From d1b6a04292f9e7b5f3c6ae23822d0b803c8f22ed Mon Sep 17 00:00:00 2001
From: HRN <hamid.r.norouzi@gmail.com>
Date: Fri, 24 May 2024 00:10:49 +0330
Subject: [PATCH 1/3] makeing beforeIteration step-wise for boundaryBase to
 implement non-bloking communications

---
 .../boundaries/boundaryBase/boundaryBase.hpp         |  2 +-
 .../boundaries/boundaryExit/boundaryExit.cpp         |  3 ++-
 .../boundaries/boundaryExit/boundaryExit.hpp         |  2 +-
 .../structuredData/boundaries/boundaryList.cpp       | 12 +++++++++++-
 .../boundaries/boundaryNone/boundaryNone.cpp         |  1 +
 .../boundaries/boundaryNone/boundaryNone.hpp         |  2 +-
 .../boundaries/boundaryPeriodic/boundaryPeriodic.cpp |  2 ++
 .../boundaries/boundaryPeriodic/boundaryPeriodic.hpp |  2 +-
 .../boundaryReflective/boundaryReflective.cpp        |  1 +
 .../boundaryReflective/boundaryReflective.hpp        |  2 +-
 10 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp b/src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp
index 978f674b..b1f8008a 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp
@@ -339,7 +339,7 @@ public:
 	
 
 	virtual 
-    bool beforeIteration(uint32 iterNum, real t, real dt) = 0 ;
+    bool beforeIteration(uint32 step, uint32 iterNum, real t, real dt) = 0 ;
 
 	virtual 
     bool iterate(uint32 iterNum, real t, real dt) = 0;
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
index 9937433c..0f530418 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
@@ -42,12 +42,13 @@ pFlow::boundaryExit::boundaryExit
 
 bool pFlow::boundaryExit::beforeIteration
 (
+	uint32 step,
 	uint32 iterNum, 
 	real t,
 	real dt
 )
 {
-
+	if(step!= 2 )return true;
 	if( !boundaryListUpdate(iterNum))return true;
 
 	// nothing have to be done
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.hpp b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.hpp
index f8aa61c5..b4763e26 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.hpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.hpp
@@ -63,7 +63,7 @@ public:
 		dictionary
 	);
 
-	bool beforeIteration(uint32 iterNum, real t, real dt) override;
+	bool beforeIteration(uint32 step, uint32 iterNum, real t, real dt) override;
 
 	bool iterate(uint32 iterNum, real t, real dt) override;
 
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryList.cpp b/src/phasicFlow/structuredData/boundaries/boundaryList.cpp
index 0e5ddfed..707e00ea 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryList.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryList.cpp
@@ -172,7 +172,17 @@ pFlow::boundaryList::beforeIteration(uint32 iter, real t, real dt, bool force)
 	
 	for (auto bdry : *this)
 	{
-		if (!bdry->beforeIteration(iter, t, dt))
+		if (!bdry->beforeIteration(1, iter, t, dt))
+		{
+			fatalErrorInFunction << "Error in beforeIteration in boundary "
+			                     << bdry->name() << endl;
+			return false;
+		}
+	}
+
+	for (auto bdry : *this)
+	{
+		if (!bdry->beforeIteration(2, iter, t, dt))
 		{
 			fatalErrorInFunction << "Error in beforeIteration in boundary "
 			                     << bdry->name() << endl;
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.cpp b/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.cpp
index 327330dd..7f228562 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.cpp
@@ -34,6 +34,7 @@ pFlow::boundaryNone::boundaryNone
 
 bool pFlow::boundaryNone::beforeIteration
 (
+	uint32 step,
 	uint32 iterNum, 
 	real t,
 	real dt
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.hpp b/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.hpp
index 8e103d39..68ddf33f 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.hpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.hpp
@@ -52,7 +52,7 @@ public:
 		dictionary
 	);
 
-	bool beforeIteration(uint32 iterNum, real t, real dt) final;
+	bool beforeIteration(uint32 step, uint32 iterNum, real t, real dt) final;
 
 	bool iterate(uint32 iterNum, real t, real dt) final;
 
