Merge branch 'master' into 'master'

merge of xdmf3 from running xdmf3 update script plus commit to resolve confict in xdmf3/vtkxdmf3/core/CMakeLists.txt file

merge of xdmf3 from running xdmf3 update script plus commit to resolve confict in xdmf3/vtkxdmf3/core/CMakeLists.txt file

See merge request !1988

ThirdParty/xdmf3/vtkxdmf3/CMake/VersionSuite/SetUpVersion.cmake

@@ -62,7 +62,7 @@ MACRO(VersionWrite vProjectName export_name)
     FOREACH(il ${include_list})
         SET(includes "${includes}\n\#include \"${il}\"")
     ENDFOREACH()
-    FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${vProjectName}Version.hpp
+    FILE(WRITE ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${vProjectName}Version.hpp
 "/* Current Version of ${vProjectName}
  * Major is: ${vMajor}
  * Minor is: ${vMinor}
@@ -73,7 +73,7 @@ ${includes}
 extern ${export_name} ProjectVersion ${vProjectName}Version;\n"
     )
 
-        FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${vProjectName}Version.cpp
+        FILE(WRITE ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${vProjectName}Version.cpp
 "/* Current Version of ${vProjectName}
  * Make sure to include this file in your built sources
  */

ThirdParty/xdmf3/vtkxdmf3/CMakeLists.txt

@@ -59,10 +59,13 @@ include(XdmfFunctions)
 get_filename_component(CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}" ABSOLUTE)
 
 # RPath
-#set(CMAKE_SKIP_BUILD_RPATH  FALSE)
-#set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-#set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib)
-#set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+option(XDMF_SET_RPATH ON)
+if (XDMF_SET_RPATH)
+  set(CMAKE_SKIP_BUILD_RPATH  FALSE)
+  set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib)
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+endif ()
 
 # Should we build with documentation
 option(XDMF_BUILD_DOCUMENTATION OFF)
@@ -365,16 +368,16 @@ if(NOT XDMF_BUILD_CORE_ONLY)
       set_target_properties(${XDMF_LIBNAME} PROPERTIES
         PREFIX ../
         IMPORT_PREFIX ../
-        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
-        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
-        ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/
+        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/
+        ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/)
       if(XDMF_STATIC_AND_SHARED AND BUILD_SHARED_LIBS)
         set_target_properties(Xdmf_Static PROPERTIES
           PREFIX ../
           IMPORT_PREFIX ../
-          RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
-          LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
-          ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+          RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/
+          LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/
+          ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/)
       endif ()
     endif()
   endif()

