Formatting changes and removing warnings

XdmfGraph.cpp

@@ -54,7 +54,7 @@ XdmfGraph::getItemTag() const
 unsigned int
 XdmfGraph::getNumberNodes() const
 {
-  //The number of nodes is equal to the number of rows or columns. Either will work.
+  // The number of nodes is equal to the number of rows or columns. Either will work.
   return this->getNumberRows();
 }
 

XdmfMap.cpp

@@ -219,19 +219,18 @@ XdmfMap::populateItem(const std::map<std::string, std::string> & itemProperties,
     }
     else {
 
-	//this needs to be changed to account for controllers being a vector now
       mRemoteTaskIdsControllers.clear();
-      for (unsigned int i = 0; i <  arrayVector[0]->getNumberHeavyDataControllers(); i++)
+      for (unsigned int i = 0; i <  arrayVector[0]->getNumberHeavyDataControllers(); ++i)
       {
         mRemoteTaskIdsControllers.push_back(arrayVector[0]->getHeavyDataController(i));
       }
       mLocalNodeIdsControllers.clear();
-      for (unsigned int i = 0; i <  arrayVector[1]->getNumberHeavyDataControllers(); i++)
+      for (unsigned int i = 0; i <  arrayVector[1]->getNumberHeavyDataControllers(); ++i)
       {
         mLocalNodeIdsControllers.push_back(arrayVector[1]->getHeavyDataController(i));
       }
       mRemoteLocalNodeIdsControllers.clear();
-      for (unsigned int i = 0; i <  arrayVector[2]->getNumberHeavyDataControllers(); i++)
+      for (unsigned int i = 0; i <  arrayVector[2]->getNumberHeavyDataControllers(); ++i)
       {
         mRemoteLocalNodeIdsControllers.push_back(arrayVector[2]->getHeavyDataController(i));
       }
@@ -247,17 +246,17 @@ XdmfMap::read()
      mRemoteLocalNodeIdsControllers.size() > 0) {
 
     unsigned int localNodeCount = 0;
-    for (unsigned int i = 0; i< mLocalNodeIdsControllers.size(); i++)
+    for (unsigned int i = 0; i< mLocalNodeIdsControllers.size(); ++i)
     {
       localNodeCount += mLocalNodeIdsControllers[i]->getSize();
     }
     unsigned int remoteTaskCount = 0;
-    for (unsigned int i = 0; i< mRemoteTaskIdsControllers.size(); i++)
+    for (unsigned int i = 0; i< mRemoteTaskIdsControllers.size(); ++i)
     {
       remoteTaskCount += mRemoteTaskIdsControllers[i]->getSize();
     }
     unsigned int remoteNodeCount = 0;
-    for (unsigned int i = 0; i< mRemoteLocalNodeIdsControllers.size(); i++)
+    for (unsigned int i = 0; i< mRemoteLocalNodeIdsControllers.size(); ++i)
     {
       remoteNodeCount += mRemoteLocalNodeIdsControllers[i]->getSize();
     }
@@ -280,21 +279,21 @@ XdmfMap::read()
     shared_ptr<XdmfArray> remoteLocalNodeIds = XdmfArray::New();
 