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp b/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp
index cbdecf71..cf111eb5 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp
@@ -51,10 +51,12 @@ pFlow::realx3 pFlow::boundaryPeriodic::boundaryExtensionLength() const
 
 
 bool pFlow::boundaryPeriodic::beforeIteration(
+	uint32 step,
     uint32 iterNum,
     real t,
     real dt)
 {
+	if(step!=2)return true;
 	// nothing have to be done
 	if(empty())
 	{
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp b/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp
index 88983fa3..69b0413a 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp
@@ -64,7 +64,7 @@ public:
 
 	//const plane& boundaryPlane()const override;*/
 
-	bool beforeIteration(uint32 iterNum, real t, real dt) override;
+	bool beforeIteration(uint32 step, uint32 iterNum, real t, real dt) override;
 
 	bool iterate(uint32 iterNum, real t, real dt) override;
 
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.cpp b/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.cpp
index 74ee4d75..8de9b74f 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.cpp
@@ -46,6 +46,7 @@ pFlow::boundaryReflective::boundaryReflective
 }
 
 bool pFlow::boundaryReflective::beforeIteration(
+    uint32 step,
     uint32 iterNum,
     real t,
     real dt)
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.hpp b/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.hpp
index 43e1ce13..3f3bc64c 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.hpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.hpp
@@ -59,7 +59,7 @@ public:
 		dictionary
 	);
 
-	bool beforeIteration(uint32 iterNum, real t, real dt) override;
+	bool beforeIteration(uint32 step, uint32 iterNum, real t, real dt) override;
 
 	bool iterate(uint32 iterNum, real t, real dt) override;
 

From 32a2c20613b09aff311d77819d2d7477fe74fe01 Mon Sep 17 00:00:00 2001
From: HRN <hamid.r.norouzi@gmail.com>
Date: Fri, 24 May 2024 20:50:53 +0330
Subject: [PATCH 2/3] for write to file binary MPI

---
 src/phasicFlow/repository/IOobject/IOobject.cpp                 | 2 ++
 .../structuredData/boundaries/boundaryExit/boundaryExit.cpp     | 1 +
 2 files changed, 3 insertions(+)

diff --git a/src/phasicFlow/repository/IOobject/IOobject.cpp b/src/phasicFlow/repository/IOobject/IOobject.cpp
index 6fae2f0a..4442332f 100644
--- a/src/phasicFlow/repository/IOobject/IOobject.cpp
+++ b/src/phasicFlow/repository/IOobject/IOobject.cpp
@@ -126,6 +126,7 @@ bool pFlow::IOobject::writeObject() const
         {
             if(auto ptrOS = outStream(); ptrOS )
             {
+                pOutput<<"Should write field "<<name() <<" file "<<ptrOS->name()<<endl;
                 return writeObject(ptrOS());
             }
             else
@@ -140,6 +141,7 @@ bool pFlow::IOobject::writeObject() const
             
             if(auto ptrOS = dummyOutStream(); ptrOS )
             {
+                pOutput<<"Should write field "<< name()<< " file " <<ptrOS->name()<<endl;
                 return writeObject(ptrOS());
             }
             else
diff --git a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
index 0f530418..ce874e67 100644
--- a/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
+++ b/src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
@@ -49,6 +49,7 @@ bool pFlow::boundaryExit::beforeIteration
 )
 {
 	if(step!= 2 )return true;
+	
 	if( !boundaryListUpdate(iterNum))return true;
 
 	// nothing have to be done

From 6a66f1edfdc30222d98ae1a0ed642544e5bea74c Mon Sep 17 00:00:00 2001
From: HRN <hamid.r.norouzi@gmail.com>
Date: Fri, 24 May 2024 22:02:46 +0330
Subject: [PATCH 3/3] bug fix for binary file read when dealing with multiple
 Fields reading from a single file

