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-95
@@ -1,95 +0,0 @@
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*.tar.gz
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*.[oa]
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*.la
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*.lo
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*.so
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*~
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CMakeFiles
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dump_field_attributes
|
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autom4te.cache/
|
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config.guess
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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tools/h5hutcc
|
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tetmesh_adjacencies
|
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tetmesh_read
|
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tetmesh_read_tags
|
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tetmesh_write
|
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tetmesh_write1
|
||||
examples/H5Fed/tetmesh_write2
|
||||
examples/H5Fed/trimesh_2gnuplot
|
||||
examples/H5Fed/trimesh_adjacencies
|
||||
examples/H5Fed/trimesh_read
|
||||
examples/H5Fed/trimesh_write
|
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examples/H5Fed/trimesh_write_dunetest
|
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tetmesh_write_tags
|
||||
write_field
|
||||
*.gch
|
||||
ReferencePages
|
||||
vtk2h5grid
|
||||
@@ -7,4 +7,4 @@ Wes Bethel (NERSC/LBNL)
|
||||
John Shalf (NERSC/LBNL)
|
||||
Cristina Siegerist (NERSC/LBNL)
|
||||
|
||||
Please use h5part@lists.psi.ch for communication.
|
||||
Please use h5part@lists.psi.ch for communicaion.
|
||||
|
||||
@@ -1,71 +0,0 @@
|
||||
*** Copyright Notice ***
|
||||
|
||||
H5hut Copyright (c) 2006-2016, The Regents of the University of California,
|
||||
through Lawrence Berkeley National Laboratory (subject to receipt of any
|
||||
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
|
||||
Institut (Switzerland). All rights reserved.
|
||||
|
||||
If you have questions about your rights to use or distribute this
|
||||
software, please contact Berkeley Lab's Technology Transfer Department
|
||||
at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
|
||||
|
||||
NOTICE. This software was developed under partial funding from the U.S.
|
||||
Department of Energy. As such, the U.S. Government has been granted for
|
||||
itself and others acting on its behalf a paid-up, nonexclusive,
|
||||
irrevocable, worldwide license in the Software to reproduce, prepare
|
||||
derivative works, and perform publicly and display publicly. Beginning
|
||||
five (5) years after the date permission to assert copyright is obtained
|
||||
from the U.S. Department of Energy, and subject to any subsequent five
|
||||
(5) year renewals, the U.S. Government is granted for itself and others
|
||||
acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
|
||||
license in the Software to reproduce, prepare derivative works,
|
||||
distribute copies to the public, perform publicly and display publicly,
|
||||
and to permit others to do so.
|
||||
|
||||
|
||||
*** License agreement ***
|
||||
|
||||
H5hut Copyright (c) 2006-2016, The Regents of the University of California,
|
||||
through Lawrence Berkeley National Laboratory (subject to receipt of any
|
||||
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
|
||||
Institut (Switzerland). All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
|
||||
(1) Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
|
||||
(2) Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
|
||||
(3) Neither the name of the University of California, Lawrence Berkeley
|
||||
National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
|
||||
(Switzerland) nor the names of its contributors may be used to endorse
|
||||
or promote products derived from this software without specific prior
|
||||
written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
|
||||
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
|
||||
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
|
||||
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
|
||||
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
|
||||
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
|
||||
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
|
||||
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
You are under no obligation whatsoever to provide any bug fixes,
|
||||
patches, or upgrades to the features, functionality or performance of
|
||||
the source code ("Enhancements") to anyone; however, if you choose to
|
||||
make your Enhancements available either publicly, or directly to
|
||||
Lawrence Berkeley National Laboratory, without imposing a separate
|
||||
written license agreement for such Enhancements, then you hereby grant
|
||||
the following license: a non-exclusive, royalty-free perpetual license
|
||||
to install, use, modify, prepare derivative works, incorporate into
|
||||
other computer software, distribute, and sublicense such enhancements or
|
||||
derivative works thereof, in binary and source code form.
|
||||
|
||||
@@ -0,0 +1,7 @@
|
||||
*** Copyright Notice ***
|
||||
|
||||
H5Part Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland). All rights reserved.
|
||||
|
||||
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
|
||||
|
||||
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
|
||||
@@ -1,15 +0,0 @@
|
||||
2018-09-14 Gsell Achim <achi.gsell@psi.ch>
|
||||
|
||||
* C-API
|
||||
- H5PartSetNumPoints() renamed to H5PartSetNumItems()
|
||||
- H5PartGetNumPoints() renamed to H5PartGetNumItems()
|
||||
- Dataset names longer then 64 bytes are handled as error.
|
||||
- Same for step/iteration names.