ThirdParty/xdmf3/vtkxdmf3/Xdmf.dtd

+<?xml version="1.0" encoding="UTF-8"?>
+<!--Root element of dataset-->
+<!ELEMENT Xdmf (Information*, Domain+)>
+<!ATTLIST Xdmf
+    Version CDATA #IMPLIED
+>
+<!--Contains domain data information-->
+<!ELEMENT Domain (Information*, Grid+)>
+<!ATTLIST Domain
+	Name CDATA #IMPLIED
+>
+<!--Contains a collection of homogeneous elements-->
+<!ELEMENT Grid (Information*, Time*, Grid*, Topology*, Geometry*, Attribute*)>
+<!ATTLIST Grid
+	Name CDATA #IMPLIED
+	GridType (Uniform | Collection) "Uniform"
+        CollectionType   (Spatial | Temporal) "Spatial"
+>
+<!--Contains a graph of points-->
+<!ELEMENT Graph (Information*, Time*, Attribute*)>
+<!ATTLIST Graph
+        Name CDATA #IMPLIED
+        NumberColumns CDATA #REQUIRED
+        NumberRows CDATA #REQUIRED
+>
+<!-- Described Temporal Relationship -->
+<!ELEMENT Time (Information*)>
+<!ATTLIST Time
+    Value CDATA #IMPLIED
+>
+<!--Describes the general organization of the data-->
+<!ELEMENT Topology (Information*, DataItem*)>
+<!ATTLIST Topology
+        TopologyType (NoTopologyType | Polyvertex | Polyline | Polygon | Triangle | Quadrilateral | Tetrahedron | Wedge | Hexahedron | Edge_3 | Triangle_6 | Quadrilateral_8 | Quadrilateral_9 | Tetrahedron_10 | Pyramid_13 | Wedge_15 | Wedge_18 | Hexahedron_20 | Hexahedron_24 | Hexahedron_27 | Hexahedron_64 | Hexahedron_125 | Hexahedron_216 | Hexahedron_343 | Hexahedron_512 | Hexahedron_729 | Hexahedron_1000 | Hexahedron_1331 | Hexahedron_Spectral_64 | Hexahedron_Spectral_125 | Hexahedron_Spectral_216 | Hexahedron_Spectral_343 | Hexahedron_Spectral_512 | Hexahedron_Spectral_729 | Hexahedron_Spectral_1000 | Hexahedron_Spectral_1331 | Mixed | 2DSMesh | 2DRectMesh | 2DCoRectMesh | 3DSMesh | 3DRectMesh | 3DCoRectMesh) #REQUIRED
+	Dimensions CDATA #IMPLIED
+	Order CDATA #IMPLIED
+	NodesPerElement CDATA #IMPLIED
+>
+<!--Describes the XYZ values of the mesh-->
+<!ELEMENT Geometry (Information*, DataItem+)>
+<!ATTLIST Geometry
+	Name CDATA #IMPLIED
+	GeometryType (XYZ | XY | X_Y_Z | VXVYVZ | ORIGIN_DXDYDZ) "XYZ"
+>
+<!--Lowest level element, describes the data that is present in the XDMF dataset-->
+<!ELEMENT DataItem (#PCDATA | DataItem)*>
+<!ATTLIST DataItem
+	Name CDATA #IMPLIED
+        ItemType (Uniform | HyperSlab | Function) "Uniform"
+	Dimensions CDATA #REQUIRED
+	NumberType (Char | UChar | Float | Int | UInt) "Float"
+	Precision (1 | 4 | 8) "4"
+	Reference CDATA #IMPLIED
+        Endian (Big | Little | Native) "Native"
+	Format (XML | HDF | Binary | TIFF) "XML"
+>
+<!--Describes the values on the mesh-->
+<!ELEMENT Attribute (Information*, DataItem)>
+<!ATTLIST Attribute
+	Name CDATA #IMPLIED
+	Center (Node | Cell | Grid | Face | Edge) "Node"
+	AttributeType (Scalar | Vector | Tensor | Tensor6 | Matrix) "Scalar"
+>
+<!--Describes subsections of a grid-->
+<!ELEMENT Set (Information*, DataItem)>
+<!ATTLIST Set
+        Name CDATA #IMPLIED
+        Type (NoSetType | Node | Cell | Face | Edge) "Node"
+>
+<!--Describes a node maping-->
+<!ELEMENT Map (Information*, DataItem*)>
+<!ATTLIST Map
+        Name CDATA #IMPLIED
+>
+<!-- Application Dependent -->
+<!ELEMENT Information (#PCDATA | Information | EMPTY)*>
+<!ATTLIST Information 
+	Name CDATA #IMPLIED
+	Value CDATA #IMPLIED
+>
+
+<!--The Definitions of these three items are extremely loose-->
+<!ELEMENT Aggregate ANY>
+<!ELEMENT Subset ANY>
+<!ELEMENT Function ANY>

ThirdParty/xdmf3/vtkxdmf3/XdmfTopology.hpp

@@ -192,7 +192,7 @@ protected:
 
 private:
 
-  XdmfTopology(const XdmfTopology &);
+  XdmfTopology(const XdmfTopology &);  // Not implemented.
   void operator=(const XdmfTopology &);  // Not implemented.
 
