volume of the region:
+
+$$ \text{volumetric result} = \frac{\text{result}}{V_{\text{region}}} $$
+
+## 10. A complete dictionary file (postprocessDataDict)
+
+```C++
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName   postprocessDataDict;
+objectType   dictionary;;
+fileFormat   ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Yes: postprocessing is active during the simulation
+// No: postprocessing is not active during the simulation
+// and it can be done after simulation
+runTimeActive yes;
+
+// shapeType: defines the type of the shape that is used in the simulation
+// (for example: sphere, grain, etc).
+// shapeType is only used when postprocessing is done after simulation 
+// to initialize the shape object for post processing operatoins 
+shapeType sphere;
+
+// default time control to be used in the postprocessing components
+defaultTimeControl
+{
+	timeControl         timeStep; // timeStep, simulationTime are the options here 
+	startTime           0;
+	endTime             1000;
+	executionInterval   150; 
+}
+
+// list of postprocessing components
+components
+(
+    // probing particles for their state variables, like velocity, position, etc
+    velocityProb
+    {
+        processMethod    particleProbe;
+        processRegion    centerPoints;
+        selector         id;
+        field            component(position,y);
+        ids              (0 10 100);
+        timeControl      default; // other options are settings, timeStep, simulationTime 
+        // settings: uses parameters from settingsDict file
+        // timeStep: uses the time step of the simulation controlling the execution of postprocessing
+        // simulationTime: uses the simulation time of the simulation controlling the execution of postprocessing
+        // default: uses the default time control (defined in defaultTimeControl).
+        // default behavior: if you do not specify it, parameters in defaultTimeControl is used.
+    }
+    
+    on_single_sphere
+    {
+        // method of performing the sum (arithmetic, uniformDistribution, GaussianDistribution)
+        processMethod    arithmetic; 
+
+        // Postprocessing is done on particles whose centers are inside this spehre
+        processRegion    sphere;  
+        
+        sphereInfo
+        {
+            radius  0.01; // radius of sphere
+            center  (-0.08 -0.08 0.015); // center of sphere
+        }
+        
+        timeControl default;
+        
+        /// all the postprocess operations to be done on sphere region
+        operations
+        (
+            // computes the arithmetic mean of particle velocity 
+            averageVel
+            {
+                function	    average;
+                field           velocity;
+                fluctuation2    yes;
+                divideByVolume 	no;  // default is no
+                threshold 	    3;   // default is 1
+                includeMask     all; // default is all
+            }
+            // - function: average, sum, and other derived ones from sum and average 
+            // - field: names of the fields in the simulation. Some special fields 
+            //   are: mass, density, volume, position, one, I. 
+            // - divideByVolume: whether the result is divided by the volume of the region 
+            // - threshold: exclude regions that contains particles less than threshold
+            // - includeMask: all, lessThan, greaterThan, between, lessThanOrEq, greaterThanEq, betweenEq
+            
+            
+            // computes the fraction of par1 in the region 
+            par1Fraction
+            {
+                function        average;
+                field           one; // default 
+                phi             one; // default
+                divideByVolume  no;
+                includeMask     lessThan;
+                
+                // diameter of par1 is 0.003, so these settings 
+                // will select only particles of type par1
+                lessThanInfo
+                {
+                    field      diameter;
+                    value      0.0031;  
+                }
+            }
+
+            numberDensity
+            {
+                function        sum;
+                field           one;
+                phi             one;
+                divideByVolume  yes;
+                
+            }
+        );
+    }
+    
+    along_a_line
+    {
+        processMethod    arithmetic;
+
+        processRegion    line;
+
+        // the time interval for executing the post-processing 
+        // other options: timeStep, default, and settings
+        timeControl simulationTime; 
+        startTime   1.0;
+        endTime     3.0;
+        executionInterval 0.1;
+        
+        // 10 spheres with radius 0.01 along the straight line defined by p1 and  p2 
+        lineInfo
+        {
+          p1        (0 0 0);
+          p2        (0 0.15 0.15);
+          nSpheres  10;
+          radius    0.01;
+        }
+
+        operations
+        (
+            // computes the arithmetic mean of particle velocity 
+            numberDensity
+            {
+                function	    sum;
+                field           one;
+                divideByVolume  yes;  //default is no 
+            }
+            
+            volumeDensity
+            {
+                function         sum;
+                field            volume; // 
+                divideByVolume   yes;    //default is no 
+            }
+        );
+    }
+    
+);
+
+```

src/PostprocessData/region/regionFields/regionField.hpp

@@ -25,7 +25,7 @@ Licence:
 #include "regionPoints.hpp"
 #include "Field.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 template<typename T> 
@@ -119,7 +119,7 @@ public:
 };
 
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 #include "regionFieldTemplate.cpp"
 

src/PostprocessData/region/regionFields/regionFieldTemplate.cpp

@@ -1,6 +1,8 @@
+namespace pFlow::postprocessData
+{
 
 template<typename T> 
-pFlow::regionField<T>::regionField(
+regionField<T>::regionField(
     const word& name, 
     const regionPoints& rPoints,
     const T defaultVal)
@@ -8,3 +10,5 @@ pFlow::regionField<T>::regionField(
     field_(name, "regionFieldValue", rPoints.size(), rPoints.size(), defaultVal),
     regionPoints_(rPoints)
 {}
+
+} // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/centerPointsRegionPoints/centerPointsRegionPoints.cpp

@@ -3,7 +3,10 @@
 #include "Set.hpp"
 #include "pStructSelector.hpp"
 
-bool pFlow::centerPointsRegionPoints::selectIds()
+namespace pFlow::postprocessData
+{
+
+bool centerPointsRegionPoints::selectIds()
 {
     if(!firstTimeUpdate_) return true;
     firstTimeUpdate_ = false;
@@ -42,7 +45,7 @@ bool pFlow::centerPointsRegionPoints::selectIds()
     return true;
 }
 
-pFlow::centerPointsRegionPoints::centerPointsRegionPoints(
+centerPointsRegionPoints::centerPointsRegionPoints(
     const dictionary &dict,
     fieldsDataBase &fieldsDataBase)
     : regionPoints(dict, fieldsDataBase),
@@ -50,7 +53,7 @@ pFlow::centerPointsRegionPoints::centerPointsRegionPoints(
       probDict_(dict)
 {}
 
-bool pFlow::centerPointsRegionPoints::update()
+bool centerPointsRegionPoints::update()
 {
     if(!selectIds()) return false;
     
@@ -74,7 +77,7 @@ bool pFlow::centerPointsRegionPoints::update()
     return true;
 }
 
-bool pFlow::centerPointsRegionPoints::write(iOstream &os) const
+bool centerPointsRegionPoints::write(iOstream &os) const
 {
     if(firstTimeUpdate_)
     {
@@ -95,3 +98,5 @@ bool pFlow::centerPointsRegionPoints::write(iOstream &os) const
 
     return true;
 }
+
+} // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/centerPointsRegionPoints/centerPointsRegionPoints.hpp

@@ -23,7 +23,7 @@ Licence:
 
 #include "regionPoints.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 /**
@@ -163,7 +163,7 @@ public:
 
 }; // class centerPointsRegionPoints
 
-} // namespace pFlow
+} // namespace pFlow::postprocessData
 
 
 

src/PostprocessData/region/regionPoints/lineRegionPoints/lineRegionPoints.cpp

@@ -1,7 +1,10 @@
 #include "lineRegionPoints.hpp"
 #include "fieldsDataBase.hpp"
 
-pFlow::lineRegionPoints::lineRegionPoints
+namespace pFlow::postprocessData
+{
+
+lineRegionPoints::lineRegionPoints
 (
     const dictionary &dict, 
     fieldsDataBase &fieldsDataBase
@@ -14,7 +17,7 @@ pFlow::lineRegionPoints::lineRegionPoints
     selectedPoints_("selectedPoints")
 {
     const auto& lDict = dict.subDict("lineInfo");
-    uint32 nPoints = lDict.getValMax<uint32>("numPoints",2);
+    uint32 nSpheres = lDict.getValMax<uint32>("nSpheres",2);
     realList raddi;
 
     if( lDict.containsDataEntry("radii"))
@@ -24,24 +27,24 @@ pFlow::lineRegionPoints::lineRegionPoints
     else
     {
         auto r = lDict.getVal<real>("radius");
-        raddi = realList(nPoints, r);
+        raddi = realList(nSpheres, r);
     }
 