|
||||
* core API
|
||||
- we use the term 'iteration' instead of 'step'
|
||||
- we use the term 'item' instead of 'point'
|
||||
- re-factor function and variable names
|
||||
- in printing messages/debug output fixed
|
||||
- do not flush (sync to disk) after writing a dataset by default,
|
||||
can be controlled by a property
|
||||
|
||||
|
||||
Executable
+133
@@ -0,0 +1,133 @@
|
||||
UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
|
||||
# for host specific options
|
||||
HOST := $(shell hostname)
|
||||
|
||||
# for processor-specific options
|
||||
ifeq ($(UNAME), Linux)
|
||||
PROC := $(shell uname -p)
|
||||
endif
|
||||
|
||||
CXX = c++
|
||||
CC = cc
|
||||
H5HOME = /usr/local/hdf5
|
||||
CFLAGS = -g -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
|
||||
# MacOS-X Serial
|
||||
ifeq ($(UNAME), Darwin)
|
||||
ifeq ($(PARALLEL), yes)
|
||||
CXX = g++
|
||||
CC = mpicc
|
||||
H5HOME = /usr/local
|
||||
CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
|
||||
LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
|
||||
else
|
||||
CXX = c++
|
||||
CC = cc
|
||||
F90 = xlf
|
||||
H5HOME = /usr/local
|
||||
CFLAGS = -O -g -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
endif
|
||||
endif
|
||||
|
||||
# SGI MIPS/Irix
|
||||
ifeq ($(UNAME), IRIX64)
|
||||
CXX = CC
|
||||
CC = cc
|
||||
F90 = f90
|
||||
ifeq ($(PARALLEL), yes)
|
||||
H5HOME = $(HDF5_DIR)
|
||||
CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
|
||||
LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
|
||||
else
|
||||
H5HOME = /usr/local
|
||||
CFLAGS = -O3 -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
endif
|
||||
endif
|
||||
|
||||
# AIX/SP-2 Parallel/serial : Seaborg
|
||||
ifeq ($(UNAME), AIX)
|
||||
ifeq ($(PARALLEL), yes) # parallel
|
||||
CXX = mpCC_r
|
||||
CC = mpxlc_r
|
||||
# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
|
||||
H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
|
||||
# /usr/common/usg/hdf5/1.4.4/parallel
|
||||
H4HOME = /usr/common/usg/hdf/default
|
||||
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
|
||||
CFLAGS = -q64 -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
|
||||
else # serial
|
||||
CXX = xlC
|
||||
CC = xlc
|
||||
H5HOME = /usr/common/usg/hdf5/1.4.4/serial
|
||||
H4HOME = /usr/common/usg/hdf/default
|
||||
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
|
||||
CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
|
||||
endif
|
||||
endif
|
||||
|
||||
# Linux
|
||||
ifeq ($(UNAME), Linux)
|
||||
# if this machine is NERSC/Davinci Altix system
|
||||
ifeq ($(PROC), ia64)
|
||||
CC = icc
|
||||
CXX = icc
|
||||
|
||||
ifeq ($(PARALLEL), yes)
|
||||
# IA64 Linux Parallel
|
||||
ifeq ($(HOST), davinci)
|
||||
H5HOME = $(HDF5_PAR)
|
||||
MPILIB = -lmpi
|
||||
else
|
||||
H5HOME = /usr/local
|
||||
HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
HDF5_PAR_INCLUDE = -I$(H5HOME)/include
|
||||
MPIHOME = /usr/local
|
||||
MPILIB = -lmpich
|
||||
endif # HOST
|
||||
CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE)
|
||||
LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
|
||||
else # IA64 Linux Serial
|
||||
CFLAGS = -O3 $(HDF5_INCLUDE)
|
||||
LDFLAGS = $(HDF5_LIB) -lm
|
||||
endif # PARALLEL
|
||||
|
||||
# else this is standard IA32 linux
|
||||
else
|
||||
ifeq ($(PARALLEL), yes)
|
||||
# Linux Parallel
|
||||
CC = gcc
|
||||
CXX = g++
|
||||
H5HOME = /usr/local
|
||||
MPIHOME = /usr/local
|
||||
CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
|
||||
else # Linux Serial
|
||||
CXX = g++
|
||||
CC = gcc
|
||||
CFLAGS = -O -g -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
endif # !PARALLEL
|
||||
endif # PROC!ia64
|
||||
|
||||
endif # !Linux
|
||||
|
||||
ifeq ($(PARALLEL), yes) #parallel
|
||||
ifdef F90
|
||||
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
|
||||
else
|
||||
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
|
||||
endif
|
||||
else
|
||||
ifdef F90
|
||||
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
|
||||
else
|
||||
all: H5PartTest H5PartTest.o H5Part.o
|
||||
endif
|
||||
endif
|
||||
|
||||
include rules.make
|
||||
@@ -0,0 +1,427 @@
|
||||
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
|
||||
// all rights reserved
|
||||
// project - gmsh2h5fed
|
||||
// file name - gmsh2h5fed.cc
|
||||
// file type - c++ implementaton file
|
||||
// objective - main file for the gmsh to hdf5fed converter
|
||||
// modified - 2006 jun 26, creation, patrick leidenberger
|
||||
// modified - 2006 aug 25, extend, patrick leidenberger
|
||||
// modified - 2006 aug 26, pl, integrate automatic index mapping.
|
||||
//
|
||||
// feature - Implements the a mesh preprocessor.
|
||||
// feature - It will read gmsh's mesh files of version 2.0 and write the mesh
|
||||
// feature - into an HDF5/FiniteElementData file.
|
||||
// required software - rlog library, boost library
|
||||
|
||||
#include <gmsh2h5fed.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 gmshInputFile;
|
||||
string hdf5fedOutputFile;
|
||||
bool writeFileForce = false;
|
||||
|
||||
//==================================================//
|
||||
// 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>(),
|
||||
"gmsh v2.0 input file")
|
||||
("output-file", boost::program_options::value<string>(),
|
||||
"hdf5fed output file")
|
||||
("force", "if output file already exists, overwrite");
|
||||
// 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"))
|
||||
&& (varMap.count("output-file")))
|
||||
{
|
||||
gmshInputFile = varMap["input-file"].as<string>();
|
||||
hdf5fedOutputFile = varMap["output-file"].as<string>();
|
||||
rInfo("Input filename: %s",
|
||||
gmshInputFile.c_str());
|
||||
rInfo("Output filename: %s",
|
||||
hdf5fedOutputFile.c_str());
|
||||
// Check it --force is set.