   shared_ptr<const XdmfTopologyType> mType;

ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt

@@ -9,7 +9,7 @@ include(SetUpVersion)
 include(TestBigEndian)
 
 if(VERSION_CONTROL_AUTOUPDATE OR
-    NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/XdmfVersion.hpp)
+    NOT EXISTS ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/XdmfVersion.hpp)
   VersionCreate("Xdmf" "3" "3" "0" "XDMFCORE_EXPORT" "XdmfCore.hpp")
 endif()
 
@@ -54,11 +54,13 @@ endif ()
 mark_as_advanced(CLEAR HDF5_C_INCLUDE_DIR)
 mark_as_advanced(CLEAR HDF5_hdf5_LIBRARY_DEBUG)
 mark_as_advanced(CLEAR HDF5_hdf5_LIBRARY_RELEASE)
-set(HDF5_LIBRARIES ${vtkhdf5_LIBRARIES})
-set(HDF5_hdf5_LIBRARY_RELEASE ${vtkhdf5_LIBRARIES})
-set(HDF5_INCLUDE_DIRS ${vtkhdf5_INCLUDE_DIRS})
-set(HDF5_C_INCLUDE_DIR ${vtkhdf5_INCLUDE_DIRS})
-set(HDF5_FOUND TRUE)
+if (NOT ("${vtkhdf5_LIBRARIES}" STREQUAL ""))
+  set(HDF5_LIBRARIES ${vtkhdf5_LIBRARIES})
+  set(HDF5_hdf5_LIBRARY_RELEASE ${vtkhdf5_LIBRARIES})
+  set(HDF5_INCLUDE_DIRS ${vtkhdf5_INCLUDE_DIRS})
+  set(HDF5_C_INCLUDE_DIR ${vtkhdf5_INCLUDE_DIRS})
+  set(HDF5_FOUND TRUE)
+endif ()
 find_package(HDF5 REQUIRED)
 if(HDF5_FOUND)
   mark_as_advanced(FORCE HDF5_C_INCLUDE_DIR)
@@ -149,7 +151,7 @@ set(XdmfCoreSources
   XdmfSparseMatrix
   XdmfSubset
   XdmfSystemUtils
-  ${CMAKE_CURRENT_BINARY_DIR}/XdmfVersion
+  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/XdmfVersion
   XdmfVisitor
   XdmfWriter)
 
@@ -198,16 +200,16 @@ if(WIN32)
     set_target_properties(XdmfCore PROPERTIES
       PREFIX ../
       IMPORT_PREFIX ../
-      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/
+      LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/
+      ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/)
     if (XDMF_STATIC_AND_SHARED AND BUILD_SHARED_LIBS)
       set_target_properties(XdmfCore_Static PROPERTIES
         PREFIX ../
         IMPORT_PREFIX ../
-        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/
+        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/
+        ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/${CMAKE_CFG_INTDIR}/)
     endif ()
   endif()
 endif()

ThirdParty/xdmf3/vtkxdmf3/core/XdmfArray.hpp

@@ -26,9 +26,9 @@
 
 // C Compatible Includes
 #include "XdmfCore.hpp"
+#include "XdmfItem.hpp"
 #include "XdmfArrayReference.hpp"
 #include "XdmfHeavyDataController.hpp"
-#include "XdmfItem.hpp"
 