-    if(raddi.size() != nPoints)
+    if(raddi.size() != nSpheres)
     {
         fatalErrorInFunction
-            << "The number elements in of radii list should be equal to the "
+            << "The number of elements in the radii list should be equal to the "
-            << "number of points"<<endl;
+            << "nSpheres"<<endl;
             fatalExit;
     }
     
-    sphereRegions_.resize(nPoints, sphere(realx3(0,0,0),1));
+    sphereRegions_.resize(nSpheres, sphere(realx3(0,0,0),1));
-    centerPoints_.resize(nPoints);
+    centerPoints_.resize(nSpheres);
-    volumes_.resize(nPoints);
+    volumes_.resize(nSpheres);
-    diameters_.resize(nPoints);
+    diameters_.resize(nSpheres);
-    selectedPoints_.resize(nPoints);
+    selectedPoints_.resize(nSpheres);
-    real dt = 1.0/(nPoints-1);
+    real dt = 1.0/(nSpheres-1);
-    for(uint32 i = 0; i < nPoints; ++i)
+    for(uint32 i = 0; i < nSpheres; ++i)
     {
         centerPoints_[i] = line_.point(i*dt);
         sphereRegions_[i] = pFlow::sphere(centerPoints_[i], raddi[i]);
@@ -50,7 +53,7 @@ pFlow::lineRegionPoints::lineRegionPoints
     }
 }
 
-pFlow::span<const pFlow::uint32> pFlow::lineRegionPoints::indices(uint32 elem) const
+pFlow::span<const pFlow::uint32> lineRegionPoints::indices(uint32 elem) const
 {
     if(elem >= size())
     {
@@ -65,7 +68,7 @@ pFlow::span<const pFlow::uint32> pFlow::lineRegionPoints::indices(uint32 elem) c
         selectedPoints_[elem].size());
 }
 
-pFlow::span<pFlow::uint32> pFlow::lineRegionPoints::indices(uint32 elem)
+pFlow::span<pFlow::uint32> lineRegionPoints::indices(uint32 elem)
 {
     if(elem >= size())
     {
@@ -80,7 +83,7 @@ pFlow::span<pFlow::uint32> pFlow::lineRegionPoints::indices(uint32 elem)
         selectedPoints_[elem].size());
 }
 
-bool pFlow::lineRegionPoints::update()
+bool lineRegionPoints::update()
 {
     const auto points = database().updatePoints();
     for(auto& elem : selectedPoints_)
@@ -101,7 +104,7 @@ bool pFlow::lineRegionPoints::update()
     return true;
 }
 
-bool pFlow::lineRegionPoints::write(iOstream &os) const
+bool lineRegionPoints::write(iOstream &os) const
 {
     os << "# Spheres along a straight line \n";
     os << "#  No." << tab << "centerPoint" << tab << "diameter" << endl;
@@ -118,3 +121,5 @@ bool pFlow::lineRegionPoints::write(iOstream &os) const
     os << endl;
     return true;
 }
+
+} // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/lineRegionPoints/lineRegionPoints.hpp

@@ -54,7 +54,7 @@ Licence:
 #include "Vectors.hpp"
 
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 class lineRegionPoints

src/PostprocessData/region/regionPoints/multipleSpheresRegionPoints/multipleSpheresRegionPoints.cpp

@@ -1,7 +1,10 @@
 #include "multipleSpheresRegionPoints.hpp"
 #include "fieldsDataBase.hpp"
 
-pFlow::multipleSpheresRegionPoints::multipleSpheresRegionPoints
+namespace pFlow::postprocessData
+{
+
+multipleSpheresRegionPoints::multipleSpheresRegionPoints
 (
     const dictionary &dict, 
     fieldsDataBase &fieldsDataBase
@@ -46,7 +49,7 @@ pFlow::multipleSpheresRegionPoints::multipleSpheresRegionPoints
     }
 }
 
-pFlow::span<const pFlow::uint32> pFlow::multipleSpheresRegionPoints::indices(uint32 elem) const
+pFlow::span<const pFlow::uint32> multipleSpheresRegionPoints::indices(uint32 elem) const
 {
     if (elem >= size())
     {
@@ -59,7 +62,7 @@ pFlow::span<const pFlow::uint32> pFlow::multipleSpheresRegionPoints::indices(uin
     return span<const uint32>(selectedPoints_[elem].data(), selectedPoints_[elem].size());
 }
 
-pFlow::span<pFlow::uint32> pFlow::multipleSpheresRegionPoints::indices(uint32 elem)
+pFlow::span<pFlow::uint32> multipleSpheresRegionPoints::indices(uint32 elem)
 {
     if (elem >= size())
     {
@@ -73,7 +76,7 @@ pFlow::span<pFlow::uint32> pFlow::multipleSpheresRegionPoints::indices(uint32 el
 }
 
 
-bool pFlow::multipleSpheresRegionPoints::update()
+bool multipleSpheresRegionPoints::update()
 {
     const auto points = database().updatePoints();
     for (auto& elem : selectedPoints_)
@@ -94,7 +97,7 @@ bool pFlow::multipleSpheresRegionPoints::update()
     return true;
 }
 
-bool pFlow::multipleSpheresRegionPoints::write(iOstream &os) const
+bool multipleSpheresRegionPoints::write(iOstream &os) const
 {
     os << "# Multiple spheres region points\n";
     os << "#  No." << tab << "centerPoint" << tab << "diameter" << endl;
@@ -110,3 +113,5 @@ bool pFlow::multipleSpheresRegionPoints::write(iOstream &os) const
     os << endl;
     return true;
 }
+
+} // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/multipleSpheresRegionPoints/multipleSpheresRegionPoints.hpp

@@ -51,7 +51,7 @@ Licence:
 #include "sphere.hpp"
 #include "Vectors.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 class multipleSpheresRegionPoints

src/PostprocessData/region/regionPoints/regionPoints/regionPoints.cpp

@@ -2,7 +2,10 @@
 #include "fieldsDataBase.hpp"
 #include "Time.hpp"
 
-pFlow::regionPoints::regionPoints
+namespace pFlow::postprocessData
+{
+
+regionPoints::regionPoints
 (
     const dictionary &dict, 
     fieldsDataBase &fieldsDataBase
@@ -11,18 +14,20 @@ pFlow::regionPoints::regionPoints
     fieldsDataBase_(fieldsDataBase)
 {}
 
-const pFlow::Time& pFlow::regionPoints::time() const
+const Time& regionPoints::time() const
 {
     return fieldsDataBase_.time();
 }
 
-const pFlow::fieldsDataBase & pFlow::regionPoints::database() const
+const fieldsDataBase & regionPoints::database() const
 {
     return fieldsDataBase_;
 }
 
-pFlow::fieldsDataBase& pFlow::regionPoints::database()
+fieldsDataBase& regionPoints::database()
 {
     return fieldsDataBase_;
 }
 
+} // namespace pFlow::postprocessData
+

src/PostprocessData/region/regionPoints/regionPoints/regionPoints.hpp

@@ -25,12 +25,16 @@ Licence:
 #include "dictionary.hpp"
 #include "pointStructure.hpp"
 
-
 namespace pFlow
+{
+    class Time;
+}
+
+namespace pFlow::postprocessData
 {
 
 class fieldsDataBase;
-class Time;
+
 
 /**
  * @class regionPoints

src/PostprocessData/region/regionPoints/sphereRegionPoints/sphereRegionPoints.cpp

@@ -1,7 +1,10 @@
 #include "sphereRegionPoints.hpp"
 #include "fieldsDataBase.hpp"
 
-pFlow::sphereRegionPoints::sphereRegionPoints
+namespace pFlow::postprocessData
+{
+
+sphereRegionPoints::sphereRegionPoints
 (
     const dictionary &dict, 
     fieldsDataBase &fieldsDataBase
@@ -15,7 +18,7 @@ pFlow::sphereRegionPoints::sphereRegionPoints
 {
 }
 