     mRemoteTaskIdsControllers[0]->read(remoteTaskIds.get());
-    for (unsigned int i = 1; i < mRemoteTaskIdsControllers.size(); i++)
+    for (unsigned int i = 1; i < mRemoteTaskIdsControllers.size(); ++i)
     {
       shared_ptr<XdmfArray> tempArray = XdmfArray::New();
       mRemoteTaskIdsControllers[i]->read(tempArray.get());
       remoteTaskIds->insert(remoteTaskIds->getSize(), tempArray, 0, tempArray->getSize());
     }
     mLocalNodeIdsControllers[0]->read(localNodeIds.get());
-    for (unsigned int i = 1; i < mLocalNodeIdsControllers.size(); i++)
+    for (unsigned int i = 1; i < mLocalNodeIdsControllers.size(); ++i)
     {
       shared_ptr<XdmfArray> tempArray = XdmfArray::New();
       mLocalNodeIdsControllers[i]->read(tempArray.get());
       localNodeIds->insert(localNodeIds->getSize(), tempArray, 0, tempArray->getSize());
     }
     mRemoteLocalNodeIdsControllers[0]->read(remoteLocalNodeIds.get());
-    for (unsigned int i = 1; i < mRemoteLocalNodeIdsControllers.size(); i++)
+    for (unsigned int i = 1; i < mRemoteLocalNodeIdsControllers.size(); ++i)
     {
       shared_ptr<XdmfArray> tempArray = XdmfArray::New();
       mRemoteLocalNodeIdsControllers[i]->read(tempArray.get());
@@ -324,17 +323,17 @@ XdmfMap::setHeavyDataControllers(std::vector<shared_ptr<XdmfHeavyDataController>
                                  std::vector<shared_ptr<XdmfHeavyDataController> > remoteLocalNodeIdsControllers)
 {
   unsigned int localNodeCount = 0;
-  for (unsigned int i = 0; i< localNodeIdsControllers.size(); i++)
+  for (unsigned int i = 0; i< localNodeIdsControllers.size(); ++i)
   {
     localNodeCount += localNodeIdsControllers[i]->getSize();
   }
   unsigned int remoteTaskCount = 0;
-  for (unsigned int i = 0; i< remoteTaskIdsControllers.size(); i++)
+  for (unsigned int i = 0; i< remoteTaskIdsControllers.size(); ++i)
   {
     remoteTaskCount += remoteTaskIdsControllers[i]->getSize();
   }
   unsigned int remoteNodeCount = 0;
-  for (unsigned int i = 0; i< remoteLocalNodeIdsControllers.size(); i++)
+  for (unsigned int i = 0; i< remoteLocalNodeIdsControllers.size(); ++i)
   {
     remoteNodeCount += remoteLocalNodeIdsControllers[i]->getSize();
   }
@@ -396,15 +395,15 @@ XdmfMap::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
     }
   }
 
-  for (unsigned int i = 0; i < mRemoteTaskIdsControllers.size(); i++)
+  for (unsigned int i = 0; i < mRemoteTaskIdsControllers.size(); ++i)
   {
     remoteTaskIds->insert(mRemoteTaskIdsControllers[i]);
   }
-  for (unsigned int i = 0; i < mLocalNodeIdsControllers.size(); i++)
+  for (unsigned int i = 0; i < mLocalNodeIdsControllers.size(); ++i)
   {
     localNodeIds->insert(mLocalNodeIdsControllers[i]);
   }
-  for (unsigned int i = 0; i < mRemoteLocalNodeIdsControllers.size(); i++)
+  for (unsigned int i = 0; i < mRemoteLocalNodeIdsControllers.size(); ++i)
   {
     remoteLocalNodeIds->insert(mRemoteLocalNodeIdsControllers[i]);
   }
@@ -417,15 +416,15 @@ XdmfMap::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
   mRemoteTaskIdsControllers.clear();
   mRemoteLocalNodeIdsControllers.clear();
 
-  for (unsigned int i = 0; i < remoteTaskIds->getNumberHeavyDataControllers(); i++)
+  for (unsigned int i = 0; i < remoteTaskIds->getNumberHeavyDataControllers(); ++i)
   {
     mRemoteTaskIdsControllers.push_back(remoteTaskIds->getHeavyDataController(i));
   }
-  for (unsigned int i = 0; i < localNodeIds->getNumberHeavyDataControllers(); i++)
+  for (unsigned int i = 0; i < localNodeIds->getNumberHeavyDataControllers(); ++i)
   {
     mLocalNodeIdsControllers.push_back(localNodeIds->getHeavyDataController(i));
   }
-  for (unsigned int i = 0; i < remoteLocalNodeIds->getNumberHeavyDataControllers(); i++)
+  for (unsigned int i = 0; i < remoteLocalNodeIds->getNumberHeavyDataControllers(); ++i)
   {
     mRemoteLocalNodeIdsControllers.push_back(remoteLocalNodeIds->getHeavyDataController(i));
   }