 #ifdef __cplusplus
 

ThirdParty/xdmf3/vtkxdmf3/core/XdmfArray.tpp

@@ -662,9 +662,7 @@ XdmfArray::initialize(const std::vector<unsigned int> & dimensions)
 {
   mDimensions = dimensions;
   const unsigned int size = static_cast<unsigned int>(
-    std::accumulate(dimensions.begin(),
-                                            dimensions.end(),
-                                            1,
+    std::accumulate(dimensions.begin(), dimensions.end(), 1,
                     std::multiplies<unsigned int>()));
   return this->initialize<T>(size);
 }
@@ -707,10 +705,11 @@ template <typename T>
 void
 XdmfArray::pushBack(const T & value)
 {
+  this->setIsChanged(true);
   return boost::apply_visitor(PushBack<T>(value,
                                           this),
                               mArray);
-  this->setIsChanged(true);
+
 }
 
 template<typename T>
@@ -718,11 +717,12 @@ void
 XdmfArray::resize(const unsigned int numValues,
                   const T & value)
 {
+  this->setIsChanged(true);
   return boost::apply_visitor(Resize<T>(this,
                                         numValues,
                                         value),
                               mArray);
-  this->setIsChanged(true);
+
 }
 
 template<typename T>
@@ -730,11 +730,8 @@ void
 XdmfArray::resize(const std::vector<unsigned int> & dimensions,
                   const T & value)
 {
-  const unsigned int size = static_cast<unsigned int>(
-    std::accumulate(dimensions.begin(),
-                                            dimensions.end(),
-                                            1,
-                    std::multiplies<unsigned int>()));
+  const unsigned int size = static_cast<unsigned int>(std::accumulate(dimensions.begin(), dimensions.end(), 1,
+                                                                      std::multiplies<unsigned int>()));
   this->resize(size, value);
   mDimensions = dimensions;
   this->setIsChanged(true);

ThirdParty/xdmf3/vtkxdmf3/core/XdmfCoreReader.cpp

@@ -21,9 +21,6 @@
 /*                                                                           */
 /*****************************************************************************/
 
-#include <libxml/uri.h>
-#include <libxml/xpointer.h>
-#include <libxml/xmlreader.h>
 #include <boost/algorithm/string/trim.hpp>
 #include <boost/tokenizer.hpp>
 #include <cstring>
@@ -215,7 +212,6 @@ public:
         if (mItemFactory->isArrayTag((char *)currNode->name)) {
           while(childNode != NULL) {
             if(childNode->type == XML_TEXT_NODE && childNode->content) {
-#if 1 //ARL's side
               const char * content = (char*)childNode->content;
 
               // Determine if content is whitespace
@@ -237,16 +233,6 @@ public:
                 itemProperties.insert(std::make_pair("XMLDir", mXMLDir));
                 break;
               }
-#else //VTK's side, breaks XDMF's tests, revisit if problematic in VTK
-              std::string content((char *)childNode->content);
-              boost::algorithm::trim(content);
-
-              if(content.size() != 0) {
-                itemProperties.insert(std::make_pair("Content", content));
-                itemProperties.insert(std::make_pair("XMLDir", mXMLDir));
-                break;
-              }
-#endif
             }
             childNode = childNode->next;
           }

ThirdParty/xdmf3/vtkxdmf3/core/XdmfError.hpp

@@ -323,4 +323,4 @@ catch (XdmfError & e) {                  \
 }
 #endif
 
-#endif
+#endif /* XDMFERROR_HPP_ */

ThirdParty/xdmf3/vtkxdmf3/core/XdmfHDF5Writer.cpp

@@ -123,6 +123,7 @@ XdmfHDF5Writer::New(const std::string & filePath,
   return p;
 }
 
+//Set mUseDeflate(true), and mDeflateFactor(6) for default compression
 XdmfHDF5Writer::XdmfHDF5Writer(const std::string & filePath) :
   XdmfHeavyDataWriter(filePath, 1, 800),
   mImpl(new XdmfHDF5WriterImpl()),
@@ -131,6 +132,7 @@ XdmfHDF5Writer::XdmfHDF5Writer(const std::string & filePath) :
 {
 }
 
