Addaped H5Fed api to Dune.

H5hut/src

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This commit is contained in:

Patrik Leidenberger

2006-09-24 12:15:09 +00:00

parent bb7f1c5f38

commit 0e2cc3ec8c

3 changed files with 63 additions and 65 deletions

									
										H5Fed/libsrc/h5fed/h5fed.cc
									
		+2
		
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				@@ -17,6 +17,7 @@

				/* include proprietary files */

				/*

				#include "h5fed.hh"

				#ifdef HAVE_HDF5

				@@ -35,3 +36,4 @@ namespace hdf5em

				//

				}

				#endif // HAVE_HDF5

				*/

									
										H5Fed/libsrc/h5fed/h5fed.hh
									
		+29
		-40
	
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				@@ -26,12 +26,14 @@

				#include <vector>

				// 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 <rlog/RLogTime.h>

				#ifdef HAVE_RLOG

				  #include <rlog/rlog.h>

				  #include <rlog/rloglocation.h>

				  #include <rlog/Error.h>

				  #include <rlog/RLogChannel.h>

				  #include <rlog/StdioNode.h>

				  #include <rlog/RLogTime.h>

				#endif // HAVE_RLOG    

				// Include HDF5 headers.

				#include <hdf5.h>

				@@ -40,18 +42,22 @@

				#include "h5fedconst.hh"

				/* include standard proprietary header files */

				/*

				#include "nonsciconst.h"

				#include "physicomath.h"

				*/

				using namespace std;

				using namespace physicomath;

				using namespace nonsciconst;

				// Don't use this: doesn't working with dune.

				//using namespace std;

				//using namespace physicomath;

				//using namespace nonsciconst;

				namespace H5Fed

				{

				class H5Fed {

				public:

				  /** \brief constructor and destructor */

				  H5Fed()

				  {

				@@ -66,9 +72,8 @@ public:

				  // The Destructor.

				  ~H5Fed(){};

				  //! Open an hdf5 finite element data file with appropriate access.

				  int open(string fileName, string fileAccess)

				  int open(std::string fileName, std::string fileAccess)

				  {

				    // Store filename and file access in private variable.

				    fileName_ = fileName;

				@@ -174,7 +179,7 @@ public:

				    // Copy the old index to the map as map-key.

				    for(unsigned int varI = 0; varI < indexVec.size(); varI++)

				    {

				      indexMap_.insert(make_pair(indexVec[varI],0));

				      indexMap_.insert(std::make_pair(indexVec[varI],0));

				    }

				    // Number all elements in the map consecutive, starting with zero, that

				    // is the new index set.

				@@ -190,7 +195,7 @@ public:

				    // of the coordinate in the vector.

				    for(unsigned int varI = 0; varI < indexVec.size(); varI++)

				    {

				      positionMap_.insert(make_pair(

				      positionMap_.insert(std::make_pair(

				                           (indexMap_.find(indexVec[varI]))->second,varI));

				    }

				    return OKCODE;

				@@ -330,15 +335,6 @@ public:

				      return ERRORCODE;

				    }

				  };

				  // Write 3dim coordinates to h5fed file.

				  int rCoord3d (std::vector<std::vector<double> >& coord)

				@@ -453,13 +449,6 @@ public:

				    }

				  };

				  // Read and return tetrahedrons and respective material index of the

				  // given level.

				  int rTetrahedron(unsigned int level,

				@@ -467,7 +456,7 @@ public:

				                   std::vector<unsigned int>& materialIndex)

				  {

				    // Set the name of the dataset, we want to read.

				    string datasetName = H5FED_D_TETMESH;

				    std::string datasetName = H5FED_D_TETMESH;

				    rElement_(datasetName, level, elem, materialIndex);

				    return OKCODE;

				  };

				@@ -480,7 +469,7 @@ public:

				    // Set dimension of an elements vector.

				    unsigned int elemDim = H5FED_TET_N_NODE;

				    // Set the name of the dataset, we want to operate.

				    string datasetName = H5FED_D_TETMESH;

				    std::string datasetName = H5FED_D_TETMESH;

				    // Select the data type in which the elements should be stored.

				    hid_t dataType = H5FED_MESH_ELEM_DATATYPE;

				    // This function does the real work for all elements.