|
||||
// --force writes the output file, if the file already exists.
|
||||
if (varMap.count("force"))
|
||||
writeFileForce = true;
|
||||
else
|
||||
writeFileForce = false;
|
||||
}
|
||||
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 //
|
||||
//==========================//
|
||||
//---------------------------------------//
|
||||
// Variables for the data form gmsh file //
|
||||
//---------------------------------------//
|
||||
// Variable for the gmsh nodes.
|
||||
std::vector<vector<double> > gmshNodes;
|
||||
gmshNodes.clear();
|
||||
// Vector for the gmshs nodes index.
|
||||
std::vector<unsigned int> gmshNodesIndex;
|
||||
gmshNodesIndex.clear();
|
||||
// Vector for the gmshs tetrahedrons.
|
||||
std::vector<std::vector<unsigned int> > gmshTetrahedron;
|
||||
gmshTetrahedron.clear();
|
||||
// Vector for the gmshs tetrahedrons.
|
||||
std::vector<std::vector<unsigned int> > gmshTetrahedronTag;
|
||||
gmshTetrahedronTag.clear();
|
||||
|
||||
// Make an instance of the vtk class.
|
||||
gmsh gmshInFile;
|
||||
|
||||
// Set the file name of the input file
|
||||
gmshInFile.gmshFileName(gmshInputFile);
|
||||
|
||||
// Open the gmsh mesh file, write the content to a string and close the
|
||||
// file.
|
||||
gmshInFile.gmshOpen();
|
||||
|
||||
// Parse the gmsh mesh file.
|
||||
gmshInFile.gmshParseFile(&gmshInFile);
|
||||
|
||||
// Get a vector with all node coordinates from the gmsh file.
|
||||
gmshNodes = gmshInFile.gmshNode();
|
||||
|
||||
// Put all H5Fed funktions in here.
|
||||
#ifdef HAVE_HDF5
|
||||
// Create H5Fed class instance.
|
||||
H5Fed::H5Fed h5fedFile;
|
||||
|
||||
// Open H5Fed file for writing. Filename and file write access comes
|
||||
// from command line parameters.
|
||||
if (writeFileForce == false)
|
||||
h5fedFile.open(hdf5fedOutputFile,FILE_CREATE);
|
||||
else
|
||||
h5fedFile.open(hdf5fedOutputFile,FILE_CREATE_FORCE);
|
||||
|
||||
// Create the group hierarchie in the hdf5fed file.
|
||||
h5fedFile.createGroupHierarchie();
|
||||
|
||||
// Get the gmsh node index vector
|
||||
gmshNodesIndex = gmshInFile.gmshNodeNumber();
|
||||
|
||||
// The gmsh node index has gaps and is not consecutive.
|
||||
// So we activate the automatic index mapping from the h5fed api.
|
||||
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);
|
||||
// Every node in h5fed file, so we can save memory.
|
||||
gmshNodes.clear();
|
||||
|
||||
//Get a vector with all tetrahedrons from gmsh file.
|
||||
gmshTetrahedron = gmshInFile.gmshTetrahedron();
|
||||
for(int varI = 0; varI<gmshTetrahedron.size(); varI++)
|
||||
{
|
||||
// rDebug("Elem: %d Nodes: %d; %d; %d; %d", varI, gmshTetrahedron[varI][0], gmshTetrahedron[varI][1], gmshTetrahedron[varI][2], gmshTetrahedron[varI][3]);
|
||||
}
|
||||
// Write the tetrahedrons to the h5fed file on the respective level.
|
||||
h5fedFile.tetrahedron(0,&gmshTetrahedron);
|
||||
// Every terahedron in h5fed file, so we can save memory.
|
||||
gmshTetrahedron.clear();
|
||||
|
||||
//Get a vector with all tetrahedrons from gmsh file.
|
||||
gmshTetrahedronTag = gmshInFile.gmshTetrahedronTag();
|
||||
for(int varI = 0; varI<gmshTetrahedronTag.size(); varI++)
|
||||
{
|
||||
// rDebug("Elem: %d Nodes: %d; %d", varI, gmshTetrahedronTag[varI][0], gmshTetrahedronTag[varI][1]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
// End with the automatic index mapping because we have no further actcion
|
||||
// with an gmsh file index.
|
||||
h5fedFile.endIndexMapping();
|
||||
|
||||
// Close H5Fed file.
|
||||
h5fedFile.close();
|
||||
|
||||
|
||||
#endif // HAVE_HDF5
|
||||
/*
|
||||
// Write all vtkPoints_ to the screen.
|
||||
for (int i = 0; i<(gmshInFile.getVtkVecSize()); i++)
|
||||
{
|
||||
rDebug("%d vtkPoint x, y, z: %e %e %e",
|
||||
i, gmshInFile.getVtkVec(i,0),gmshInFile.getVtkVec(i,1),gmshInFile.getVtkVec(i,2));
|
||||
}
|
||||
*/
|
||||
/*
|
||||
//Write all vktCells_ with cell types and cell points on the screen.
