Extension of the H5Fed API and adding a dump program to test the API.

.gitattributes

@@ -5,6 +5,8 @@
 /GNUmakefile.orig -text
 H5Fed/applications/gmsh2h5fed.cc -text
 H5Fed/applications/gmsh2h5fed.hh -text
+H5Fed/applications/h5feddump.cc -text
+H5Fed/applications/h5feddump.hh -text
 H5Fed/applications/makefile.am -text
 H5Fed/autogen.sh -text
 H5Fed/configure.ac -text

H5Fed/applications/gmsh2h5fed.cc

@@ -7,6 +7,7 @@
 // modified  - 2006 jun 26, creation, patrick leidenberger
 // modified  - 2006 aug 25, extend, patrick leidenberger
 // modified  - 2006 aug 26, pl, integrate automatic index mapping.
+// modified  - 2006 sep 22, pl, addaped to h5fed api changes.
 //
 // feature - Implements the a mesh preprocessor.
 // feature - It will read gmsh's mesh files of version 2.0 and write the mesh
@@ -159,12 +160,12 @@ int main(int argc, char **argv)
   
   // The gmsh node index has gaps and is not consecutive.
   // So we activate the automatic index mapping from the h5fed api.
-  h5fedFile.beginIndexMapping(&gmshNodesIndex);
+  h5fedFile.beginIndexMapping(gmshNodesIndex);
 
     // Get a vector with all node coordinates from the gmsh file.
     gmshNodes = gmshInFile.gmshNode();
     // Write the nodes to the h5fed file.
-    h5fedFile.coord3d(&gmshNodes);
+    h5fedFile.wCoord3d(gmshNodes);
     // Every node in h5fed file, so we can save memory.
     gmshNodes.clear();
   
@@ -174,8 +175,10 @@ int main(int argc, char **argv)
     {
 //      rDebug("Elem: %d Nodes: %d; %d; %d; %d", varI, gmshTetrahedron[varI][0], gmshTetrahedron[varI][1], gmshTetrahedron[varI][2], gmshTetrahedron[varI][3]);
     }
+    std::vector<unsigned int> gmshTetrahedronMatIndex;
+    gmshTetrahedronMatIndex.resize(0,gmshTetrahedron.size());
     // Write the tetrahedrons to the h5fed file on the respective level.
-    h5fedFile.tetrahedron(0,&gmshTetrahedron);
+    h5fedFile.wTetrahedron(0,gmshTetrahedron, gmshTetrahedronMatIndex);
     // Every terahedron in h5fed file, so we can save memory.
     gmshTetrahedron.clear();
     