---
 src/phasicFlow/containers/Field/Field.cpp     | 19 +++++++++++++++----
 src/phasicFlow/containers/Field/Field.hpp     |  4 ++--
 .../repository/IOobject/IOobject.cpp          |  2 --
 src/phasicFlow/triSurface/triSurface.cpp      |  4 ++--
 4 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/src/phasicFlow/containers/Field/Field.cpp b/src/phasicFlow/containers/Field/Field.cpp
index 335fbe49..10e14df8 100644
--- a/src/phasicFlow/containers/Field/Field.cpp
+++ b/src/phasicFlow/containers/Field/Field.cpp
@@ -21,13 +21,17 @@ Licence:
 template<class T, class MemorySpace>
 bool pFlow::Field<T, MemorySpace>::read
 (
-	iIstream& is
+	iIstream& is,
+	bool resume
 )
 {
 	
 	bool tokenFound = true;
 	
-    tokenFound = is.findToken(fieldKey_);
+	if(resume)
+		tokenFound = is.findTokenResume(fieldKey_);
+	else
+		tokenFound = is.findToken(fieldKey_);
 
 	if( !tokenFound )
 	{
@@ -53,14 +57,21 @@ template<class T, class MemorySpace>
 bool pFlow::Field<T, MemorySpace>::read
 (
 	iIstream& is,
-	const IOPattern& iop
+	const IOPattern& iop,
+	bool resume
 )
 {
 	
 	bool tokenFound = true;
 	
     if(iop.thisProcReadData())
-        tokenFound = is.findToken(fieldKey_);
+	{
+		if(resume)
+			tokenFound = is.findTokenResume(fieldKey_);
+		else
+			tokenFound = is.findToken(fieldKey_);
+	}
+	
 
 	if( !tokenFound )
 	{
diff --git a/src/phasicFlow/containers/Field/Field.hpp b/src/phasicFlow/containers/Field/Field.hpp
index 738811bc..b38d3017 100644
--- a/src/phasicFlow/containers/Field/Field.hpp
+++ b/src/phasicFlow/containers/Field/Field.hpp
@@ -197,12 +197,12 @@ public:
 		
 	//// - IO operations 
 		
-		bool read(iIstream& is);
+		bool read(iIstream& is, bool resume = false);
 		
 		bool write(iOstream& os)const;			
 
 
-		bool read(iIstream& is, const IOPattern& iop);
+		bool read(iIstream& is, const IOPattern& iop, bool resume = false);
 		
 
 		bool write(iOstream& os, const IOPattern& iop )const;			
diff --git a/src/phasicFlow/repository/IOobject/IOobject.cpp b/src/phasicFlow/repository/IOobject/IOobject.cpp
index 4442332f..6fae2f0a 100644
--- a/src/phasicFlow/repository/IOobject/IOobject.cpp
+++ b/src/phasicFlow/repository/IOobject/IOobject.cpp
@@ -126,7 +126,6 @@ bool pFlow::IOobject::writeObject() const
         {
             if(auto ptrOS = outStream(); ptrOS )
             {
-                pOutput<<"Should write field "<<name() <<" file "<<ptrOS->name()<<endl;
                 return writeObject(ptrOS());
             }
             else
@@ -141,7 +140,6 @@ bool pFlow::IOobject::writeObject() const
             
             if(auto ptrOS = dummyOutStream(); ptrOS )
             {
-                pOutput<<"Should write field "<< name()<< " file " <<ptrOS->name()<<endl;
                 return writeObject(ptrOS());
             }
             else
diff --git a/src/phasicFlow/triSurface/triSurface.cpp b/src/phasicFlow/triSurface/triSurface.cpp
index 4daf1387..ab18bb36 100644
--- a/src/phasicFlow/triSurface/triSurface.cpp
+++ b/src/phasicFlow/triSurface/triSurface.cpp
@@ -257,7 +257,7 @@ pFlow::triSurface::triSurface
 bool pFlow::triSurface::read(iIstream &is, const IOPattern &iop)
 {
 	points_.clear();
-	if(!points_.read(is, iop))
+	if(!points_.read(is, iop, true))
 	{
 		ioErrorInFile(is.name(), is.lineNumber())<<
 		" when reading field "<< points_.name()<<endl;
@@ -265,7 +265,7 @@ bool pFlow::triSurface::read(iIstream &is, const IOPattern &iop)
 	}
 
 	vertices_.clear();
-	if(!vertices_.read(is, iop))
+	if(!vertices_.read(is, iop, true))
 	{
 		ioErrorInFile(is.name(), is.lineNumber())<<
 		" when reading field "<< vertices_.name()<<endl;