|
||||
for (int i = 0;
|
||||
(i<(gmshInFile.getVtkCellTypesN())) && (i<(gmshInFile.getVtkCellsN()));
|
||||
i++)
|
||||
{
|
||||
rDebug("vtkCellType: %d", gmshInFile.getVtkCellType(i));
|
||||
for (int j = 0; j<(gmshInFile.getVtkCellPointN(i)); j++)
|
||||
{
|
||||
rDebug(" vtkPoint: %d", gmshInFile.getVtkCellPoint(i,j));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
// Write all vtk point datas on the screen.
|
||||
//rDebug("size: %d", gmshInFile.vtkVectorSize("vtkPointData_"));
|
||||
for (int i = 0;
|
||||
i<(gmshInFile.vtkVectorSize("vtkPointData_"));
|
||||
i++)
|
||||
{
|
||||
for (int j = 0; j<(gmshInFile.vtkVectorSize("vtkPointData_",i)); j++)
|
||||
{
|
||||
for(int k = 0; k<(gmshInFile.vtkVectorSize("vtkPointData_",i,j)); k++)
|
||||
rDebug("vtk point vector element i, j, k, value: %d %d %d %e",
|
||||
i,j,k,gmshInFile.vtkVector("vtkPointData_",i,j,k));
|
||||
}
|
||||
}
|
||||
|
||||
// Write all vtkPointsType_ to the screen.
|
||||
rDebug("size of vtkPointDataType_: %d", gmshInFile.vtkVectorSize("vtkPointDataType_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataType_")); i++)
|
||||
{
|
||||
rDebug("vtkPointDataType_ %s", gmshInFile.vtkVector("vtkPointDataType_",i).c_str());
|
||||
}
|
||||
// Write all vtkPointsName_ to the screen.
|
||||
rDebug("size of vtkPointDataName_: %d", gmshInFile.vtkVectorSize("vtkPointDataName_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataName_")); i++)
|
||||
{
|
||||
rDebug("vtkPointName_ %s", gmshInFile.vtkVector("vtkPointDataName_",i).c_str());
|
||||
}
|
||||
// Write all vtkPointsFormat_ to the screen.
|
||||
rDebug("size of vtkPointDataFormat_: %d", gmshInFile.vtkVectorSize("vtkPointDataFormat_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataFormat_")); i++)
|
||||
{
|
||||
rDebug("vtkPointFormat_ %s", (gmshInFile.vtkVector("vtkPointDataFormat_",i)).c_str());
|
||||
}
|
||||
|
||||
|
||||
// Write all vtk point datas on the screen.
|
||||
//rDebug("size: %d", gmshInFile.vtkVectorSize("vtkCellData_"));
|
||||
for (int i = 0;
|
||||
i<(gmshInFile.vtkVectorSize("vtkCellData_"));
|
||||
i++)
|
||||
{
|
||||
for (int j = 0; j<(gmshInFile.vtkVectorSize("vtkCellData_",i)); j++)
|
||||
{
|
||||
for(int k = 0; k<(gmshInFile.vtkVectorSize("vtkCellData_",i,j)); k++)
|
||||
rDebug("vtk cell vector element i, j, k, value: %d %d %d %e",
|
||||
i,j,k,gmshInFile.vtkVector("vtkCellData_",i,j,k));
|
||||
}
|
||||
}
|
||||
|
||||
// Write all vtkCellsType_ to the screen.
|
||||
rDebug("size of vtkCellDataType_: %d", gmshInFile.vtkVectorSize("vtkCellDataType_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataType_")); i++)
|
||||
{
|
||||
rDebug("vtkCellDataType_ %s", (gmshInFile.vtkVector("vtkCellDataType_",i)).c_str());
|
||||
}
|
||||
// Write all vtkCellsName_ to the screen.
|
||||
rDebug("size of vtkCellDataName_: %d", gmshInFile.vtkVectorSize("vtkCellDataName_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataName_")); i++)
|
||||
{
|
||||
rDebug("vtkCellDataName_ %s", (gmshInFile.vtkVector("vtkCellDataName_",i)).c_str());
|
||||
}
|
||||
// Write all vtkCellsFormat_ to the screen.
|
||||
rDebug("size of vtkCellDataFormat_: %d", gmshInFile.vtkVectorSize("vtkCellDataFormat_"));
|
||||
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataFormat_")); i++)
|
||||
{
|
||||
rDebug("vtkCellDataFormat_ %s", (gmshInFile.vtkVector("vtkCellDataFormat_",i)).c_str());
|
||||
}
|
||||
*/
|
||||
|
||||
// cout <<"\n\n" <<gmshInFile.getUg PointsN()<< "\n\n";
|
||||
|
||||
// int i = gmshInFile.openVtk();
|
||||
//vtk* vtkPt;
|
||||
//vtkPt = &gmshInFile;
|
||||
//vtkPt->vtkVersion();
|
||||
|
||||
//gmshInFile.vtkVersion();
|
||||
|
||||
// This vector is used in loops to transport datas from vtk to ristream.
|
||||
vector<double> dataVector1;
|
||||
/*
|
||||
// Scaling factor for the vtk input data.
|
||||
double scale = 15.0;
|
||||
ristream rib;
|
||||
// Set the filname of the .rib file.
|
||||
rib.RibsFile(ribOutputFile);
|
||||
rib.openRibs();
|
||||
rib.RibsFormat(1024,768);
|
||||
rib.RibsLightSource("distantlight");
|
||||
rib.RibsProjection("perspective");
|
||||
//rib.RibsProjection("orthographic");
|
||||
|
||||
// Give the center or the rotation.