H5Fed/applications/h5feddump.cc

+// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
+//                 all rights reserved
+// project   - h5feddump
+// file name - h5feddump.cc
+// file type - c++ implementaton file
+// objective - main file h5fed dump program
+// modified  - 2006 sep 21, creation, patrick leidenberger.
+// modified  - 2006 sep 22, pl, add dump for coordinates.
+//
+// feature - Implements the a dump tool for h5fed files.
+// feature - It will read hf5ed file and write the data to the standard 
+// feature - output.
+// feature - There are different options on command line what to dump.
+// required software - rlog library, boost library 
+
+#include <h5feddump.hh>
+
+using namespace rlog;
+
+int main(int argc, char **argv)
+{
+  //=================//
+  // Initialize RLog //
+  //=================//
+  // Make a instance of the class for RLog.
+  StdioNode stdLog;
+
+  /** Subscchar* inFile_;ribe output channels.
+   * Compile with -DRLOG_DEBUG to get the debug output.
+   **/
+  #ifdef USE_RLOG_DEBUG_CHANNEL
+    stdLog.subscribeTo(GetGlobalChannel("debug"));
+  #endif //USE_RLOG_DEBUG_CHANNEL
+  #ifdef USE_RLOG_ERROR_CHANNEL
+    stdLog.subscribeTo(GetGlobalChannel("error"));
+  #endif //USE_RLOG_ERROR_CHANNEL
+  #ifdef USE_RLOG_INFO_CHANNEL
+    stdLog.subscribeTo(GetGlobalChannel("info"));
+  #endif //USE_RLOG_INFO_CHANNEL
+  #ifdef USE_RLOG_WARNING_CHANNEL
+    stdLog.subscribeTo(GetGlobalChannel("warning"));
+  #endif //USE_RLOG_WARNING_CHANNEL
+
+  // Define variables that hold the command line parameters.
+  string hdf5fedFile;
+ 
+  //==================================================//
+  // Parse the comand line options                    //
+  // with the program_options from the boost library. //
+  //==================================================//
+  try
+  {
+    // Define and instance of the program_options class and name it.
+    boost::program_options::options_description 
+      desc("Allowed program options");
+    // Define the command line options parsing rules.
+    desc.add_options()
+      ("help", "produce this help")
+      ("input-file", boost::program_options::value<string>(),
+       "hdf5fed file to dump");
+    // Parse the command line.
+    boost::program_options::variables_map varMap;
+    boost::program_options::store
+      (boost::program_options::parse_command_line(argc, argv, desc),
+       varMap);
+    boost::program_options::notify(varMap);
+    // Action in relation to the command line options.
+    if (varMap.count("help"))
+    {
+      cout << desc << "\n";
+      return ERRORCODE;
+    }
+    else if (varMap.count("input-file")) 
+    {
+      hdf5fedFile = varMap["input-file"].as<string>();
+      rInfo("Input filename: %s",
+            hdf5fedFile.c_str());
+    }    
+    else
+    {
+      rError("You have insert wrong options.");
+      rError("For details use: --help.");
+      return ERRORCODE;
+    }    
+  }
+  catch(exception& error)
+  {
+    rError("Error: %d",error.what());
+    return ERRORCODE;
+  }  
+
+  //==========================//
+  // Start with the main work //
+  //==========================//
+
+  // Put all H5Fed funktions in here.
+  #ifdef HAVE_HDF5
+  // Create H5Fed class instance. 
+  H5Fed::H5Fed h5fedFile;
+  
+  // Open H5Fed file for reading. Filename comes from 
+  // command line parameters. 
+  h5fedFile.open(hdf5fedFile,FILE_READ);
+
+  // Vector for the tetrahedorn nodes and the material tag.
+  std::vector< std::vector<unsigned int> > elem;
+  std::vector<unsigned int> materialIndex;
+
+
+  // Read the tetrahedrons of the h5fed file an print them.
+  h5fedFile.rTetrahedron((unsigned int)0, elem, materialIndex);
+  for(int varI = 0; varI<elem.size(); varI++)
+  {
+    rDebug("Tet number: %d; nodes: %d %d; %d %d; material index: %d",
+           varI,
+           elem[varI][0],
+           elem[varI][1],
+           elem[varI][2],
+           elem[varI][3],
+           materialIndex[varI]);
+  }
+
+
+  // Read the 3d coordinates of the h5fed file an print them.
+  std::vector<std::vector< double> > coord;
+  h5fedFile.rCoord3d(coord);
+  for(int varI = 0; varI<coord.size(); varI++)
+  {
+    rDebug("Coor Number %d; Coord3d: %f;  %f;  %f",
+           varI,
+           coord[varI][0],
+           coord[varI][1],
+           coord[varI][2]);
+  }
+  // Close H5Fed file.
+  h5fedFile.close();
+    
+  #endif // HAVE_HDF5
+
+  return(0);
+}
+

H5Fed/applications/h5feddump.hh

+// rights    - 2006-, copyright by 
+//                    benedikt oswald and patrick leidenberger,
+//                    all rights reserved
+// project   - h5feddump
+// file name - h5feddump.hh
+// file type - c++ header file
+// objective - header file for the h5feddump
+// modified  - 2006 sep 21, creation, Patrick Leidenberger
+// modified  - 2006 sep 22, pl, add dump for coordinates.
+
+#ifndef H5FEDDUMP_H_
+#define H5FEDDUMP_H_
+
+/* include standard header files */
+#include <cmath>
+#include <complex>
+#include <string>
+#include <vector>
+#include <iostream>
+#include <iterator>
+#include <math.h>
+
+/* Include the files for rlog. */
+#include <rlog/rlog.h>
+#include <rlog/rloglocation.h>
+#include <rlog/Error.h>
+#include <rlog/RLogChannel.h>
+#include <rlog/StdioNode.h>
+// Include this if you want to log the time.
+#include <rlog/RLogTime.h>
+
+// Include the boost program program_options to parse the comand line
+// options.
+#include <boost/program_options.hpp>
+
+
+/* include standard proprietary header files */
+#include <nonsciconst.h>
+#include <physicomath.h>
+
+// Include the Hdf5FiniteElementData API.
+#ifdef HAVE_HDF5
+  // Include the Hdf5FiniteElementData API.
+  #include <h5fed.hh>
+  // Include h5fed specific constants.
+  #include <h5fedconst.hh>
+#else
+  #warning No hdf5 lib found!!
+#endif
+
+using namespace physicomath;
+using namespace nonsciconst;
+using namespace H5Fed;
+//using namespace gmshtohdf5fed;
+
+#endif /*PHIDIAS3D_H_*/