-bool pFlow::sphereRegionPoints::update()
+bool sphereRegionPoints::update()
 {
     const auto points = database().updatePoints();
     selectedPoints_.clear();
@@ -30,7 +33,7 @@ bool pFlow::sphereRegionPoints::update()
     return true;
 }
 
-bool pFlow::sphereRegionPoints::write(iOstream &os) const
+bool sphereRegionPoints::write(iOstream &os) const
 {
     os <<"# Single sphere\n";
     os <<"# center point: "<<sphereRegion_.center()<<endl;
@@ -39,3 +42,5 @@ bool pFlow::sphereRegionPoints::write(iOstream &os) const
     
     return true;
 }
+
+} // End namespace pFlow::postprocessData

src/PostprocessData/region/regionPoints/sphereRegionPoints/sphereRegionPoints.hpp

@@ -38,7 +38,7 @@ Licence:
 #include "sphere.hpp"
 #include "Vectors.hpp"
 
-namespace pFlow
+namespace pFlow::postprocessData
 {
 
 class sphereRegionPoints

src/PostprocessData/sampleDictionary/postprocessDataDict

@@ -7,18 +7,30 @@ objectType   dictionary;;
 fileFormat   ASCII;
 /*---------------------------------------------------------------------------*/
 
+// Yes: postprocessing is active during the simulation
+// No: postprocessing is not active during the simulation
+// and it can be done after simulation
 runTimeActive yes;
 
+// shapeType: defines the type of the shape that is used in the simulation
+// (for example: sphere, grain, etc).
+// shapeType is only used when postprocessing is done after simulation 
+// to initialize the shape object for post processing operatoins 
+shapeType sphere;
+
+// default time control to be used in the postprocessing components
 defaultTimeControl
 {
-	timeControl         timeStep;
+	timeControl         timeStep; // timeStep, simulationTime are the options here 
 	startTime           0;
 	endTime             1000;
 	executionInterval   150; 
 }
 
+// list of postprocessing components
 components
 (
+    // probing particles for their state variables, like velocity, position, etc
     velocityProb
     {
         processMethod    particleProbe;
@@ -26,23 +38,31 @@ components
         selector         id;
         field            component(position,y);
         ids              (0 10 100);
+        timeControl      default; // other options are settings, timeStep, simulationTime 
+        // settings: uses parameters from settingsDict file
+        // timeStep: uses the time step of the simulation controlling the execution of postprocessing
+        // simulationTime: uses the simulation time of the simulation controlling the execution of postprocessing
+        // default: uses the default time control (defined in defaultTimeControl).
+        // default behavior: if you do not specify it, parameters in defaultTimeControl is used.
     }
     
-      onSingleSphere
+    on_single_sphere
     {
         // method of performing the sum (arithmetic, uniformDistribution, GaussianDistribution)
         processMethod    arithmetic; 
-          processRegion    sphere; // type of region on which processing is performed 
+
+        // Postprocessing is done on particles whose centers are inside this spehre
+        processRegion    sphere;  
         
         sphereInfo
         {
-              radius 0.01;
+            radius  0.01; // radius of sphere
-              center (-0.08 -0.08 0.015);
+            center  (-0.08 -0.08 0.015); // center of sphere
         }
         
-          timeControl default; // settings, timeStep, simulationTime 
+        timeControl default;
         
-          /// all the post process operations to be done 
+        /// all the postprocess operations to be done on sphere region
         operations
         (
             // computes the arithmetic mean of particle velocity 
@@ -50,16 +70,24 @@ components
             {
                 function	    average;
                 field           velocity;
-                  divideByVolume 	  no;  //default 
+                fluctuation2    yes;
-                  threshold 	  3;   //default is 1;
+                divideByVolume 	no;  // default is no
-                  includeMask     all;
+                threshold 	    3;   // default is 1
+                includeMask     all; // default is all
             }
+            // - function: average, sum, and other derived ones from sum and average 
+            // - field: names of the fields in the simulation. Some special fields 
+            //   are: mass, density, volume, position, one, I. 
+            // - divideByVolume: whether the result is divided by the volume of the region 
+            // - threshold: exclude regions that contains particles less than threshold
+            // - includeMask: all, lessThan, greaterThan, between, lessThanOrEq, greaterThanEq, betweenEq
+            
             
             // computes the fraction of par1 in the region 
             par1Fraction
             {
                 function        average;
-                  field           one;
+                field           one; // default 
                 phi             one; // default
                 divideByVolume  no;
                 includeMask     lessThan;
@@ -69,7 +97,6 @@ components
                 lessThanInfo
                 {
                     field      diameter;
-                      
                     value      0.0031;  
                 }
             }
@@ -78,16 +105,17 @@ components
             {
                 function        sum;
                 field           one;
-                  phi             one; // default
+                phi             one; 
                 divideByVolume  yes;
                 
             }
         );
     }
     
-    alongALine
+    along_a_line
     {
         processMethod    arithmetic;
+
         processRegion    line;
 
         // the time interval for executing the post-processing 
@@ -103,7 +131,7 @@ components
         {
             p1        (0 0 0);
             p2        (0 0.15 0.15);
-            numPoints 10;
+            nSpheres  10;
             radius    0.01;
         }
 
@@ -120,7 +148,7 @@ components
             volumeDensity
             {
                 function         sum;
-                field            cube(diameter); // d^3, although it differs by pi/6
+                field            volume; // 
                 divideByVolume   yes;    //default is no 
             }
         );

tutorials/README.md

@@ -0,0 +1,40 @@
+# phasicFlow Tutorials
+
+This directory contains various tutorial examples to help you learn how to use phasicFlow for different particle simulation scenarios. Each tutorial provides a complete working example with configuration files and instructions.
+
+
+## 1. Sphere DEM Simulations (`sphereGranFlow`)
+
+The most comprehensive collection of tutorials using spherical particles for DEM simulations:
+
+- [Rotating Drum (Small)](./sphereGranFlow/rotatingDrumSmall/) - Simple rotating drum simulation with 30,000 spherical particles (4 mm diameter)
+- [Rotating Drum (Medium)](./sphereGranFlow/rotatingDrumMedium/) - Medium-sized rotating drum simulation
+- [Rotating Drum with Baffles](./sphereGranFlow/RotatingDrumWithBaffles/) - Rotating drum with internal baffles and binary particle mixture
+- [Rotating Drum with Periodic Boundaries](./sphereGranFlow/drum-PeriodicBoundary/) - Simulates an "infinite length" drum using periodic boundaries
+- [V-blender](./sphereGranFlow/V-blender/) - V-shaped blender simulation for particle mixing
+- [Tote Blender](./sphereGranFlow/toteBlender/) - Double pedestal tote blender simulation with 24,000 particles
+- [Binary System of Particles](./sphereGranFlow/binarySystemOfParticles/) - Demonstrates particle segregation in a rotating drum with two particle sizes
+- [Screw Conveyor](./sphereGranFlow/screwConveyor/) - Simulates particle transport using a screw conveyor
+- [Conveyor Belt](./sphereGranFlow/conveyorBelt/) - Simulates particles on a moving conveyor belt
+- [Rotary Air Lock Valve](./sphereGranFlow/RotaryAirLockValve/) - Simulates a rotary air lock valve with particle insertion
+- [Layered Silo Filling](./sphereGranFlow/layeredSiloFilling/) - Demonstrates filling a silo with layers of particles
+- [Homogenization Silo (Periodic Boundaries)](./sphereGranFlow/homogenizationSilo-PeriodicBoundary/) - Simulates homogenization in a silo with periodic boundaries
+
+## 2. Course-grained (Grain) DEM Simulations (`grainGranFlow`)
+
+Tutorials for simulations with non-spherical (grain-shaped) particles:
+
+- [Rotating Drum](./grainGranFlow/rotatingDrum/) - Demonstrates non-spherical grain particles in a rotating drum
+
+## 3. Geometry Iteration (`iterateGeometry`)
+
+Tutorials focused on geometry handling and visualization:
+
+- [Inclined Screw Conveyor](./iterateGeometry/inclinedScrewConveyor/) - Visualizes the geometry of an inclined screw conveyor without particles
+
+## 4. Post-processing (`postprocessPhasicFlow`)
+
+Tutorials focused on post-processing and analysis:
+
+- [Segregation Analysis](./postprocessPhasicFlow/segregation/) - Demonstrates how to analyze particle segregation in simulation results
+

tutorials/grainGranFlow/rotatingDrum/settings/particlesDict

@@ -44,8 +44,8 @@ positionParticles
 	
 	orderedInfo
 	{
-		// minimum space between centers of particles
+		// minimum distance between particles centers
-		diameter 0.001;
+		distance 0.001;
 		