|
||||
double rotCenterX = 0.0;
|
||||
double rotCenterY = 0.0;
|
||||
double rotRadius = 1.6;
|
||||
double cameraPosX = sqrt(3.92); // Only the camera postion if nLoop = 1;
|
||||
double cameraPosY = 0;
|
||||
cameraPosX = 1; // Only the camera postion if nLoop = 1;
|
||||
cameraPosY = -1;
|
||||
|
||||
char filename[20];
|
||||
|
||||
const int nLoop = 1;
|
||||
for(int i = 0; i<nLoop; i++)
|
||||
{
|
||||
if (nLoop > 1)
|
||||
{
|
||||
cameraPosX = -rotRadius*cos(2*PI*i/(double)nLoop) + rotCenterX;
|
||||
cameraPosY = -rotRadius*sin(2*PI*i/(double)nLoop) + rotCenterY;
|
||||
}
|
||||
|
||||
rib.RibsFrameBegin();
|
||||
// Set the file name for the renderer output image.
|
||||
string tempstring = "";
|
||||
tempstring = "tests/movie_data/Hallo";
|
||||
//tempstring.append("%d.tiff",i);
|
||||
//tempstring.append((string)i);
|
||||
tempstring.append(".tiff");
|
||||
//sprintf ( tempchar ,"tests/movie_data/Hallo%d.tiff",i );
|
||||
// rib.RibsFrameFilename("");
|
||||
rib.RibsDisplay(frameName);
|
||||
|
||||
rDebug(tempstring.c_str());
|
||||
|
||||
// Camera Position and orientation:
|
||||
// The default camera postion is the world coordinate origin and it
|
||||
// looks in the -z-direction.
|
||||
|
||||
// The function RibsPlaceCamera set the position of the camera in world
|
||||
// coordinates and the point, where to look at in world coordinates.
|
||||
// To get a skew view, you can roll the camera.
|
||||
// This function must be called befor RibsWorldBegin!
|
||||
rib.RibsPlaceCamera(1.5*cameraPosX, 1.5*cameraPosY, 2.0, // position
|
||||
0.0, 0.0, 1.2, // look-at point
|
||||
0.0) ; // roll angle (in degree)
|
||||
|
||||
rib.RibsWorldBegin();
|
||||
rib.RibsSurface("plastic");
|
||||
rib.RibsCoordinateSystem();
|
||||
|
||||
//Write all vktCells_ with cell types and cell points on the screen.
|
||||
//rDebug("getVtkCellTypesN(): %d", gmshInFile.getVtkCellTypesN());
|
||||
for (int i = 0; i<(gmshInFile.getVtkCellTypesN()); i++)
|
||||
{
|
||||
// Look if there is a thetrahedron.
|
||||
if (gmshInFile.getVtkCellType(i) == 10)
|
||||
{
|
||||
// Clear the data structur to save the point cooridnates temporal.
|
||||
dataVector1.clear();
|
||||
|
||||
// Read the points of a tetrahedron.
|
||||
//rDebug("getVtkCellPointN(%d): %d", i, gmshInFile.getVtkCellPointN(i));
|
||||
for (int j = 0; j<(gmshInFile.getVtkCellPointN(i)); j++)
|
||||
{
|
||||
int tempInt = gmshInFile.getVtkCellPoint(i,j);
|
||||
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 0));
|
||||
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 1));
|
||||
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 2));
|
||||
//rDebug("vtkPoint: %d, %f %f %f", tempInt,
|
||||
// gmshInFile.getVtkVec(tempInt, 0),
|
||||
// gmshInFile.getVtkVec(tempInt, 1),
|
||||
// gmshInFile.getVtkVec(tempInt, 2));
|
||||
|
||||
}
|
||||
rib.RibsColor(0.0,0,1.0,1.0);
|
||||
rib.RibsTetrahedron(scale*dataVector1[0], scale*dataVector1[1], scale*dataVector1[2],
|
||||
scale*dataVector1[3], scale*dataVector1[4], scale*dataVector1[5],
|
||||
scale*dataVector1[6], scale*dataVector1[7], scale*dataVector1[8],
|
||||
scale*dataVector1[9], scale*dataVector1[10],scale*dataVector1[11],
|
||||
0.8);
|
||||
}
|
||||
}
|
||||
*/
|
||||
/*
|
||||
rib.RibsColor(1.0,0,0,0.6);
|
||||
rib.RibsTetrahedron(0.3, 0.3, 0.0,
|
||||
2.0, 0.3, 0.0,
|
||||
0.3, 2.0, 0.0,
|
||||
0.3, 0.3, 0.5,
|
||||
1.0);
|
||||
rib.RibsColor(0,1.0,0,0.7);
|
||||
rib.RibsTetrahedron(0.3, 0.3, 0.0,
|
||||
2.0, 0.3, 0.0,
|
||||
0.3, 2.0, 0.0,
|
||||
0.3, 0.3, 0.5,
|
||||
0.6);
|
||||
|
||||
rib.RibsColor(0.0,0,1.0,1.0);
|
||||
rib.RibsTetrahedron(0.3, 0.3, 0.0,
|
||||
2.0, 0.3, 0.0,
|
||||
0.3, 2.0, 0.0,
|
||||
0.3, 0.3, 0.5,
|
||||
0.3);
|
||||
*/
|
||||
// rib,RibsAxes();
|
||||
// rib.RibsVector(0,0,0,0.5);
|
||||
/*
|
||||
rib.RibsWorldEnd();
|
||||
rib.RibsFrameEnd();
|
||||
}
|
||||
rib.closeRibs();
|
||||
*/
|
||||
// return(0);
|
||||
}
|
||||
|
||||
@@ -0,0 +1,69 @@
|
||||
// rights - 2006-, copyright benedikt oswald and patrick leidenberger, all rights reserved
|
||||
// project - phidias3d
|
||||
// file name - phidias3d.h
|
||||
// file type - c++ header file
|
||||
// objective - header file for the phidias3d visualization postprocessor
|
||||
// modified - 2006 jun 26, creation, benedikt oswald
|
||||
// modified - 2006 jun 28,
|
||||
// modified - 2006 jul 30, Add include for command line argument parser
|
||||
// with boost::program_options, pl.