core/XdmfCore.i

@@ -950,6 +950,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %include XdmfItem.hpp
 %include XdmfItemProperty.hpp
 %include XdmfSparseMatrix.hpp
+%include XdmfSystemUtils.hpp
 %include XdmfVisitor.hpp
 %include XdmfHeavyDataController.hpp
 %include XdmfHeavyDataWriter.hpp

core/XdmfError.cpp

@@ -68,8 +68,8 @@ XdmfError::setBuffer(std::streambuf* buf)
  *** Private Static Functions ***
  ********************************/
 
-//automatically writes the message to the provided buffer
-//by default this is basically a print statement
+// automatically writes the message to the provided buffer
+// by default this is basically a print statement
 void
 XdmfError::WriteToStream(std::string msg)
 {

core/XdmfSparseMatrix.cpp

@@ -202,8 +202,8 @@ XdmfSparseMatrix::populateItem(const std::map<std::string, std::string> & itemPr
   }
 
   if(arrayVector.size() < 3) {
-    //The three required arrays are for the row pointer, column index, and the contained values.
-    //Without these arrays the object can't be properly built.
+    // The three required arrays are for the row pointer, column index, and the contained values.
+    // Without these arrays the object can't be properly built.
     try {
       XdmfError::message(XdmfError::FATAL,
                          "Expected 3 arrays attached to "

core/XdmfWriter.cpp

@@ -73,6 +73,7 @@ public:
   {
     mXPath.clear();
 
+    //this section writes to file
     std::ofstream fileStream;
     if(!mStream) {
       fileStream.open(mXMLFilePath.c_str());
@@ -96,7 +97,7 @@ public:
     
     xmlFreeDoc(mXMLDocument);
     xmlCleanupParser();
-    
+
     if(mHeavyDataWriter->getMode() == XdmfHeavyDataWriter::Default) {
       mHeavyDataWriter->closeFile();
     }
@@ -285,6 +286,7 @@ XdmfWriter::visit(XdmfArray & array,
   const bool isSubclassed = 
     array.getItemTag().compare(XdmfArray::ItemTag) != 0;
 
+
   if(isSubclassed) {
     try {
       this->visit(dynamic_cast<XdmfItem &>(array), visitor);
@@ -294,10 +296,10 @@ XdmfWriter::visit(XdmfArray & array,
     }
   }
 
+
   if(array.getSize() > 0 && !(mImpl->mLastXPathed && isSubclassed)) {
     std::vector<std::string> xmlTextValues;
 
-    //adjust for multifile write
     // Take care of writing to single heavy data file (Default behavior)
     if(!array.isInitialized() && array.getHeavyDataController(0) &&
        array.getHeavyDataController(0)->getFilePath().compare(mImpl->mHeavyDataWriter->getFilePath()) != 0 &&
@@ -307,36 +309,42 @@ XdmfWriter::visit(XdmfArray & array,
 