				@@ -513,7 +502,7 @@ public:

				    if (hdf5FileIdent_ >= 0)

				    {

				      // Make datasetName with the datasetNameBlank and the level.

				      string datasetName = datasetNameBlank + stringify(level);

				      std::string datasetName = datasetNameBlank + stringify(level);

				      // Check if the dataset with the given datasetName already exists:

				      // if it exists, abort; 

				@@ -627,7 +616,7 @@ public:

				          // Set the appropriate material list!

				          // ===> This is not implementes yet! <===

				          // See warning above.

				          element[dim_out[1]-1] = 0;

				          element[dim_out[1]-1] = materialIndex[varI];

				          // Select hyperslab ('region') in file dataspace.

				          hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,

				@@ -683,7 +672,7 @@ public:

				    if (hdf5FileIdent_ >= 0)

				    {

				      // Make datasetName with the datasetNameBlank and the level.

				      string datasetName = datasetNameBlank + stringify(level);

				      std::string datasetName = datasetNameBlank + stringify(level);

				      // Check if the dataset with the given datasetName exists:

				      // if it does not return errorcode, else continue. 

				@@ -840,7 +829,6 @@ public:

				    }

				  }

				  /** \brief Inquire existence of HDF5 groups */

				//  existsVolumeMesh()

				@@ -966,15 +954,14 @@ public:

				//________________________________________________________________

				//		protected:

				//		

				private:

				  //-----------------------------------------------------------------------//

				  // Private data structure.                                               //

				  //-----------------------------------------------------------------------//

				  // Store the filename of the H5Fed here.

				  string fileName_;

				  std::string fileName_;

				  // Store the file access rights of the H5Fed here.

				  string fileAccess_;

				  std::string fileAccess_;

				  // Hdf5 error variable stores the success of an Hdf5 action.

				  herr_t hdf5Status_;

				@@ -1006,7 +993,7 @@ private:

				    {

				      oStream << value;

				    }

				    catch(exception& error)

				    catch(std::exception& error)

				    {

				      rError("Cannot convert this variable to a string.");

				      rError("Error: %d",error.what());

				@@ -1014,11 +1001,13 @@ private:

				    }  

				    return oStream.str();

				  }

				};

				} // End of namespace H5Fed

				#elif

				#warning "No HDF5 found. You cannot use h5fed."

				#endif // HAVE_HDF5

				#endif //H5FED_HH_

									
										H5Fed/libsrc/h5fed/h5fedconst.hh
									
		+32
		-25
	
												View File
												
				@@ -6,41 +6,47 @@

				// Include HDF5 headers.

				#include <hdf5.h>

				using namespace std;

				namespace H5Fed

				{

				// Return values.

				const int OKCODE    = 0;

				const int ERRORCODE = 1;

				//! Hdf5 specific file access:

				// "r" for read only access.

				// "w" for read and write access.

				// "c" create a new a new file with if it does not exist already.

				// "cf" create a new file, overwrite it if it exists already.

				const string FILE_READ("r");

				const string FILE_READ_WRITE("w");

				const string FILE_CREATE("c");

				const string FILE_CREATE_FORCE("cf");

				const std::string FILE_READ("r");

				const std::string FILE_READ_WRITE("w");

				const std::string FILE_CREATE("c");

				const std::string FILE_CREATE_FORCE("cf");

				// Define the group names of the H5Fed starndard groups.

				const string H5FED_G_ROOT                ("/HDF5_FINITE_ELEMENT_DATA");

				  const string H5FED_G_COORD             (H5FED_G_ROOT+"/COORD");

				  const string H5FED_G_VOLUME_MESH       (H5FED_G_ROOT+"/VOLUME_MESH");

				  const string H5FED_G_BOUNDARY_MESH     (H5FED_G_ROOT+"/BOUNDARY_MESH");

				  const string H5FED_G_MATERIAL          (H5FED_G_ROOT+"/MATERIAL");

				    const string H5FED_G_ELECTROMAGNETIC (H5FED_G_MATERIAL+"/ELECTROMAGNETIC");

				      const string H5FED_G_DISCRETE      (H5FED_G_ELECTROMAGNETIC+"/DISCRETE");

				      const string H5FED_G_PHYSICAL      (H5FED_G_ELECTROMAGNETIC+"/PHYSICAL");