|
||||
// inheritance -
|
||||
// feature - implements the phidias3d visualization postprocessor; the features
|
||||
// feature - will be (1) read VTK legacy formatted files (2) read HDF5/ELECTROMAGNETIC
|
||||
// feature - structures files (3) export VTK legacy formatted files (4) export
|
||||
// feature - data, both meshes and fields, throught the Renderman Interface
|
||||
// feature - routines.
|
||||
// required software -
|
||||
|
||||
|
||||
/* 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 <ristream.h>
|
||||
#include <gmsh.hh>
|
||||
|
||||
// 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
|
||||
|
||||
|
||||
|
||||
#ifndef PHIDIAS3D_H_
|
||||
#define PHIDIAS3D_H_
|
||||
|
||||
using namespace physicomath;
|
||||
using namespace nonsciconst;
|
||||
using namespace gmshtohdf5fed;
|
||||
|
||||
|
||||
|
||||
#endif /*PHIDIAS3D_H_*/
|
||||
@@ -0,0 +1,26 @@
|
||||
## Makefile.am -- process this file with automake to produce Makefile.in
|
||||
##
|
||||
## authors - benedikt oswald and patrick leidenberger
|
||||
## 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.
|
||||
#
|
||||
## objective - automake input file for the gmsh directory
|
||||
## project - gmsh2h5fed
|
||||
|
||||
noinst_PROGRAMS = gmsh2h5fed
|
||||
|
||||
gmsh2h5fed_SOURCES = gmsh2h5fed.cc
|
||||
gmsh2h5fed_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h \
|
||||
../libsrc/stdincl/physicomath.h \
|
||||
../libsrc/gmsh/gmsh.hh \
|
||||
../libsrc/gmsh/gmsh.cc \
|
||||
../libsrc/gmsh/gmshconst.hh \
|
||||
../libsrc/gmsh/gmshgrammar.hh \
|
||||
../libsrc/gmsh/gmshsemanticaction.hh \
|
||||
../libsrc/h5fed/h5fed.hh \
|
||||
../libsrc/h5fed/h5fed.cc
|
||||
|
||||
gmsh2h5fed_LDADD = @GMSH2H5FED_LIBS@
|
||||
|
||||
#AM_CPPFLAGS = @AM_CPPFLAGS@
|
||||
Executable
+10
@@ -0,0 +1,10 @@
|
||||
libtoolize -f && \
|
||||
aclocal && \
|
||||
autoconf && \
|
||||
autoheader && \
|
||||
automake --add-missing && \
|
||||
CC='mpicc' F9X='mpif90' CXX='mpiCC' ./configure --with-rlog=$HOME/extlib/rlog-1.3.7 --with-boost='' --with-hdf5=$HOME/extlib/hdf5-1.6.5 &&\