     if(array.getHeavyDataController(0) ||
        array.getSize() > mImpl->mLightDataLimit) {
-      //this case is for if the data is smaller than the limit
-      //create case for when data is over the limit
       // Write values to heavy data
-      try {
+
+      try {// this takes about half the time needed
         mImpl->mHeavyDataWriter->visit(array, mImpl->mHeavyDataWriter);
       }
       catch (XdmfError e) {
         throw e;
       }
+
       std::stringstream valuesStream;
-      for(unsigned int i = 0; i < array.getNumberHeavyDataControllers(); i++) {
+      for(unsigned int i = 0; i < array.getNumberHeavyDataControllers(); ++i) {
         std::string heavyDataPath =
           array.getHeavyDataController(i)->getFilePath();
         size_t index = heavyDataPath.find_last_of("/\\");
-        if(index != std::string::npos) {//if path is not a folder
-          const std::string heavyDataDir = heavyDataPath.substr(0, index + 1);//put the directory path into this variable
-          if(mImpl->mXMLFilePath.find(heavyDataDir) == 0) {//if the directory is in the XML File Path
+        if(index != std::string::npos) {
+          // if path is not a folder
+          // put the directory path into this variable
+          const std::string heavyDataDir = heavyDataPath.substr(0, index + 1);
+          // if the directory is in the XML File Path
+          if(mImpl->mXMLFilePath.find(heavyDataDir) == 0) {
             heavyDataPath =
               heavyDataPath.substr(heavyDataDir.size(),
-                                   heavyDataPath.size() - heavyDataDir.size());//pull the file off of the end and place it in the DataPath
-          }//otherwise the full path is required
+                                   heavyDataPath.size() - heavyDataDir.size());
+            // pull the file off of the end and place it in the DataPath
+          }
+          // otherwise the full path is required
         }
         std::stringstream dimensionStream;
-        for (unsigned int j = 0; j < array.getHeavyDataController(i)->getDimensions().size(); j++) {
+        for (unsigned int j = 0; j < array.getHeavyDataController(i)->getDimensions().size(); ++j) {
           dimensionStream << array.getHeavyDataController(i)->getDimensions()[j];
           if (j < array.getHeavyDataController(i)->getDimensions().size() - 1) {
             dimensionStream << " ";
           }
         }
-        valuesStream.str(std::string());//clear the stream
+        // clear the stream
+        valuesStream.str(std::string());
 	if (array.getNumberHeavyDataControllers() > 1) {
           valuesStream << heavyDataPath << ":"
                        << array.getHeavyDataController(i)->getDataSetPath()
@@ -366,7 +374,7 @@ XdmfWriter::visit(XdmfArray & array,
       array.swap(arrayToWrite);
       mImpl->mXMLCurrentNode = mImpl->mXMLCurrentNode->last;
       this->visit(dynamic_cast<XdmfItem &>(*arrayToWrite.get()), visitor);
-      for(unsigned int i = 0; i<xmlTextValues.size(); i++) {
+      for(unsigned int i = 0; i<xmlTextValues.size(); ++i) {
         xmlAddChild(mImpl->mXMLCurrentNode->last,
                     xmlNewText((xmlChar*)xmlTextValues[i].c_str()));
       }
@@ -375,7 +383,7 @@ XdmfWriter::visit(XdmfArray & array,
     }
     else {
       this->visit(dynamic_cast<XdmfItem &>(array), visitor);
-      for(unsigned int i = 0; i<xmlTextValues.size(); i++) {
+      for(unsigned int i = 0; i<xmlTextValues.size(); ++i) {
         xmlAddChild(mImpl->mXMLCurrentNode->last,
                     xmlNewText((xmlChar*)xmlTextValues[i].c_str()));
       }
@@ -415,7 +423,7 @@ XdmfWriter::visit(XdmfItem & item,
         XdmfInformation & xpathinfo = dynamic_cast<XdmfInformation &>(item);
         if (xpathinfo.getKey() == "XIncludes") {
           shared_ptr<XdmfInformation> outputinfo;
-          for (unsigned int i = 0; i < xpathinfo.getNumberInformations(); i++) {
+          for (unsigned int i = 0; i < xpathinfo.getNumberInformations(); ++i) {
             mImpl->mXPathCount++;
             outputinfo = xpathinfo.getInformation(i);
             mImpl->mXMLCurrentNode = xmlNewChild(mImpl->mXMLCurrentNode,
@@ -509,6 +517,7 @@ XdmfWriter::visit(XdmfItem & item,
         }
         else {
           // Not inserted before --- need to write all data and traverse.
+
           mImpl->mXMLCurrentNode = xmlNewChild(mImpl->mXMLCurrentNode,
                                                NULL,
                                                (xmlChar *)tag.c_str(),

core/tests/Cxx/TestXdmfError.cpp

@@ -50,7 +50,7 @@ int main(int, char **)
 	catch (XdmfError e)
 	{
 		//a print statement is redundant since the error message is sent to cout
-		//printf("The error message is:\n%s\n", e.what());
+		//std::cout << "The error message is:\n" << e.what() << std::endl;
 	}
 