H5Fed/applications/makefile.am

@@ -4,11 +4,12 @@
 ## modified  - 2006 aug 21, patrick leidenberger, creation
 ## modified  - 2006 aug 23, pl, adaped to changed directory structure.
 ## modified  - 2006 aug 25, pl, adaped to changed directory structure.
+## modified  - 2006 sep 21, pl, add the h5feddump application.
 #
 ## objective - automake input file for the gmsh directory
 ## project   - gmsh2h5fed
 
-noinst_PROGRAMS = gmsh2h5fed
+noinst_PROGRAMS = gmsh2h5fed h5feddump
 
 gmsh2h5fed_SOURCES = gmsh2h5fed.cc
 gmsh2h5fed_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h      \
@@ -23,4 +24,14 @@ gmsh2h5fed_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h      \
 
 gmsh2h5fed_LDADD = @GMSH2H5FED_LIBS@
 
+
+h5feddump_SOURCES = h5feddump.cc
+h5feddump_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h      \
+                         ../libsrc/stdincl/physicomath.h      \
+                         ../libsrc/h5fed/h5fed.hh             \
+                         ../libsrc/h5fed/h5fed.cc
+
+h5feddump_LDADD = @H5FEDDUMP_LIBS@
+
+
 #AM_CPPFLAGS = @AM_CPPFLAGS@

H5Fed/configure.ac

@@ -3,6 +3,7 @@
 ## author    - benedikt oswald and patrick leidenberger
 ## modified  - 2006 aug 21, pl, creation.
 ## modified  - 2006 aug 24, pl, add h5fed path.
+## modified  - 2006 sep 21, pl, add h5feddump libs.
 ##
 ## to do     : The rlog lib needs a -DRLOG_COMPONENT="some name", I don't know
 ##             how tho do this so that the quotation marks are in the output
@@ -33,6 +34,7 @@ CXXFLAGS=""
 # provide include directories
 AC_SUBST([AM_CPPFLAGS], '-I$(top_srcdir)/libsrc/stdincl -I$(top_srcdir)/libsrc/gmsh -I$(top_srcdir)/libsrc/h5fed')
 AC_SUBST([GMSH2H5FED_LIBS],'$(top_srcdir)/libsrc/gmsh/libgmsh.la $(top_srcdir)/libsrc/h5fed/libh5fed.la')
+AC_SUBST([H5FEDDUMP_LIBS],'$(top_srcdir)/libsrc/h5fed/libh5fed.la')
 
 # Make available external libraries
 AC_ARG_WITH(boost,

H5Fed/libsrc/h5fed/h5fedconst.hh

@@ -2,6 +2,10 @@
 #define H5FEDCONST_HH_
 
 #include<string>
+
+// Include HDF5 headers.
+#include <hdf5.h>
+
 using namespace std;
 
 //! Hdf5 specific file access:
@@ -46,5 +50,10 @@ const unsigned short int H5FED_PYRAMID_N_NODE    = 5;
 const unsigned short int H5FED_TRIANGLE_N_NODE   = 3;
 const unsigned short int H5FED_QUADRANGLE_N_NODE = 4;
 
+// In which format should a single element of a mesh entity and the
+// index to the material list be stored.
+const hid_t H5FED_MESH_ELEM_DATATYPE = H5T_STD_U32LE;
+const hid_t H5FED_COORD_DATATYPE = H5T_IEEE_F64LE;
+
 
 #endif /*H5FEDCONST_HH_*/