|
||||
make clean && \
|
||||
make all
|
||||
|
||||
|
||||
@@ -0,0 +1,106 @@
|
||||
## Process this file with autoconf to produce a configure script
|
||||
##
|
||||
## author - benedikt oswald and patrick leidenberger
|
||||
## modified - 2006 aug 21, pl, creation.
|
||||
## modified - 2006 aug 24, pl, add h5fed path.
|
||||
##
|
||||
## to do : The rlog lib needs a -DRLOG_COMPONENT="some name", I don't know
|
||||
## how tho do this so that the quotation marks are in the output
|
||||
## stream as well, pl, 2006 jul 04.
|
||||
##
|
||||
## objective - develop input file for GNU autotools/configure
|
||||
## project - H5Fed
|
||||
##
|
||||
|
||||
AC_PREREQ(2.59)
|
||||
AC_COPYRIGHT([This configure script is copyright by Benedikt Oswald and Patrick Leidenberger, 2006])
|
||||
|
||||
AC_INIT([gmshtohdf5fed], [1.0], [in case of problems mail to: benedikt.oswald@psi.ch or patrick.leidenberger@psi.ch])
|
||||
|
||||
# library creation
|
||||
AC_PROG_LIBTOOL
|
||||
|
||||
# standard macros
|
||||
AC_CONFIG_AUX_DIR(./)
|
||||
AM_INIT_AUTOMAKE
|
||||
AC_CONFIG_HEADER([./config.h:./config.in])
|
||||
|
||||
# set cppflags to zero
|
||||
CPPFLAGS=""
|
||||
CFFLAGS=""
|
||||
CXXFLAGS=""
|
||||
|
||||
# provide include directories
|
||||
AC_SUBST([AM_CPPFLAGS], '-I$(top_srcdir)/libsrc/stdincl -I$(top_srcdir)/libsrc/gmsh -I$(top_srcdir)/libsrc/h5fed')
|
||||
AC_SUBST([GMSH2H5FED_LIBS],'$(top_srcdir)/libsrc/gmsh/libgmsh.la $(top_srcdir)/libsrc/h5fed/libh5fed.la')
|
||||
|
||||
# Make available external libraries
|
||||
AC_ARG_WITH(boost,
|
||||
AC_HELP_STRING([--with-boost=PREFIX],
|
||||
[prefix where the Boost libraries and include files are to be found]),
|
||||
[BOOST_PREFIX=$withval
|
||||
LDFLAGS="-lz -lboost_program_options "])
|
||||
|
||||
AC_ARG_WITH(rlog,
|
||||
AC_HELP_STRING([--with-rlog=PREFIX],
|
||||
[prefix where the rlog libraries and include files are to be found]),
|
||||
[RLOG_PREFIX=$withval
|
||||
CPPFLAGS="-I"$RLOG_PREFIX"/include "${CPPFLAGS}
|
||||
LDFLAGS=$RLOG_PREFIX"/lib/librlog.la "${LDFLAGS}])
|
||||
|
||||
AC_ARG_ENABLE(rlog-debug,
|
||||
AC_HELP_STRING([--disable-rlog-debug],
|
||||
[disable the debug output channel of rlog]),
|
||||
[],
|
||||
[CFFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CFFLAGS}
|
||||
CXXFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CXXFLAGS}])
|
||||
|
||||
AC_ARG_ENABLE(rlog-error,
|
||||
AC_HELP_STRING([--disable-rlog-error],
|
||||
[disable the error output channel of rlog]),
|
||||
[],
|
||||
[CFFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CFFLAGS}
|
||||
CXXFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CXXFLAGS}])
|
||||
|
||||
AC_ARG_ENABLE(rlog-info,
|
||||
AC_HELP_STRING([--disable-rlog-info],
|
||||
[disable the info output channel of rlog]),
|
||||
[],
|
||||
[CFFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CFFLAGS}
|
||||
CXXFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CXXFLAGS}])
|
||||
|
||||
AC_ARG_ENABLE(rlog-warning,
|
||||
AC_HELP_STRING([--disable-rlog-warning],
|
||||
[disable the warning output channel of rlog]),
|
||||
[],
|
||||
[CFFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CFFLAGS}
|
||||
CXXFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CXXFLAGS}])
|
||||
|
||||
AC_ARG_WITH(hdf5,
|
||||
AC_HELP_STRING([--with-hdf5=PREFIX],
|
||||
[prefix to hdf5 libraries and include files]),
|
||||
[HDF5_PREFIX=$withval
|
||||
CPPFLAGS="-DHAVE_HDF5 -I"$HDF5_PREFIX"/include "${CPPFLAGS}
|
||||
LDFLAGS="-L"$HDF5_PREFIX"/lib -lhdf5 "${LDFLAGS}])
|
||||
# LDFLAGS=$HDF5_PREFIX"/lib/libhdf5.la "${LDFLAGS}])
|
||||
|
||||
|
||||
# Set C/C++ compiler flags.
|
||||
CPPFLAGS=${CPPFLAGS}
|
||||
CFFLAGS="-g3 "${CFFLAGS}
|
||||
CXXFLAGS="-g3 "${CXXFLAGS}
|
||||
|
||||
AM_INIT_AUTOMAKE([1.9 foreign])
|
||||
|
||||
AC_PROG_CC
|
||||
AC_PROG_MAKE_SET
|
||||
AC_PROG_INSTALL([install])
|
||||
|
||||
AC_CONFIG_FILES([makefile
|
||||
applications/makefile
|
||||
libsrc/makefile
|
||||
libsrc/gmsh/makefile
|
||||
libsrc/h5fed/makefile])
|
||||
|
||||
|
||||
AC_OUTPUT
|
||||
@@ -0,0 +1,114 @@
|
||||
// rights - 2002-2005, benedikt oswald,
|
||||
// project - aq
|
||||
// file name - cube0.geo
|
||||
// file type - GMSH script file
|
||||
// objective - model cube fundamental cube
|
||||
// modified - 2005 jan 25, benedikt oswald, creation
|
||||
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
|
||||
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
|
||||
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
|
||||
// modified - 2005 mar 22, benedikt oswald, adapted to model fundamental cube
|
||||
// inheritance -
|
||||
// feature - models fundamental cube, used for benchmark calculations of a Hertzian dipole
|
||||
// feature - radiating into free space; the model uses standard physical domain tags;
|
||||
|
||||
|
||||
// 1 modeling constants
|
||||
|
||||
lcl1=0.50; // characteristic length in fractions of lambda@1 GHz for air domain
|
||||
lcl2=0.50; // characteristic length in fractions of lambda@1 GHz for air domain
|
||||
|
||||
lambda=0.30; // wavelength of electromagntic wave at a frequency of 1 GHz
|
||||
|
||||
lx=2.0; // x dim of computational domain
|
||||
ly=2.0; // y dim of computational domain
|