 	return 0;

examples/Cxx/ExampleXdmfArray.cpp

@@ -189,7 +189,7 @@ int main(int, char **)
         dimensionVector.push_back(5);
         dimensionVector.push_back(4);
         writtenArray->initialize<int>(dimensionVector);
-        for (int i = 0; i < 20; i++)
+        for (int i = 0; i < 20; ++i)
         {
                 writtenArray->insert(i, i + 1);
         }
@@ -234,9 +234,9 @@ shared_ptr<XdmfArray> maximum(std::vector<shared_ptr<XdmfArray> > values)
 	else
 	{
 		double maxVal = values[0]->getValue<double>(0);
-		for (int i = 0; i < values.size(); i++)
+		for (int i = 0; i < values.size(); ++i)
 		{
-			for (int j = 0; j < values[i]->getSize(); j++)
+			for (int j = 0; j < values[i]->getSize(); ++j)
 			{
 				if (maxVal < values[i]->getValue<double>(j))
 				{

examples/Cxx/ExampleXdmfDSMSelfcontained.cpp

@@ -36,7 +36,7 @@ int main(int argc, char *argv[])
 
 	shared_ptr<XdmfArray> testArray = XdmfArray::New();
 
-	for (unsigned int i = 1; i <= 4; i++)
+	for (unsigned int i = 1; i <= 4; ++i)
 	{
 		testArray->pushBack(i*id);
 	}
@@ -95,7 +95,7 @@ int main(int argc, char *argv[])
 
 	testArray->insert(writeController);
 
-	for (unsigned int i = 0; i<size; i++)
+	for (unsigned int i = 0; i<size; ++i)
 	{
 		MPI_Barrier(comm);
 		if (i == id)
@@ -106,26 +106,26 @@ int main(int argc, char *argv[])
 			std::cout << "filepath = " << testArray->getHeavyDataController(0)->getFilePath() << std::endl;
 			outputVector = testArray->getHeavyDataController(0)->getDataspaceDimensions();
 			std::cout << "Data space dimensions" << std::endl;
-			for (int j=0; j<outputVector.size(); j++)
+			for (int j=0; j<outputVector.size(); ++j)
 			{
 				std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
 			}
 			std::cout << "Controller Dimensions" << std::endl;
 			outputVector = testArray->getHeavyDataController(0)->getDimensions();
-			for (int j=0; j<outputVector.size(); j++)
+			for (int j=0; j<outputVector.size(); ++j)
 			{
 				std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
 			}
 			std::cout << "Controller size" << testArray->getHeavyDataController(0)->getSize() << std::endl;
 			std::cout << "Controller starts" << std::endl;
 			outputVector = testArray->getHeavyDataController(0)->getStart();
-			for (int j=0; j<outputVector.size(); j++)
+			for (int j=0; j<outputVector.size(); ++j)
 			{
 				std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
 			}
 			std::cout << "Controller strides" << std::endl;
 			outputVector = testArray->getHeavyDataController(0)->getStride();
-			for (int j=0; j<outputVector.size(); j++)
+			for (int j=0; j<outputVector.size(); ++j)
 			{
 				std::cout << "[" << j << "] =" << outputVector[j] << "\n" << std::endl;
 			}
@@ -169,7 +169,7 @@ int main(int argc, char *argv[])
 	std::cout << "done testing read" << std::endl;
 	