 		// number of particles in the simulation 	 	
 		numPoints 50000;

tutorials/postprocessPhasicFlow/segregation/settings/particlesDict

@@ -24,7 +24,7 @@ positionParticles
 		
 	positionOrderedInfo
 	{		
-		diameter 0.005; 	// minimum space between centers of particles
+		distance 0.005; 	// minimum distance between particles centers
 		numPoints 30000; 	// number of particles in the simulation 
 		axisOrder (z x y);  // axis order for filling the space with particles
 	}
@@ -41,7 +41,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		r	Velocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
+		rVelocity 		realx3 	(0 0 0); // rotational velocity (rad/s)
 		shapeName 		word	smallSphere; // name of the particle shape 
 	}
 
@@ -54,6 +54,7 @@ setFields
 			{
 				begin 	0;			// begin index of points
 				end 	29999;		// end index of points
+				number 	10000;	    // number of points to be selected 
 			}
 			fieldValue  // fields that the selector is applied to 
 			{

tutorials/sphereGranFlow/RotaryAirLockValve/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

tutorials/sphereGranFlow/RotaryAirLockValve/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

tutorials/sphereGranFlow/RotaryAirLockValve/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
 {
     min     (0.397538 0.178212 0.00);
     

tutorials/sphereGranFlow/RotaryAirLockValve/settings/settingsDict

@@ -25,10 +25,12 @@ g               (0 -9.8 0);                 // gravity vector (m/s2)
 includeObjects (diameter mass);
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1);
+excludeObjects ();
 
 integrationMethod       AdamsBashforth2;
 
+integrationHistory      off;
+
 writeFormat     ascii;                      // data writting format (ascii or binary)
 
 timersReport    Yes;                        // report timers: Yes or No

tutorials/sphereGranFlow/RotatingDrumWithBaffles/ReadMe.md

@@ -1,4 +1,5 @@
 # Problem Definition (v-1.0)
+
 The problem is to simulate a rotating drum with a diameter of 0.24 m, a length of 0.1 m and 6 baffles rotating at 15 rpm. This drum is filled with 20000 particles, the integration time step is 0.00001 s. There are 2 types of particles in this drum, each of which is inserted during the simulation to fill the drum.
 * **12500** Particles with **4 mm** diameter, at the rate of 12500 particles/s for 1 sec. 
 * **7500** Particles with **5mm** diameter, at the rate of 7500 particles/s for 1 sec.   
@@ -15,10 +16,13 @@ The problem is to simulate a rotating drum with a diameter of 0.24 m, a length o
 </html>
 
 # Setting up the Case
+
 As it has been explained in the previous cases, the simulation case setup is based on text-based scripts. Here, the simulation case setup are sorted in three folders: `caseSetup`, `setting` and `stl`.
 
 ## Defining small and large particles 
+
 Then in the `caseSetup/shapes` the diameter and the material name of the particles are defined.  Two sizes are defined: 4 and 5 mm.
+
 ```C++
 // names of shapes 
 names 		(smallSphere largeSphere);
@@ -28,8 +32,8 @@ diameters 	(0.004 0.005);
 materials	(lightMat heavyMat);
 ```
 
-
 ## Particle Insertion
+
 In this case we have two regions for inserting the particles. In both regions we define the insertion rate, the start and end time of the insertion, information about the volume of space through which the particles are inserted. The insertion phase in the simulation is performed between times 0 and 1 second.   
 For example, for the insertion region for inserting light particles is shown below.
 
@@ -39,31 +43,44 @@ in <b>caseSetup/particleInsertion</b> file
 
 
 ```C++
-// Right Layer Region
+// Right Region
-layerrightregion 
+right_region 
 {
-// type of insertion region
+   // type of insertion region
-   timeControl           simulationTime;
    regionType	         cylinder;
-// insertion rate (particles/s)    
+   // insertion rate (particles/s)    
    rate 	  12500;
-// Start time of LightParticles insertion (s)
+
+   timeControl           simulationTime;  
+   // Start time of insertion (s)   
    startTime 	  0; 
-// End time of LightParticles insertion (s)      
+   // End time of  insertion (s)      
    endTime   	  1;
-// Time Interval of LightParticles insertion (s)
+   // Time Interval of insertion (s)
    insertionInterval       0.025; 
 
    cylinderInfo 
    {
-// Coordinates of cylinderRegion (m,m,m)
+       // Coordinates of cylinderRegion (m,m,m)
    	   p2 (-0.15 0.25 0.05);
    	   p1 (-0.15 0.24	0.05);
-// radius of cylinder (m)
+       // radius of cylinder (m)
    	   radius 0.035;
    }
+   
+   setFields
+   {
+        velocity   realx3 (0.0 -0.6 0.0); // initial velocity of inserted particles
+   }
+   
+   mixture
+   {
+        smallSphere     1;              // mixture composition of inserted particles
+   }
 }
 ```
+
+
 ## Interaction between particles and walls
 The `caseSetup/interaction` file defines the material names and properties as well as the interaction parameters: the interaction between the particles and the shell of the rotating drum. Since we define 3 materials for simulation, the interaction matrix is 3x3, while we only need to enter upper triangle elements (interactions are symmetric). 
 
@@ -78,31 +95,32 @@ densities   (1000 1500 2500);
                                  heavyMat-heavyMat    heavyMat-wallMat
                                                       wallMat-wallMat );
    */
-// Young modulus [Pa]
+   // Young modulus [Pa]
    Yeff (1.0e6 1.0e6 1.0e6  
                1.0e6 1.0e6
                      1.0e6);
-// Shear modulus [Pa]   
+   // Shear modulus [Pa]   
    Geff (0.8e6 0.8e6 0.8e6  
                0.8e6 0.8e6
                      0.8e6);
-// Poisson's ratio [-]
+   // Poisson's ratio [-]
    nu    (0.25 0.25  0.25  
                0.25  0.25
                      0.25);
-// coefficient of normal restitution
+   // coefficient of normal restitution
    en (0.97  0.97    0.85   
              0.97    0.85
                      1.00);
-// dynamic friction 
+   // dynamic friction 
    mu (0.65   0.65 0.35   
               0.65 0.35
                    0.35);
-// rolling friction 
+   // rolling friction 
    mur (0.1  0.1 0.1    
              0.1 0.1
                  0.1);      
 ```
+
 ## Settings
 ### Geometry
 In the `settings/geometryDict` file, the geometry and axis of rotation is defined for the drum. The geometry is composed of a body, front and rear ends. 
@@ -163,7 +181,9 @@ surfaces
 In this part of `geometryDict` the information of rotating axis and speed of rotation are defined. The start of rotation is at 2 s. The first 2 seconds of simulation is for allowing particles to settle donw in the drum. 
 