+//Set mUseDeflate(true), and mDeflateFactor(6) for default compression
 XdmfHDF5Writer::XdmfHDF5Writer(const XdmfHDF5Writer & writerRef) :
   XdmfHeavyDataWriter(writerRef.getFilePath(), 1, 800),
   mImpl(new XdmfHDF5WriterImpl()),
@@ -1399,7 +1401,7 @@ XdmfHDF5Writer::write(XdmfArray & array)
           const hsize_t totalDimensionsSize =
             std::accumulate(current_dims.begin(),
                             current_dims.end(),
-                            1,
+                            (hsize_t) 1,
                             std::multiplies<hsize_t>());
           // The Nth root of the chunk size divided by the dimensions added together
           const double factor =

ThirdParty/xdmf3/vtkxdmf3/core/XdmfHeavyDataDescription.cpp

@@ -76,6 +76,8 @@ XdmfHeavyDataDescription::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
 
 }
 
+// C Wrappers
+
 XDMFHEAVYDATADESCRIPTION *
 XdmfHeavyDataDescriptionNew(char * key, char * value)
 {

ThirdParty/xdmf3/vtkxdmf3/core/XdmfInformation.hpp

@@ -221,7 +221,7 @@ protected:
 
 private:
 
-  XdmfInformation(const XdmfInformation &);
+  XdmfInformation(const XdmfInformation &);  // Not implemented.
   void operator=(const XdmfInformation &);  // Not implemented.
 
   std::string mKey;

ThirdParty/xdmf3/vtkxdmf3/core/XdmfItem.cpp

@@ -34,7 +34,7 @@ XdmfItem::XdmfItem() :
 {
 }
 
-XdmfItem::XdmfItem(XdmfItem &refItem) :
+XdmfItem::XdmfItem(const XdmfItem &refItem) :
   mInformations(refItem.mInformations),
   mIsChanged(true)
 {

ThirdParty/xdmf3/vtkxdmf3/core/XdmfItem.hpp

@@ -37,8 +37,12 @@ class XdmfVisitor;
 
 // Includes
 #include <loki/Visitor.h>
+#define vtk_libxml2_reference reference // Reversing VTK name mangling
 #include <libxml/xmlexports.h>
 #include <libxml/tree.h>
+#include <libxml/uri.h>
+#include <libxml/xpointer.h>
+#include <libxml/xmlreader.h>
 #include <map>
 #include <set>
 #include <string>
@@ -377,7 +381,7 @@ public:
    */
   virtual void traverse(const shared_ptr<XdmfBaseVisitor> visitor);
 
-  XdmfItem(XdmfItem &);
+  XdmfItem(const XdmfItem &);
 
 protected:
 
@@ -411,7 +415,7 @@ protected:
 
 private:
 
-  XdmfItem(const XdmfItem &);  // Not implemented.
+//  XdmfItem(const XdmfItem &);  // It is implemented for C wrappers.
   void operator=(const XdmfItem &);  // Not implemented.
 
 };

ThirdParty/xdmf3/vtkxdmf3/core/XdmfWriter.cpp

@@ -22,7 +22,6 @@
 /*****************************************************************************/
 
 #include <fstream>
-#include <libxml/tree.h>
 #include <sstream>
 #include <utility>
 #include "XdmfArray.hpp"
@@ -120,6 +119,9 @@ public:
                (xmlChar*)"Version",
                (xmlChar*)mVersionString.c_str());
     xmlDocSetRootElement(mXMLDocument, mXMLCurrentNode);
+    if(mHeavyDataWriter->getMode() == XdmfHeavyDataWriter::Default) {
+      mHeavyDataWriter->openFile();
+    }
   }
 
   int mDepth;
@@ -374,9 +376,11 @@ XdmfWriter::visit(XdmfArray & array,
 
       // 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 &&
          mImpl->mMode == Default) {
-        array.read();
+        if (array.getHeavyDataController(0)->getFilePath().compare(mImpl->mHeavyDataWriter->getFilePath()) != 0)
+        {
+          array.read();
+        }
       }
 
       if(array.getHeavyDataController(0) ||