 
-        for (unsigned int i = 0; i<size; i++)
+        for (unsigned int i = 0; i<size; ++i)
         {
                 MPI_Barrier(comm);
                 if (i == id)
@@ -180,26 +180,26 @@ int main(int argc, char *argv[])
                         std::cout << "filepath = " << readArray->getHeavyDataController(0)->getFilePath() << std::endl;
                         outputVector = readArray->getHeavyDataController(0)->getDataspaceDimensions();
                         std::cout << "Data space dimensions" << std::endl;
-                        for (int j=0; j<outputVector.size(); j++)
+                        for (int j=0; j<outputVector.size(); ++j)
                         {
                                 std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
                         }
                         std::cout << "Controller Dimensions" << std::endl;
                         outputVector = readArray->getHeavyDataController(0)->getDimensions();
-                        for (int j=0; j<outputVector.size(); j++)
+                        for (int j=0; j<outputVector.size(); ++j)
                         {
                                 std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
                         }
                         std::cout << "Controller size" << readArray->getHeavyDataController(0)->getSize() << std::endl;
                         std::cout << "Controller starts" << std::endl;
                         outputVector = readArray->getHeavyDataController(0)->getStart();
-                        for (int j=0; j<outputVector.size(); j++)
+                        for (int j=0; j<outputVector.size(); ++j)
                         {
                                 std::cout << "[" << j << "] =" << outputVector[j] << std::endl;
                         }
                         std::cout << "Controller strides" << std::endl;
                         outputVector = readArray->getHeavyDataController(0)->getStride();
-                        for (int j=0; j<outputVector.size(); j++)
+                        for (int j=0; j<outputVector.size(); ++j)
                         {
                                 std::cout << "[" << j << "] =" << outputVector[j] << "\n" << std::endl;
                         }

examples/Cxx/ExampleXdmfWrite.cpp

@@ -190,7 +190,7 @@ int main(int, char **)
         /*
         the version of XdmfMap::New() used here returns a number of maps equal to the number of attributes it was provided with.
         */
-        for (int i = 0; i<mapcollection.size(); i++)
+        for (int i = 0; i<mapcollection.size(); ++i)
 	{
 		gridHolder->insert(mapcollection[i]);
 	}
@@ -226,14 +226,14 @@ int main(int, char **)
         primaryDomain->accept(exampleWriter);
 
         exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Append);
-	for (int i = 0; i <= 408; i++)
+	for (int i = 0; i <= 408; ++i)
 	{//overflow occurs a little after the end of this loop
 		primaryDomain->accept(exampleHeavyWriter);
 	}
 	exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Default);
 	primaryDomain->accept(exampleHeavyWriter);
 	exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Append);
-	for (int i = 0; i<5; i++)
+	for (int i = 0; i<5; ++i)
 	{//this loop covers the overflow of the fileSizeLimit
 		primaryDomain->accept(exampleHeavyWriter);
 	}

tests/Cxx/ExampleXdmfWrite.cpp

@@ -222,28 +222,23 @@ int main(int, char **)
 	exampleHeavyWriter->setFileSizeLimit(1);
 
 	primaryDomain->accept(exampleHeavyWriter);
-	printf("default mode\n");
 	exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Overwrite);//do this so that the data isn't in the hdf5 file twice.
-	printf("overwrite mode\n");
 	exampleHeavyWriter->setFileIndex(0);
         exampleWriter->setLightDataLimit(1);
 	primaryDomain->accept(exampleWriter);
 
         exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Append);
-	printf("append mode\n");
 	for (int i = 0; i <= 797; i++)
 	{//overflow occurs at around 509
 		primaryDomain->accept(exampleHeavyWriter);
 	}
-	/*exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Default);
-	printf("default mode\n");
+	exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Default);
 	primaryDomain->accept(exampleHeavyWriter);
-	printf("append mode\n");
 	exampleHeavyWriter->setMode(XdmfHeavyDataWriter::Append);
 	for (int i = 0; i<500; i++)
 	{
 		primaryDomain->accept(exampleHeavyWriter);
-	}*/
+	}
 	primaryDomain->accept(exampleWriter);
   return 0;
 }

tests/Cxx/HugeReadArray.cpp

@@ -9,6 +9,6 @@ int main(int, char **)
 	shared_ptr<XdmfReader> testReader = XdmfReader::New();
 	shared_ptr<XdmfArray> readArray = shared_dynamic_cast<XdmfArray>(testReader->read("arraydata.xmf"));
 	readArray->read();
-	printf("Array ocntains %s\n", readArray->getValuesString());
+	std::cout << "Array ocntains " << readArray->getValuesString() << std::endl;
 	return 0;
 }