 ```C++
+
 motionModel rotatingAxis;
+
 rotatingAxisInfo
 {
     rotAxis 
@@ -181,7 +201,9 @@ rotatingAxisInfo
     }
 }
 ```
+
 ## Performing Simulation
+
 To run simulations, type the following commands in the terminal one at a time.
 
 Enter `particlesPhasicFlow` command to create the initial fields for particles.  

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/interaction

@@ -6,6 +6,7 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 materials           (lightMat heavyMat wallMat); // a list of materials names
 
 densities           (1000 1500 2500);            // density of materials [kg/m3]  
@@ -14,7 +15,7 @@ contactListType     sortedContactList;
 
 contactSearch
 {
-    method             NBS;                       // method for broad search 
+    method             NBS;
     
     updateInterval     10;
 

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/particleInsertion

@@ -6,14 +6,14 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 active     Yes;                         // is insertion active -> Yes or No
 
 /*
       Two layers of particles are packed one-by-one using 1 insertion steps 
 */
 
-
+right_region                                 
-layerrightregion                                 // Right Layer Region
 {
     timeControl           simulationTime;
 
@@ -21,11 +21,11 @@ layerrightregion                                 // Right Layer Region
  
     rate                  12500;        // Right Region Particles Insertion Rate (particles/s)
 
-    startTime 	          0;                     // Start time of LightParticles insertion (s)
+    startTime             0;            // Start time of insertion (s)
     
-    endTime   	          1;                     // End time of LightParticles insertion (s) 
+    endTime               1;            // End time of insertion (s) 
 
-    insertionInterval     0.025;                 // Time Interval of LightParticles insertion (s)
+    insertionInterval     0.025;        // Time Interval of particles insertion (s)
 
     cylinderInfo 
     {
@@ -47,7 +47,7 @@ layerrightregion                                 // Right Layer Region
     }
 }
 
-layerleftregion                                  // Left Layer Region
+left_region                                  
 {
     timeControl           simulationTime;
 
@@ -55,11 +55,11 @@ layerleftregion                                  // Left Layer Region
 
     rate                  7500;          // Left Region Particles Insertion Rate (particles/s)
 
-    startTime             0;                      // Start time of LightParticles insertion (s)
+    startTime             0;             // Start time of  insertion (s)
   
-    endTime               1;                      // End time of LightParticles insertion (s)
+    endTime               1;             // End time of  insertion (s)
 
-    insertionInterval     0.025;                  // Time Interval of LightParticles insertion (s)
+    insertionInterval     0.025;         // Time Interval of  insertion (s)
 
     cylinderInfo 
     {

tutorials/sphereGranFlow/RotatingDrumWithBaffles/caseSetup/shapes

@@ -6,6 +6,7 @@ objectName 	sphereDict;
 objectType  sphereShape;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 names         (smallSphere largeSphere);  // names of shapes 
     
 diameters     (0.004 0.005);              // diameter of shapes (m) 

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                                        
 {
     min (-0.328 0.095 -0.025);      // lower corner point of the box 
 
@@ -22,26 +24,26 @@ boundaries
 
 	right
 	{
-		type     exit;                           // other options: periodict, reflective 
+		type     exit;         // other options: periodic, reflective 
 	}
 
 	bottom
 	{
-		type     exit;                           // other options: periodict, reflective 
+		type     exit;         // other options: periodic, reflective 
 	}
 
 	top
 	{
-		type     exit;                           // other options: periodict, reflective 
+		type     exit;         // other options: periodic, reflective 
 	}
 
 	rear
 	{
-		type     exit;                           // other options: periodict, reflective 
+		type     exit;         // other options: periodic, reflective 
 	}
 
 	front
 	{
-		type     exit;                           // other options: periodict, reflective 
+		type     exit;         // other options: periodic, reflective 
 	}
 }

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/geometryDict

@@ -6,6 +6,7 @@ objectName 	geometryDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 motionModel rotatingAxis;                        
 
 rotatingAxisInfo

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/particlesDict

@@ -10,9 +10,7 @@ setFields
 {
 	/*
 	    Default value for fields defined for particles
-
 		These fields should always be defined for simulations with 
-
 		spherical particles.
 	*/
 
@@ -29,30 +27,13 @@ setFields
 
 	selectors
 	{
-		shapeAssigne
-		{
-			selector     stridedRange; 	         // other options: box, cylinder, sphere, randomPoints 
 		
-			stridedRangeInfo
-			{
-				begin 	   0;			         // begin index of points
-
-				end 	   20000;		 		 // end index of points 
-
-				stride     3;			 		 // stride for selector 
-			}
-
-			fieldValue  					     // fields that the selector is applied to 
-			{
-				shapeName 	word    sphere1;     // sets shapeName of the selected points to largeSphere
-			}
-		}
 	}
 }
 
-positionParticles                                // positions particles 
+positionParticles 
 {
-	method empty;     		                     // other options: random and ordered
+	method empty;    // other options: random, file and ordered
 }
 
 

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/settingsDict

@@ -20,14 +20,16 @@ timePrecision     6;		                     // maximum number of digits for time
 
 g                (0 -9.8 0);                     // gravity vector (m/s2) 
 
-// save necessary (i.e., required) data on disk
+// save necessary data on disk
 includeObjects (diameter);                       
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+excludeObjects (); 
 
 integrationMethod        AdamsBashforth2;        // integration method
 
+integrationHistory       off;                    // to sace space on disk 
+
 writeFormat              ascii;                  // data writting format (ascii or binary)
 
 timersReport             Yes;                    // report timers (Yes or No)

tutorials/sphereGranFlow/V-blender/README.md

@@ -0,0 +1,251 @@
+# V-blender Simulation (phasicFlow v-1.0)
+
+This tutorial demonstrates the simulation of a V-blender, a common mixing device used in pharmaceutical and powder processing industries. The V-blender consists of a V-shaped vessel that rotates around a horizontal axis, allowing for efficient mixing of particulate materials.
+
+
+<div align ="center">
+  <img src="./v-blender.png" style="width: 400px;">
+</div>
+<div align ="center">  
+  <b>
+    V-blender simulation with two layers of particles
+  </b>
+</div>
+
+## Problem Definition
+
+The simulation represents a V-blender with the following characteristics:
+
+- The blender is initially empty and is filled with two different particle types in sequence
+- First layer: Small particles (10 mm diameter) are inserted from the right side
+- Second layer: Slightly larger particles (10.1 mm diameter) are inserted from the left side
+- The blender begins rotation at t = 3.0 s and continues until t = 10.0 s
+- The rotation speed is set to 3.14 rad/s (approximately 0.5 Hz or 30 RPM)
+- The simulation runs for a total of 10 seconds
+
+## Case Setup
+
+The simulation case setup files are organized in the `settings/` and `caseSetup/` folders.
+
+### Particles Definition
+
+Two particle types are defined in the `caseSetup/shapes` file:
+
+```C++
+names       (smallSphere largeSphere);     // names of particles
+diameters               (0.01 0.0101);     // diameter of particles (m)
+materials         (lightMat lightMat);     // material names for particles
+```
+
+Both particle types share the same material properties but differ slightly in size to allow for visual distinction during mixing.
+
+### Particle Insertion
+
+Particles are inserted in two sequential phases, as defined in `caseSetup/particleInsertion`:
+
+```C++
+active              Yes;      // is insertion active -> Yes or No
+
+rightregion
+{
+    timeControl    simulationTime;    // Controls insertion based on simulation time
+    
+    regionType     cylinder;          // Defines a cylindrical insertion region
+    
+    rate           10000;             // Inserts 10,000 particles per second
+    
+    startTime      0.0;               // Starts inserting at t = 0s (beginning of simulation)
+    
+    endTime        1.0;               // Stops inserting at t = 1s
+    
+    insertionInterval 0.025;          // Inserts particles every 0.025s
+                                      // (40 insertion events during the 1s period)
+    
+    cylinderInfo {
+        // Defines cylinder endpoints and radius
+        p1 (0.0950615  0.12 0.5011585);  // First endpoint coordinates (x,y,z) in meters
+        p2 (0.1150615  0.12 0.4811585);  // Second endpoint coordinates (x,y,z) in meters
+        radius 0.1;                       // Cylinder radius in meters
+    }
+    
+    setFields {
+        // Initial properties for inserted particles
+        velocity realx3 (1.2 0.0 -1.2);   // Initial velocity vector (x,y,z) in m/s
+                                          // Particles move to the right and downward
+    }
+    
+    mixture {
+        // Particle type distribution
+        smallSphere 1;                    // 100% of inserted particles are "smallSphere" type
+    }
+}
+
+leftregion
+{
+    timeControl    simulationTime;    // Controls insertion based on simulation time
+    
+    regionType     cylinder;          // Defines a cylindrical insertion region
+    
+    rate           10000;             // Inserts 10,000 particles per second
+    
+    startTime      1.5;               // Starts inserting at t = 1.5s
+                                      // (after the first insertion phase)
+    
+    endTime        2.5;               // Stops inserting at t = 2.5s
+    
+    insertionInterval 0.025;          // Inserts particles every 0.025s
+                                      // (40 insertion events during the 1s period)
+    
+    cylinderInfo {
+        // Defines cylinder endpoints and radius
+        p1 (0.7562545 0.12 0.50079);    // First endpoint coordinates (x,y,z) in meters
+        p2 (0.7362545 0.12 0.48079);    // Second endpoint coordinates (x,y,z) in meters
+        radius 0.1;                      // Cylinder radius in meters
+    }
+    
+    setFields {
+        // Initial properties for inserted particles
+        velocity realx3 (-1.2 0.0 -1.2); // Initial velocity vector (x,y,z) in m/s
+                                         // Particles move to the left and downward
+    }
+    
+    mixture {
+        // Particle type distribution
+        largeSphere 1;                   // 100% of inserted particles are "largeSphere" type
+    }
+}
+```
+
+#### Detailed Explanation of Insertion Parameters
+
+1. **`rightregion` Dictionary**:
+   - Creates a cylindrical insertion region on the right side of the V-blender
+   - Active during t=0s to t=1s at the beginning of the simulation
+   - Particles are inserted from randomly generated positions within the cylinder
+   - Inserts "smallSphere" particles with 10mm diameter
+   - Initial velocity (1.2, 0.0, -1.2) m/s directs particles toward the center and bottom of the blender
+   - 40 insertion events occur (every 0.025s), each adding approximately 250 particles
+
+2. **`leftregion` Dictionary**:
+   - Creates a symmetrical cylindrical insertion region on the left side of the V-blender
+   - Active during t=1.5s to t=2.5s, after the first batch of particles has settled
+   - Inserts "largeSphere" particles with 10.1mm diameter
+   - Initial velocity (-1.2, 0.0, -1.2) m/s directs particles toward the center and bottom of the blender
+   - Mirror image of the first insertion but with slightly larger particles
+
+3. **Insertion Region Selection**:
+   - Cylindrical insertion regions are positioned above each arm of the V-blender
+   - This arrangement ensures particles fall naturally into the V-blender without initial overlap
+
+4. **Timing Strategy**:
+   - Sequential insertion with a 0.5s gap between phases allows the first batch to settle
+   - All particles settle for 0.5s after the second insertion (t=2.5s to t=3.0s)
+   - Blender rotation begins after all particles have settled (t=3.0s)
+
+### Geometry and Motion
+
+The V-blender geometry is defined in `settings/geometryDict` using an STL file:
+
+```C++
+motionModel rotatingAxis;                        // motion model: rotating object around an axis
+
+rotatingAxisInfo                                 // information for rotatingAxis motion model 
+{
+    rotAxis 
+    {  
