merging in from main branch

core/XdmfArray.cpp

@@ -85,7 +85,8 @@ public:
                          mArray->mArray);
   }
 
-private: 
+private:
+ 
   XdmfArray * const mArray;
 };
 
@@ -390,10 +391,10 @@ public:
   void
   operator()(const shared_ptr<std::vector<T> > & array) const
   {
-    unsigned int size = mStartIndex + mNumValues;
-    if(mArrayStride > 1) {
-      size = mStartIndex + (mNumValues - 1) * mArrayStride + 1;
-    }
+    unsigned int size =
+      mStartIndex + (mNumValues) * mArrayStride + 1;
+
+
     if(array->size() < size) {
       array->resize(size);
       mDimensions.clear();
@@ -463,6 +464,34 @@ private:
   XdmfArray * const mArray;
 };
 
+class XdmfArray::IsInitialized : public boost::static_visitor<bool> {
+public:
+
+  IsInitialized()
+  {
+  }
+
+  bool
+  operator()(const boost::blank &) const
+  {
+    return false;
+  }
+
+  template<typename T>
+  bool
+  operator()(const shared_ptr<std::vector<T> > &) const
+  {
+    return true;
+  }
+
+  template<typename T>
+  bool
+  operator()(const T &) const
+  {
+    return true;
+  }
+};
+
 class XdmfArray::Reserve : public boost::static_visitor<void> {
 public:
 
@@ -517,7 +546,7 @@ public:
       for (int i = 0; i < mArray->mHeavyDataControllers.size(); i++) {
         total += mArray->mHeavyDataControllers[i]->getSize();
       }
-      return total;//modify this to compile all controllers
+      return total;
     }
     return 0;
   }
@@ -1452,7 +1481,7 @@ XdmfArray::insert(const unsigned int startIndex,
 }
 
 
-//TODO
+
 void
 XdmfArray::insert(const std::vector<unsigned int> startIndex,
                   const shared_ptr<const XdmfArray> values,
@@ -1591,13 +1620,8 @@ XdmfArray::insert(const std::vector<unsigned int> startIndex,
 bool
 XdmfArray::isInitialized() const
 {
-  try {
-    boost::get<boost::blank>(mArray);
-    return false;
-  }
-  catch(const boost::bad_get & exception) {
-  }
-  return true;
+  return boost::apply_visitor(IsInitialized(),
+                                mArray);
 }
 
 void

core/XdmfArray.tpp

@@ -263,10 +263,8 @@ public:
   void
   operator()(shared_ptr<std::vector<std::string> > & array) const
   {
-    unsigned int size = mStartIndex + mNumValues;
-    if(mArrayStride > 1) {
-      size = mStartIndex + mNumValues * mArrayStride - 1;
-    }
+    const unsigned int size = 
+      mStartIndex + (mNumValues - 1) * mArrayStride + 1;
     if(array->size() < size) {
       array->resize(size);
       mDimensions.clear();
@@ -282,10 +280,8 @@ public:
   void
   operator()(shared_ptr<std::vector<U> > & array) const
   {
-    unsigned int size = mStartIndex + mNumValues;
-    if(mArrayStride > 1) {
-      size = mStartIndex + mNumValues * mArrayStride - 1;
-    }
+    const unsigned int size = 
+      mStartIndex + (mNumValues - 1) * mArrayStride + 1;
     if(array->size() < size) {
       array->resize(size);
       mDimensions.clear();
@@ -348,10 +344,8 @@ public:
   void
   operator()(shared_ptr<std::vector<std::string> > & array) const
   {
-    unsigned int size = mStartIndex + mNumValues;
-    if(mArrayStride > 1) {
-      size = mStartIndex + mNumValues * mArrayStride - 1;
-    }
+    const unsigned int size = 
+      mStartIndex + (mNumValues - 1) * mArrayStride + 1;
     if(array->size() < size) {
       array->resize(size);
       mDimensions.clear();
@@ -366,10 +360,8 @@ public:
   void
   operator()(shared_ptr<std::vector<U> > & array) const
   {
-    unsigned int size = mStartIndex + mNumValues;
-    if(mArrayStride > 1) {
-      size = mStartIndex + mNumValues * mArrayStride - 1;
-    }
+    const unsigned int size = 
+      mStartIndex + (mNumValues - 1) * mArrayStride + 1;
     if(array->size() < size) {
       array->resize(size);
       mDimensions.clear();

core/XdmfWriter.cpp

@@ -236,6 +236,12 @@ XdmfWriter::setDocumentTitle(std::string title)
   mImpl->mDocumentTitle = title;
 }
 