tests/Cxx/ReadArray.cpp

@@ -17,16 +17,16 @@ int main(int, char **)
 	shared_ptr<XdmfReader> testReader = XdmfReader::New();
 	/*
 	shared_ptr<XdmfArray> readArray = shared_dynamic_cast<XdmfArray>(testReader->read("array.xmf"));
-	printf("Array ocntains %s\n", readArray->getValuesString());
+	std::cout << "Array ocntains " << readArray->getValuesString() << std::endl;
 	*/
 	shared_ptr<XdmfDomain> readDomain = shared_dynamic_cast<XdmfDomain>(testReader->read("array.xmf"));
-	printf("pulling out unstructured grid\n");
+	std::cout << "pulling out unstructured grid" << std::endl;
 	shared_ptr<XdmfRectilinearGrid> readGrid = readDomain->getRectilinearGrid(0);
-	//printf("pulling out geometry\n");
+	//std::cout << "pulling out geometry" << std::endl;
 	//shared_ptr<XdmfGeometry> readGeometry = readGrid->getGeometry();
-	printf("pulling out dimensions\n");
+	std::cout << "pulling out dimensions" << std::endl;
 	std::vector<shared_ptr<XdmfArray> > readDimensions = readGrid->getCoordinates();
-	printf("Geometry contains %s\n", readDimensions[0]->getValuesString());
+	std::cout << "Geometry contains " << readDimensions[0]->getValuesString() << std::endl;
 	shared_ptr<XdmfWriter> testWriter = XdmfWriter::New("arrayoutput.xmf");
 	readGrid->accept(testWriter);
 	//readArray->accept(testWriter);

tests/Cxx/TestXdmfGraph.cpp

@@ -35,11 +35,9 @@ int main(int, char **)
 
   shared_ptr<XdmfWriter> writer = XdmfWriter::New("TestXdmfGraph.xmf");
   graph->accept(writer);
-	printf("after writing\n");
   shared_ptr<XdmfReader> reader = XdmfReader::New();
   shared_ptr<XdmfGraph> readGraph = 
     shared_dynamic_cast<XdmfGraph>(reader->read("TestXdmfGraph.xmf"));
-	printf("after reading\n");
   assert(readGraph);
   assert(readGraph->getNumberNodes() == graph->getNumberNodes());
   assert(readGraph->getNumberAttributes() == graph->getNumberAttributes());

tests/Cxx/XdmfPostFixCalc.cpp

@@ -211,7 +211,7 @@ double parse(std::string expression, std::map<std::string, double> variables)
 					//if it is grab the string between paranthesis
 					i = i + 2;
 					valueStart = i;
-					unsigned int numOpenParenthesis = 0;
+					int numOpenParenthesis = 0;
 					while ((expression[i] != ')' || numOpenParenthesis) && i < expression.size())
 					{
 						if (expression[i] == '(')
@@ -483,7 +483,7 @@ shared_ptr<XdmfArray> parse(std::string expression, std::map<std::string, shared
 					//if it is grab the string between paranthesis
 					i = i + 2;
 					valueStart = i;
-					unsigned int numOpenParenthesis = 0;
+					int numOpenParenthesis = 0;
 					while ((expression[i] != ')' || numOpenParenthesis) && i < expression.size())
 					{
 						if (expression[i] == '(')
@@ -996,11 +996,11 @@ shared_ptr<XdmfArray> calculation(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArr
 			if (i<arrayRatio1)
 			{
 				int amountWritten = val1->getSize()/arrayRatio1;
-				if ((unsigned int)((amountWritten * arrayRatio1) + i) < val1->getSize())
+				if (((amountWritten * arrayRatio1) + i) < (int)val1->getSize())
 				{
 					amountWritten++;
 				}
-				if (amountWritten > floor(val2->getSize()/arrayRatio2))
+				if (amountWritten > (int)floor(val2->getSize()/arrayRatio2))
 				{
 					arrayExcess1 += amountWritten - (int)floor(val2->getSize()/arrayRatio2);
 					amountWritten = (int)floor(val2->getSize()/arrayRatio2);
@@ -1010,11 +1010,11 @@ shared_ptr<XdmfArray> calculation(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArr
 			else //second array takes the rest
 			{
 				int amountWritten = val2->getSize()/arrayRatio2;
-				if ((unsigned int)((amountWritten * arrayRatio2) + i) < val2->getSize())
+				if (((amountWritten * arrayRatio2) + i) < (int)val2->getSize())
 				{
 					amountWritten++;
 				}
-				if (amountWritten > floor(val1->getSize()/arrayRatio1))
+				if (amountWritten > (int)floor(val1->getSize()/arrayRatio1))
 				{
 					arrayExcess2 += amountWritten - (int)floor(val1->getSize()/arrayRatio1);
 					amountWritten = (int)floor(val1->getSize()/arrayRatio1);