+        p1 (0.128228 0.116446 0.297901);         // first point for the axis of rotation
+        p2 (0.722596 0.116459 0.297901);         // second point for the axis of rotation
+        omega                      3.14;         // rotation speed (rad/s)
+        startTime                     3;         // start time of rotation
+        endTime                      10;         // end time of rotation
+    }
+}
+```
+
+The blender starts rotating at t = 3.0 s, after both particle types have been inserted and allowed to settle.
+
+### Simulation Domain and Boundaries
+
+The simulation domain is defined in `settings/domainDict`:
+
+```C++
+globalBox                                        
+{
+    min  (-0.1 -0.4 0);       // lower corner point of the box 
+    max (0.86 0.6 0.6);       // upper corner point of the box 
+}
+```
+
+All boundaries are set to "exit" type, meaning particles that go outside the domain will be deleted.
+
+### Particle Interaction Properties
+
+Material properties and interaction parameters are defined in `caseSetup/interaction`:
+
+```C++
+materials        (wallMat lightMat);        // a list of materials names
+densities               (1000 1000);        // density of materials [kg/m3]
+
+// Contact force models
+model
+{
+    contactForceModel    nonLinearNonLimited;
+    rollingFrictionModel              normal;
+    
+    // Material properties
+    Yeff (1.0e6 1.0e6 
+                1.0e6);      // Young modulus [Pa]
+    Geff (0.8e6 0.8e6 
+                0.8e6);      // Shear modulus [Pa]
+    nu   (0.25  0.25 
+                0.25);         // Poisson's ratio [-]
+    en   (0.97  0.85 
+                0.97);         // coefficient of normal restitution
+    mu   (0.65  0.35 
+                0.65);         // dynamic friction
+    mur  (0.1   0.1 
+                0.1);            // rolling friction
+}
+```
+
+## Running the Simulation
+
+To run this simulation, execute the following commands in sequence:
+
+1. First, create the geometry:
+
+   ```
+   geometryPhasicFlow
+   ```
+
+2. Next, initialize the particle system (note: starts with zero particles):
+   ```
+   particlesPhasicFlow
+   ```
+
+3. Finally, run the simulation:
+
+   ```
+   sphereGranFlow
+   ```
+
+The simulation will automatically insert particles according to the defined schedule and begin rotating the V-blender at the specified time.
+
+## Visualizing Results
+
+After the simulation completes, you can convert the results to VTK format for visualization:
+
+```
+pFlowToVTK  --binary 
+```
+
+The VTK files will be stored in a new directory called `./VTK` and can be visualized using tools like ParaView or VisIt.
+
+## Expected Behavior
+
+During the simulation, you should observe:
+1. Initial filling with small particles from the right side (0-1s)
+2. A brief settling period (1-1.5s)
+3. Filling with large particles from the left side (1.5-2.5s)
+4. Another settling period (2.5-3s)
+5. Rotation of the V-blender causing mixing of the two particle types (3-10s)

tutorials/sphereGranFlow/V-blender/caseSetup/interaction

@@ -6,6 +6,7 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 materials        (wallMat lightMat);        // a list of materials names
 
 densities               (1000 1000);        // density of materials [kg/m3]
@@ -14,7 +15,7 @@ contactListType   sortedContactList;
 
 contactSearch
 {
-    method         NBS;                          // method for broad search 
+    method         NBS;  
 
     updateInterval   10;
 

tutorials/sphereGranFlow/V-blender/caseSetup/particleInsertion

@@ -6,9 +6,10 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
+
 active              Yes;      // is insertion active -> Yes or No
 
-checkForCollision   Yes;           // is checked          -> Yes or No
 
 /*
    Two layers of particles are packed one-by-one using tho insertion steps
@@ -69,12 +70,11 @@ leftregion
     {
         /* coordinates of center of both ends of the insertion 
         cylinder on the left side of the V-blender (m,m,m)  */     
-
         p1 ( 0.7562545 0.12 0.50079);
 
         p2 ( 0.7362545 0.12 0.48079);
 
-        radius   0.1;                             // radius of cylinder (m)
+        radius   0.1;                 
     }
 
     setFields

tutorials/sphereGranFlow/V-blender/settings/domainDict

@@ -25,26 +25,26 @@ boundaries
 
     right
     {
-        type     exit;                           // other options: periodict, reflective 
+        type     exit;        // other options: periodic, reflective 
     }
 
     bottom
     {
-        type     exit;                           // other options: periodict, reflective 
+        type     exit;        // other options: periodic, reflective 
     }
 
     top
     {
-        type     exit;                           // other options: periodict, reflective 
+        type     exit;        // other options: periodic, reflective 
     }
 
     rear
     {
-        type     exit;                           // other options: periodict, reflective 
+        type     exit;        // other options: periodic, reflective 
     }
 
     front
     {
-        type     exit;                           // other options: periodict, reflective 
+        type     exit;        // other options: periodic, reflective 
     }
 }

tutorials/sphereGranFlow/V-blender/settings/geometryDict

@@ -6,6 +6,7 @@ objectName  geometryDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 motionModel rotatingAxis;                        // motion model: rotating object around an axis
 
 rotatingAxisInfo                                 // information for rotatingAxis motion model 

tutorials/sphereGranFlow/binarySystemOfParticles/README.md

@@ -47,7 +47,7 @@ positionParticles
     method ordered;         // other options: random or empty
     orderedInfo
     {        
-           diameter     0.005;     // minimum space between centers of particles
+        distance   0.005;     // minimum space between centers of particles
         numPoints  30000;     // number of particles in the simulation 
         axisOrder  (z x y);   // axis order for filling the space with particles
     }

tutorials/sphereGranFlow/binarySystemOfParticles/settings/domainDict

@@ -6,8 +6,8 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-// Simulation domain: every particles that goes outside this domain will be deleted
 
+// Simulation domain: every particles that goes outside this domain will be deleted
 globalBox                     
 {
     min     (-0.12 -0.12 0);

tutorials/sphereGranFlow/binarySystemOfParticles/settings/geometryDict

@@ -44,7 +44,6 @@ surfaces
     /*
         This is a plane wall at the rear end of cylinder
     */
-
     wall1
     {
         type         planeWall;                  // other options: cuboidWall and  cylinderWall
@@ -65,7 +64,6 @@ surfaces
     /*
         This is a plane wall at the front end of cylinder
     */
-
     wall2
     {
         type         planeWall;                  // other options: cuboidWall and  cylinderWall 

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -6,6 +6,7 @@ objectName 	particlesDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 setFields
 {
     /*
@@ -54,7 +55,7 @@ positionParticles 				                 // positions particles
 
     orderedInfo
     {       
-		diameter    0.005; 	                     // diameter of particles
+        distance    0.005;                       // minimum distance between particles centers
 
         numPoints   30000;                       // number of particles in the simulation
 

tutorials/sphereGranFlow/binarySystemOfParticles/settings/settingsDict

@@ -21,15 +21,15 @@ timePrecision     6;		                     // maximum number of digits for time
 g                 (0 -9.8 0);                    // gravity vector (m/s2) 
 
 // save necessary (i.e., required) data on disk
-
 includeObjects     (diameter);  
 
 // exclude unnecessary data from saving on disk
-
+excludeObjects     (); 
-excludeObjects     (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
 integrationMethod        AdamsBashforth2;        // integration method
 
+integrationHistory       off;                    // do not keep integration history on disk (saves space)
+
 writeFormat              ascii;                  // data writting format (ascii or binary)
 
 timersReport             Yes;                    // report timers

tutorials/sphereGranFlow/conveyorBelt/caseSetup/particleInsertion

@@ -6,14 +6,14 @@ objectName particleInsertion;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 active           Yes;     // is insertion active -> yes or no
 
 checkForCollision No;     // is checked          -> yes or no
 
 /*
-   one layers of particles are packed 
+   one layer of particles are packed 
 */
-
 layer0
 {  
     timeControl          simulationTime;

tutorials/sphereGranFlow/conveyorBelt/caseSetup/shapes

@@ -6,6 +6,7 @@ objectName 	sphereDict;
 objectType  sphereShape;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 names        (lightSphere heavySphere);          // names of shapes 
 
 diameters                (0.007 0.007);          // diameter of shapes 

tutorials/sphereGranFlow/conveyorBelt/settings/domainDict

@@ -6,7 +6,9 @@ objectName 	domainDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+
+// Simulation domain: every particles that goes outside this domain will be deleted
+globalBox                  
 {
     min (-0.11 -0.11 -0.41);
     
@@ -16,19 +18,15 @@ globalBox                                        // Simulation domain: every par
 boundaries
 {
     // Determines how often (how many iterations) do you want to 
-
     // rebuild the list of particles in the neighbor list 
-
     // of all boundaries in the simulation domain 
 
     neighborListUpdateInterval 30;
     
     // Determines how often do you want to update the new changes in the boundary
-
     updateInterval             10;
 
     // The distance from the boundary plane within which particles are marked to be in the boundary list 
-
     neighborLength          0.004;
 
     left

tutorials/sphereGranFlow/conveyorBelt/settings/geometryDict

@@ -6,7 +6,9 @@ objectName 	geometryDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-motionModel          conveyorBelt;               // motion model can be rotatingAxis or stationary or vibrating
+
+// motion model can be rotatingAxis or stationary or vibrating
+motionModel          conveyorBelt;               
 
 conveyorBeltInfo
 {
@@ -73,8 +75,3 @@ surfaces
     }
 }
 
-
-
-
-
-

tutorials/sphereGranFlow/conveyorBelt/settings/particlesDict

@@ -6,16 +6,14 @@ objectName 	particlesDict;
 objectType 	dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 setFields
 {
 	/*
 	    Default value for fields defined for particles
-
 		These fields should always be defined for simulations with 
-
 		spherical particles.
 	*/
-
 	defaultValue 
 	{
 		velocity 		realx3 	    (0 0 0);     // linear velocity (m/s)
@@ -31,17 +29,8 @@ setFields
 	{}
 }
 
-positionParticles                                // positions particles 
+positionParticles  
 {
-	method                empty;                 // other options: ordered and random 
+	method                empty;  // other options: file, ordered and random 
-
-	regionType              box;                 // other options: cylinder and sphere  
-
-	boxInfo                                      // box region for positioning particles 
-	{
-		min (-0.08 -0.08 0.015);                 // lower corner point of the box 
-
-		max ( 0.08  0.08 0.098);	             // upper corner point of the box 
-	} 
 }
 

tutorials/sphereGranFlow/conveyorBelt/settings/settingsDict

@@ -6,7 +6,8 @@ objectName 	settingsDict;
 objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-run   layerdSiloFilling;
+
+run        conveyorBelt;
 
 dt              0.00005;                         // time step for integration (s)
 
@@ -21,13 +22,10 @@ timePrecision         6;	                     // maximum number of digits for ti
 g            (0 0 -9.8);                         // gravity vector (m/s2) 
 
 // save data objects that are not automatically saved on disk.
-
 // overrides the default behavior 
-
 includeObjects (diameter);    
 
 // exclude unnecessary data from saving on disk
-
 excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
 
 integrationMethod       AdamsBashforth2;          // integration method 

tutorials/sphereGranFlow/drum-PeriodicBoundary/README.md

@@ -72,7 +72,7 @@ boundaries
 ## Running the Case 
 The solver for this simulation is `sphereGranFlow`. Enter the following commands in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete. 
 
-```sh
+```
 geometryPhasicFlow
 particlesPhasicFlow
 sphereGranFlow
@@ -81,6 +81,6 @@ sphereGranFlow
 ## Post Processing 
 After finishing the simulation, you can render the results in ParaView. To convert the results to VTK format, just enter the following command in the terminal. This will convert all the results (particles and geometry) to VTK format and store them in the `VTK/` folder. 
 
-```sh
+```
 pFlowToVTK --binary
 ```