+void 
+XdmfWriter::setHeavyDataWriter(shared_ptr<XdmfHeavyDataWriter> heavyDataWriter)
+{
+  mImpl->mHeavyDataWriter = heavyDataWriter;
+}
+
 void
 XdmfWriter::setLightDataLimit(const unsigned int numValues)
 {

core/tests/Cxx/TestXdmfArrayInsert.cpp

 #include "XdmfArray.hpp"
-#include "XdmfArrayType.hpp"
-
-#include <iostream>
 
 int main(int, char **)
 {
-  shared_ptr<XdmfArray> resultArray = XdmfArray::New();
+
+  // Insert from another array
+  shared_ptr<XdmfArray> array1 = XdmfArray::New();
   shared_ptr<XdmfArray> insertArray1 = XdmfArray::New();
   shared_ptr<XdmfArray> insertArray2 = XdmfArray::New();
   shared_ptr<XdmfArray> insertArray3 = XdmfArray::New();
   shared_ptr<XdmfArray> insertArray4 = XdmfArray::New();
 
-  for (int i = 0; i< 10; i++)
-  {
-   insertArray1->pushBack(1);
-  }
-
-  for (int i = 0; i< 10; i++)
-  {
-   insertArray2->pushBack(2);
-  }
-
-  for (int i = 0; i< 10; i++)
-  {
-   insertArray3->pushBack(3);
-  }
-
-  for (int i = 0; i< 10; i++)
-  {
-   insertArray4->pushBack(4);
-  }
-
-  resultArray->insert(0, insertArray1, 0, 10, 4, 1);
-  resultArray->insert(1, insertArray2, 0, 10, 4, 1);
-  resultArray->insert(2, insertArray3, 0, 10, 4, 1);
-  resultArray->insert(3, insertArray4, 0, 10, 4, 1);
-
-  printf("result array contains:\n%s\n", resultArray->getValuesString());
-  printf("result should be:\n%s\n", "1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4");
-
-  assert(resultArray->getValuesString().compare("1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4") == 0);
+  insertArray1->resize<int>(10, 1);
+  insertArray2->resize<int>(10, 2);
+  insertArray3->resize<int>(10, 3);
+  insertArray4->resize<int>(10, 4);
+
+  array1->insert(0, insertArray1, 0, 10, 4, 1);
+  array1->insert(1, insertArray2, 0, 10, 4, 1);
+  array1->insert(2, insertArray3, 0, 10, 4, 1);
+  array1->insert(3, insertArray4, 0, 10, 4, 1);
+
+  assert(array1->getValuesString().compare("1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 "
+                                           "2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 "
+                                           "3 4 1 2 3 4") == 0);
+
+  // Insert from vector
+  std::vector<int> insertArray5(10, 1);
+  std::vector<int> insertArray6(10, 2);
+  std::vector<int> insertArray7(10, 3);
+  std::vector<int> insertArray8(10, 4);
+
+  shared_ptr<XdmfArray> array2 = XdmfArray::New();
+
+  array2->insert(0, &(insertArray5[0]), 10, 4, 1);
+  array2->insert(1, &(insertArray6[0]), 10, 4, 1);
+  array2->insert(2, &(insertArray7[0]), 10, 4, 1);
+  array2->insert(3, &(insertArray8[0]), 10, 4, 1);
+
+  assert(array2->getValuesString().compare("1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 "
+                                           "2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 "
+                                           "3 4 1 2 3 4") == 0);
+
+  // Insert from vector string
+  std::vector<std::string> insertArray9(10, "1");
+  std::vector<std::string> insertArray10(10, "2");
+  std::vector<std::string> insertArray11(10, "3");
+  std::vector<std::string> insertArray12(10, "4");
+
+  shared_ptr<XdmfArray> array3 = XdmfArray::New();
+
+  array3->insert(0, &(insertArray9[0]), 10, 4, 1);
+  array3->insert(1, &(insertArray10[0]), 10, 4, 1);
+  array3->insert(2, &(insertArray11[0]), 10, 4, 1);
+  array3->insert(3, &(insertArray12[0]), 10, 4, 1);
+
+  assert(array3->getValuesString().compare("1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 "
+                                           "2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 "
+                                           "3 4 1 2 3 4") == 0);
 
   return 0;
 }

utils/XdmfFortran.cpp

@@ -40,6 +40,7 @@
 #include "XdmfGridCollectionType.hpp"
 #include "XdmfInformation.hpp"
 #include "XdmfReader.hpp"
+#include "XdmfSystemUtils.hpp"
 #include "XdmfTime.hpp"
 #include "XdmfTopology.hpp"
 #include "XdmfTopologyType.hpp"
@@ -723,12 +724,6 @@ XdmfFortran::setTopology(const int topologyType,
   return id;
 }
 