				        const string H5FED_G_DEBYE       (H5FED_G_PHYSICAL+"/DEBYE");

				        const string H5FED_G_LORENTZ     (H5FED_G_PHYSICAL+"/LORENTZ");

				        const string H5FED_G_DRUDE       (H5FED_G_PHYSICAL+"/DRUDE");

				  const string H5FED_G_DOF               (H5FED_G_ROOT+"/DOF");

				  const string H5FED_G_FIELD             (H5FED_G_ROOT+"/FIELD");

				const std::string H5FED_G_ROOT                ("/HDF5_FINITE_ELEMENT_DATA");

				  const std::string H5FED_G_COORD             (H5FED_G_ROOT+"/COORD");

				  const std::string H5FED_G_VOLUME_MESH       (H5FED_G_ROOT+"/VOLUME_MESH");

				  const std::string H5FED_G_BOUNDARY_MESH     (H5FED_G_ROOT+"/BOUNDARY_MESH");

				  const std::string H5FED_G_MATERIAL          (H5FED_G_ROOT+"/MATERIAL");

				    const std::string H5FED_G_ELECTROMAGNETIC (H5FED_G_MATERIAL+"/ELECTROMAGNETIC");

				      const std::string H5FED_G_DISCRETE      (H5FED_G_ELECTROMAGNETIC+"/DISCRETE");

				      const std::string H5FED_G_PHYSICAL      (H5FED_G_ELECTROMAGNETIC+"/PHYSICAL");

				        const std::string H5FED_G_DEBYE       (H5FED_G_PHYSICAL+"/DEBYE");

				        const std::string H5FED_G_LORENTZ     (H5FED_G_PHYSICAL+"/LORENTZ");

				        const std::string H5FED_G_DRUDE       (H5FED_G_PHYSICAL+"/DRUDE");

				  const std::string H5FED_G_DOF               (H5FED_G_ROOT+"/DOF");

				  const std::string H5FED_G_FIELD             (H5FED_G_ROOT+"/FIELD");

				// Define the dataset names of the H5Fed standard datasets.

				const string H5FED_D_COORD3D        (H5FED_G_COORD+"/COORD3D");

				const string H5FED_D_TETMESH        (H5FED_G_VOLUME_MESH+"/TETMESH_L");

				const string H5FED_D_HEXMESH        (H5FED_G_VOLUME_MESH+"/HEXMESH_L");

				const string H5FED_D_PRISMATICMESH  (H5FED_G_VOLUME_MESH+"/PRISMATICMESH_L");

				const string H5FED_D_PYRAMIDMESH    (H5FED_G_VOLUME_MESH+"/PYRAMIDMESH_L");

				const string H5FED_D_TRIANGLEMESH   (H5FED_G_VOLUME_MESH+"/TRIANGLEMESH_L");

				const string H5FED_D_QUADRANGLEMESH (H5FED_G_VOLUME_MESH+"/QUADRANGLEMESH_L");

				const std::string H5FED_D_COORD3D        (H5FED_G_COORD+"/COORD3D");

				const std::string H5FED_D_TETMESH        (H5FED_G_VOLUME_MESH+"/TETMESH_L");

				const std::string H5FED_D_HEXMESH        (H5FED_G_VOLUME_MESH+"/HEXMESH_L");

				const std::string H5FED_D_PRISMATICMESH  (H5FED_G_VOLUME_MESH+"/PRISMATICMESH_L");

				const std::string H5FED_D_PYRAMIDMESH    (H5FED_G_VOLUME_MESH+"/PYRAMIDMESH_L");

				const std::string H5FED_D_TRIANGLEMESH   (H5FED_G_VOLUME_MESH+"/TRIANGLEMESH_L");

				const std::string H5FED_D_QUADRANGLEMESH (H5FED_G_VOLUME_MESH+"/QUADRANGLEMESH_L");

				// How much nodes have a geometric figure. 

				const unsigned short int H5FED_TET_N_NODE        = 4;

				@@ -56,4 +62,5 @@ const hid_t H5FED_MESH_ELEM_DATATYPE = H5T_STD_U32LE;

				const hid_t H5FED_COORD_DATATYPE = H5T_IEEE_F64LE;

				} /* namespace H5Fed*/

				#endif /*H5FEDCONST_HH_*/