tutorials/sphereGranFlow/drum-PeriodicBoundary/settings/settingsDict

@@ -24,18 +24,12 @@ g               (0 -9.8 0);         // gravity vector (m/s2)
 includeObjects  (diameter);         // save necessary (i.e., required) data on disk
 
 // exclude unnecessary data from saving on disk
-excludeObjects  (rVelocity.dy1
+excludeObjects  (); 
-                 rVelocity.dy2
-                 rVelocity.dy3 
-                 pStructPosition.dy1
-                 pStructPosition.dy2
-                 pStructPosition.dy3 
-                 pStructVelocity.dy1
-                 pStructVelocity.dy2
-                 pStructVelocity.dy3); 
 
 integrationMethod     AdamsBashforth4;  // integration method
 
+integrationHistory    off;              // to save space on disk  
+
 writeFormat           ascii;            // data writting format (ascii or binary)
 
 timersReport          Yes;              // report timers (Yes or No)

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/README.md

@@ -3,7 +3,7 @@
 ## Problem
 A homogenization silo is used to mix particles inside a silo using the circulation of particles. A pneumatic conveying system carries particles from the exit and re-enters them from the top. Here, we use a `periodic` boundary to simulate the action of the pneumatic conveyor system for circulating particles. Particles exiting from the bottom are re-entered from the top using this boundary (`periodic`).
 
-The simulation case setup is essentially similar to the [`layeredSiloFilling`](https://github.com/PhasicFlow/phasicFlow/tree/main/tutorials/sphereGranFlow/layeredSiloFilling) tutorial. There is also another change with regard to `layeredSiloFilling`. The exit gate is opened after the filling phase of the silo (see `settings/geometryDict` for more details).
+The simulation case setup is essentially similar to the [`layeredSiloFilling`](../layeredSiloFilling/) tutorial. There is also another change with regard to `layeredSiloFilling`. The exit gate is opened after the filling phase of the silo (see `settings/geometryDict` for more details).
 