-
-
-
-
-
-
 int
 XdmfFortran::retrieveNumDomainGridCollections()
 {
@@ -1377,7 +1372,6 @@ XdmfFortran::replaceDomainGrid(int gridType, int index, char * name)
 
 			shared_ptr<XdmfCurvilinearGrid> grid = mDomain->getCurvilinearGrid(index);
 			grid->setName(name);
-
 			grid->setGeometry(mGeometry);
 			grid->setDimensions(mDimensions);
 
@@ -1385,7 +1379,6 @@ XdmfFortran::replaceDomainGrid(int gridType, int index, char * name)
 			{
 				grid->removeAttribute(0);
 			}
-
 			for(std::vector<shared_ptr<XdmfAttribute> >::const_iterator iter =
 				mAttributes.begin(); 
 				iter != mAttributes.end();

utils/XdmfFortran.hpp

@@ -44,6 +44,7 @@ class XdmfHeavyDataWriter;
 
 //Includes
 #include <stack>
+#include <map>
 #include <vector>
 #include "XdmfUtils.hpp"
 #include "XdmfSharedPtr.hpp"
@@ -532,6 +533,8 @@ public:
    * @param numValues number of connectivity values to copy.
    * @param arrayType type of connectivity values.
    * @param connectivityValues array of connectivity values.
+   * @param polyNodesPerElement for polyline and polyvertex types the
+   * number of nodes per element.
    *
    * @return int providing id to fortran if reusing.
    */
@@ -539,11 +542,15 @@ public:
                   const unsigned int numValues,
                   const int arrayType,
                   const void * const connectivityValues,
+<<<<<<< HEAD
                   const int numNodes);
 
 
 
 
+=======
+                  const int polyNodesPerElement = 0);
+>>>>>>> 6748b23947ebc47742c96d7e3a56242511c67d73
 
   /**
    * Returns the number of grid collections currently

utils/XdmfPartitioner.cpp

@@ -134,11 +134,28 @@ XdmfPartitioner::partition(const shared_ptr<XdmfGraph> graphToPartition,
     XdmfError::message(XdmfError::FATAL,
                        "Current graph's row pointer or column index is null "
                        "in XdmfPartitioner::partition");
+ 
+  graphToPartition->removeAttribute("Partition");
+
+  shared_ptr<XdmfAttribute> attribute = XdmfAttribute::New();
+  attribute->setName("Partition");
+  attribute->setCenter(XdmfAttributeCenter::Node());
+  attribute->setType(XdmfAttributeType::Scalar());
+  graphToPartition->insert(attribute);
+
+  idx_t numberVertices = graphToPartition->getNumberNodes();
+  
+  // Handle case where we partition onto 1 processor. Metis for some reason
+  // handles this incorrectly (indices are 1 instead of zero even though 
+  // correct numbering option is supplied to metis)
+  if(numberOfPartitions == 1) {
+    attribute->resize<idx_t>(numberVertices, 0);
+    return;
+  }
 
   shared_ptr<XdmfArray> rowPointer = graphToPartition->getRowPointer();
   shared_ptr<XdmfArray> columnIndex = graphToPartition->getColumnIndex();
 
-  idx_t numberVertices = graphToPartition->getNumberNodes();
   idx_t numberConstraints = 1;
 
   bool releaseRowPointer = false;
@@ -239,16 +256,9 @@ XdmfPartitioner::partition(const shared_ptr<XdmfGraph> graphToPartition,
   delete [] xadj;
   delete [] adjncy;
 
-  graphToPartition->removeAttribute("Partition");
-
-  shared_ptr<XdmfAttribute> attribute = XdmfAttribute::New();
-  attribute->setName("Partition");
-  attribute->setCenter(XdmfAttributeCenter::Node());
-  attribute->setType(XdmfAttributeType::Scalar());
   attribute->insert(0,
                     part,
                     numberVertices);
-  graphToPartition->insert(attribute);
 
   delete [] part;