tests/Python/WriteTime.py

@@ -35,7 +35,6 @@ if __name__ == "__main__":
 	startclock = time.clock()
 
 	for i in range(numTimestamps):
-		#print "timestamp " + str(i)
 		timestampGrid = XdmfGridCollection.New()
 		timestampTime = XdmfTime.New(i)
 		timestampGrid.setTime(timestampTime)
@@ -68,11 +67,15 @@ if __name__ == "__main__":
 			#sectionGrid.accept(exampleHeavyWriter)
 			#exampleHeavyWriter.closeFile()
 		primaryCollection.insert(timestampGrid)
+		writeclock = time.clock()
 		exampleHeavyWriter.openFile()
-		timestampGrid.accept(exampleHeavyWriter)
 		#primaryDomain.accept(exampleHeavyWriter)
-		#primaryDomain.accept(exampleWriter)
+		if i % 10 == 9:
+			primaryDomain.accept(exampleWriter)
+		else:
+			timestampGrid.accept(exampleHeavyWriter)
 		exampleHeavyWriter.closeFile()
+		print "iteration " + str(i) + " Time = " + str(time.clock() - writeclock)
 
 
 	exampleHeavyWriter.openFile()
@@ -81,3 +84,8 @@ if __name__ == "__main__":
 	exampleHeavyWriter.closeFile()
 
 	print (time.clock() - startclock)
+
+	print XdmfSystemUtils.getRealPath("timestamptest.xmf")
+
+	#os.remove("/usr/var/tmp/ajburns/timing.xmf")
+	#os.remove("/usr/var/tmp/ajburns/timing.h5")

utils/XdmfFortran.hpp

@@ -173,6 +173,7 @@ class XdmfHeavyDataWriter;
 #define XdmfInitHDF5 xdmfinithdf5_
 
 #define XdmfSetTopologyPolyline xdmfsettopologypolyline_
+#define XdmfSetTopologyPolygon xdmfsettopologypolygon_
 
 
 #define XdmfRetrieveNumDomainGridCollections xdmfretrievenumdomaingridcollections_
@@ -541,10 +542,6 @@ public:
                   const void * const connectivityValues,
                   const int numNodes);
 
-
-
-
-
   /**
    * Returns the number of grid collections currently
    * contained in the domain
@@ -2285,6 +2282,21 @@ public:
                           const int arrayType,
                           const void * const connectivityValues);
 
+  /**
+   * Set the topology (connectivity data) for a polygon that will be
+   * added to the next grid.
+   *
+   * @param nodesPerElement number of nodes in the polygon.
+   * @param numValues number of connectivity values to copy.
+   * @param arrayType type of connectivity values.
+   * @param connectivityValues array of connectivity values.
+   *
+   * @return int providing id to fortran if reusing.
+   */
+  int setTopologyPolygon(const unsigned int nodesPerElement,
+                         const unsigned int numValues,
+                         const int arrayType,
+                         const void * const connectivityValues);
 
 private: