fileHandler: Added flush method

This method waits until all the threads have completed IO operations and
then clears any cached information about the files on disk. This
replaces the deactivation of threading by means of zeroing the buffer
size when writing and reading of a file happen in sequence. It also
allows paraFoam to update the list of available times.

Patch contributed by Mattijs Janssens
Resolves bug report https://bugs.openfoam.org/view.php?id=2962

src/OpenFOAM/global/fileOperations/collatedFileOperation/collatedFileOperation.C

@@ -611,6 +611,18 @@ bool Foam::fileOperations::collatedFileOperation::writeObject
     }
 }
 
+void Foam::fileOperations::collatedFileOperation::flush() const
+{
+    if (debug)
+    {
+        Pout<< "collatedFileOperation::flush : clearing and waiting for thread"
+            << endl;
+    }
+    masterUncollatedFileOperation::flush();
+    // Wait for thread to finish (note: also removes thread)
+    writer_.waitAll();
+}
+
 
 Foam::word Foam::fileOperations::collatedFileOperation::processorsDir
 (

src/OpenFOAM/global/fileOperations/collatedFileOperation/collatedFileOperation.H

@@ -155,6 +155,9 @@ public:
 
         // Other
 
+            //- Forcibly wait until all output done. Flush any cached data
+            virtual void flush() const;
+
             //- Actual name of processors dir
             virtual word processorsDir(const IOobject&) const;
 

src/OpenFOAM/global/fileOperations/fileOperation/fileOperation.C

@@ -991,6 +991,17 @@ Foam::label Foam::fileOperation::nProcs
 }
 
 
+void Foam::fileOperation::flush() const
+{
+    if (debug)
+    {
+        Pout<< "fileOperation::flush : clearing processor directories cache"
+            << endl;
+    }
+    procsDirs_.clear();
+}
+
+
 Foam::fileName Foam::fileOperation::processorsCasePath
 (
     const IOobject& io,

src/OpenFOAM/global/fileOperations/fileOperation/fileOperation.H

@@ -514,6 +514,9 @@ public:
             virtual void setTime(const Time&) const
             {}
 
+            //- Forcibly wait until all output done. Flush any cached data
+            virtual void flush() const;
+
             //- Generate path (like io.path) from root+casename with any
             //  'processorXXX' replaced by procDir (usually 'processsors')
             fileName processorsCasePath

src/OpenFOAM/global/fileOperations/masterUncollatedFileOperation/masterUncollatedFileOperation.C

@@ -2561,6 +2561,13 @@ Foam::fileOperations::masterUncollatedFileOperation::NewOFstream
 }
 
 
+void Foam::fileOperations::masterUncollatedFileOperation::flush() const
+{
+    fileOperation::flush();
+    times_.clear();
+}
+
+
 Foam::label Foam::fileOperations::masterUncollatedFileOperation::addWatch
 (
     const fileName& fName

src/OpenFOAM/global/fileOperations/masterUncollatedFileOperation/masterUncollatedFileOperation.H

@@ -769,6 +769,9 @@ public:
             //- Callback for time change
             virtual void setTime(const Time&) const;
 
+            //- Forcibly wait until all output done. Flush any cached data
+            virtual void flush() const;
+
             //- Return cached times
             const HashPtrTable<instantList>& times() const
             {