 <div align ="center">
 <img src="./homoSilo.jpeg" style="width: 400px;">

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/interaction

@@ -37,7 +37,6 @@ model
                                  heavyMat-heavyMat    heavyMat-wallMat
                                                       wallMat-wallMat  );
    */
-
    Yeff (1.0e6 1.0e6 1.0e6                       // Young modulus [Pa]
                1.0e6 1.0e6
                      1.0e6);

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/caseSetup/particleInsertion

@@ -109,7 +109,6 @@ layer2
     mixture
     {
         parType1 1; // only parType1
-      
     }
 }
 
@@ -143,7 +142,6 @@ layer3
     mixture
     {
         parType2 1;
-      
     }
 }
 
@@ -176,7 +174,6 @@ layer4
     mixture
     {
         parType1 1;
-      
     }
 }
 
@@ -209,6 +206,5 @@ layer5
     mixture
     {
         parType2 1;
-      
     }
 }

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/domainDict

@@ -38,12 +38,12 @@ boundaries
         type exit;   
     }
 
-	rear
+    rear // z-
     {
         type periodic;      
     }
 
-	front
+    front // z+ 
     {
         type periodic;   
     }

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/geometryDict

@@ -61,7 +61,6 @@ surfaces
     /*
         This is a plane wall at the exit of silo
     */
-
     exitGate
     {
         type        planeWall;                   // other options: cuboidWall and cylinderWall

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/particlesDict

@@ -13,7 +13,6 @@ setFields
         These fields should always be defined for simulations with 
         spherical particles.
     */
-
     defaultValue 
     {
         velocity        realx3      (0 0 0);     // linear velocity (m/s)

tutorials/sphereGranFlow/homogenizationSilo-PeriodicBoundary/settings/settingsDict

@@ -25,12 +25,12 @@ g 			    (0 0 -9.8); // gravity vector (m/s2)
 includeObjects (diameter);    
 
 // exclude unnecessary data from saving on disk
-excludeObjects (rVelocity.dy1 rVelocity.dy2 rVelocity.dy3 
+excludeObjects (); 
-				pStructPosition.dy1 pStructPosition.dy2 pStructPosition.dy3
-				pStructVelocity.dy1 pStructVelocity.dy2 pStructVelocity.dy3); 
 
 integrationMethod       AdamsBashforth4; // integration method 
 
+integrationHistory      off;       // to save space on disk 
+
 writeFormat             binary;    // data writting format (ascii or binary)
 
 timersReport            Yes;       // report timers

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -13,7 +13,6 @@ setFields
 		These fields should always be defined for simulations with 
 		spherical particles.
 	*/
-
 	defaultValue 
 	{
 		velocity 		realx3 	    (0 0 0);     // linear velocity (m/s)

tutorials/sphereGranFlow/layeredSiloFilling/settings/settingsDict

@@ -25,10 +25,12 @@ g               (0 0 -9.8);    // gravity vector (m/s^2)
 includeObjects  (diameter mass);
 
 // exclude unnecessary data from saving on disk
-excludeObjects  (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1);
+excludeObjects  ();
 
 integrationMethod    AdamsBashforth2; // integration method
 
+integrationHistory   off;
+
 writeFormat          ascii;           // data writing format (ascii or binary)
 
 timersReport         Yes;             // report timers

tutorials/sphereGranFlow/rotatingDrumMedium/README.md

@@ -0,0 +1,161 @@
+# Simulating a Medium-Scale Rotating Drum (v-1.0)
+
+## Problem Definition
+
+This tutorial demonstrates the simulation of a medium-sized rotating drum with a diameter of 0.24 m and a length of 0.36 m. The drum is filled with 250,000 spherical glass beads with a diameter of 3 mm. The drum rotates at a constant speed, and the simulation captures the flow behavior and mixing of the particles.
+
+<div align="center">
+<b>
+A view of the rotating drum simulation
+</b>
+</div>
+
+***
+
+## Setting up the Case
+
+PhasicFlow simulation case setup is based on text-based scripts provided in two folders located in the simulation case folder: `settings` and `caseSetup`. All commands should be entered in the terminal while the current working directory is the simulation case folder.
+
+### Creating Particles
+
+In the file `settings/particlesDict`, two dictionaries, `positionParticles` and `setFields`, define how particles are positioned and what field values they have initially.
+
+The `positionParticles` dictionary specifies the ordered positioning method to place 250,000 particles within a cylindrical region:
+
+```C++
+positionParticles
+{
+    method ordered;                // other options: random and empty
+    
+    orderedInfo
+    {
+        distance   0.003;          // minimum distance between particles centers
+        numPoints  250000;         // number of particles in the simulation 
+        axisOrder  (z y x);        // axis order for filling the space with particles
+    }
+
+    regionType cylinder;           // other options: box and sphere  
+    
+    cylinderInfo
+    {
+        p1 (0.0 0.0 0.003);        // begin point of cylinder axis
+        p2 (0.0 0.0 0.357);        // end point of cylinder axis
+        radius     0.117;          // radius of cylinder 
+    }
+}
+```
+
+The `setFields` dictionary defines the initial values for particle fields:
+
+```C++
+setFields
+{
+    defaultValue 
+    {
+        velocity        realx3  (0 0 0);   // linear velocity (m/s)
+        acceleration    realx3  (0 0 0);   // linear acceleration (m/s2)
+        rVelocity       realx3  (0 0 0);   // rotational velocity (rad/s)
+        shapeName       word    glassBead; // name of the particle shape 
+    }
+}
+```
+
+To create the particles based on these settings, enter the following command in the terminal:
+
+```
+> particlesPhasicFlow
+```
+
+### Creating Geometry
+
+In the file `settings/geometryDict`, you can find information for creating the rotating drum geometry. The simulation uses the `rotatingAxis` motion model to define rotation around a fixed axis.
+
+The surfaces of the drum are defined in the `surfaces` dictionary, including the cylindrical shell and end walls.
+
+To create the geometry based on these settings, enter the following command in the terminal:
+
+```
+> geometryPhasicFlow
+```
+
+### Defining Properties and Interactions
+
+In the file `caseSetup/shapes`, the particle shape, diameter, and material are defined:
+
+```C++
+names       (glassBead);    // names of shapes 
+diameters       (0.003);    // diameter of shapes 
+materials    (glassMat);    // material names for shapes
+```
+
+In the file `caseSetup/interaction`, the material properties and interaction models are defined:
+
+```C++
+materials     (glassMat wallMat);  // a list of materials names
+densities     (2500.0 2500);       // density of materials [kg/m3]
+
+model
+{
+    contactForceModel    nonLinearLimited;
+    rollingFrictionModel           normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);          // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);          // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);           // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);           // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);           // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);            // rolling friction
+}
+```
+
+The contact search settings are also defined in this file, including the method, update interval, and other parameters.
+
+## Running the Simulation
+
+To run the simulation, follow these steps in order:
+
+1. Create the initial particle fields:
+
+   ```
+   > particlesPhasicFlow
+   ```
+
+2. Create the geometry:
+
+   ```
+   > geometryPhasicFlow
+   ```
+
+3. Start the simulation:
+
+   ```
+   > sphereGranFlow
+   ```
+
+The simulation will run according to the settings defined in `settings/settingsDict`, including the time step, start/end times, and gravity vector.
+
+## Post-Processing
+
+After the simulation is complete, you can visualize the results using ParaView. To convert the simulation results to VTK format, use the following command:
+
+```
+> pFlowToVTK --binary
+```
+
+This will create VTK files in the `VTK/` folder that can be opened in ParaView for visualization and analysis.

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/interaction

@@ -6,6 +6,7 @@ objectName interaction;
 objectType dicrionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
+
 materials         (glassMat wallMat);                       // a list of materials names
 
 densities         (2500.0 2500);                            // density of materials [kg/m3]

tutorials/sphereGranFlow/rotatingDrumMedium/caseSetup/particleInsertion

@@ -1,10 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-active         No;                                      // is checked          -> Yes or No
-