||||
lz=2.0; // z dim of computational domain
|
||||
|
||||
cx=0.5*lx; // calculate center of computational domain
|
||||
cy=0.5*ly; // calculate center of computational domain
|
||||
cz=0.5*lz; // calculate center of computational domain
|
||||
|
||||
|
||||
// 1.2 Define physical material domains
|
||||
|
||||
vacuum=609; // physical entity vacuum
|
||||
air=709; // physical entity air
|
||||
subsurface=809; // physical entity subsurface
|
||||
pml=1301; // physical entity pml material
|
||||
icelens=4001; // physical entity icelens
|
||||
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
|
||||
interelement_bnd=12702; // interior boundary, separating different material domains
|
||||
|
||||
|
||||
|
||||
// 2 Define cubes
|
||||
// 2.1.1 Define points of cube
|
||||
|
||||
p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcl1};
|
||||
p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcl1};
|
||||
p2=newp; Point(p2) = { lx, ly, 0.0, lambda * lcl1};
|
||||
p3=newp; Point(p3) = {0.0, ly, 0.0, lambda * lcl1};
|
||||
p4=newp; Point(p4) = {0.0, 0.0, lz, lambda * lcl1};
|
||||
p5=newp; Point(p5) = { lx, 0.0, lz, lambda * lcl1};
|
||||
p6=newp; Point(p6) = { lx, ly, lz, lambda * lcl1};
|
||||
p7=newp; Point(p7) = {0.0, ly, lz, lambda * lcl1};
|
||||
|
||||
// 2.1.3 Define lines of cube
|
||||
|
||||
// lower xy plane
|
||||
li0=newl; Line(li0) = {p0,p1};
|
||||
li1=newl; Line(li1) = {p1,p2};
|
||||
li2=newl; Line(li2) = {p2,p3};
|
||||
li3=newl; Line(li3) = {p3,p0};
|
||||
|
||||
// upper xy plane
|
||||
li4=newl; Line(li4) = {p4,p5};
|
||||
li5=newl; Line(li5) = {p5,p6};
|
||||
li6=newl; Line(li6) = {p6,p7};
|
||||
li7=newl; Line(li7) = {p7,p4};
|
||||
|
||||
// vertical lines
|
||||
li8=newl; Line(li8) = {p0,p4};
|
||||
li9=newl; Line(li9) = {p1,p5};
|
||||
li10=newl; Line(li10) = {p2,p6};
|
||||
li11=newl; Line(li11) = {p3,p7};
|
||||
|
||||
|
||||
// 2.1.5 Define line 6 line loops for the 6 faces of the cube
|
||||
|
||||
lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
|
||||
lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
|
||||
|
||||
lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
|
||||
lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
|
||||
|
||||
lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
|
||||
lloop5= newreg; Line Loop(lloop5) = { li3, li8, -li7, -li11};
|
||||
|
||||
|
||||
// 2.1.7 define plane surfaces for the cube
|
||||
|
||||
s0=news; Plane Surface(s0) = {lloop0};
|
||||
s1=news; Plane Surface(s1) = {lloop1};
|
||||
s2=news; Plane Surface(s2) = {lloop2};
|
||||
s3=news; Plane Surface(s3) = {lloop3};
|
||||
s4=news; Plane Surface(s4) = {lloop4};
|
||||
s5=news; Plane Surface(s5) = {lloop5};
|
||||
|
||||
|
||||
// 2.1.9 Define surface loops required for volume definition of the cube
|
||||
|
||||
sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
|
||||
|
||||
// 2.1.10 Define volume of the cube
|
||||
|
||||
v0=newv; Volume(v0) = {sloop0};
|
||||
|
||||
// 3.0 define physical entitites
|
||||
|
||||
Physical Point(vacuum_background_bnd) = {p0:p7};
|
||||
Physical Line(vacuum_background_bnd) = {li0:li11};
|
||||
Physical Surface(vacuum_background_bnd) = {s0:s5};
|
||||
Physical Volume(air) = {v0};
|
||||
|
||||
|
||||
+21463
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,206 @@
|
||||
// rights - 2002-2005, benedikt oswald,
|
||||
// project - aq
|
||||
// file name - cubeincube.geo
|
||||
// file type - GMSH script file
|
||||
// objective - model cube in a cube mesh, useful for PML booundary conditions
|
||||
// modified - 2005 jan 25, benedikt oswald, creation
|
||||
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
|
||||
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
|
||||
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
|
||||
// inheritance -
|
||||
// feature - models a cube in a cube mesh, useful for PML booundary conditions;
|
||||
// feature - the PML boundary model is based on a 3D region with special electromagnetic
|
||||
// feature - material properties which guarantee, in theory, perfect absorption of incident
|
||||
// feature - electromagnetic waves independent of the angle between the wave vector
|
||||
// feature - and the boundary; in order to model the PML material domain a separate mesh
|
||||
// feature - region is created so that there is a clean boundary between the PML and
|
||||
// feature - and the air region.
|
||||
|
||||
|
||||
// 1 modeling constants
|
||||
|
||||
lcair=0.90; // characteristic length in fractions of lambda@1 GHz for air domain
|
||||
lcpml=0.70; // characteristic length in fractions of lambda@1 GHz for PML region
|
||||
lambda=0.30; // wavelength of electromagntic wave at a frequency of 1 GHz
|
||||
|
||||
lx=1.0; // x dim of computational domain
|
||||
ly=1.0; // y dim of computational domain
|
||||
lz=1.0; // z dim of computational domain
|
||||
|
||||
cx=0.5*lx; // calculate center of computational domain
|
||||
cy=0.5*ly; // calculate center of computational domain
|
||||
cz=0.5*lz; // calculate center of computational domain
|
||||
|
||||
lpmlxl=0.1; // thickness of PML region
|
||||
lpmlxh=0.1; // thickness of PML region
|
||||
|
||||
lpmlyl=0.1; // thickness of PML region
|
||||
lpmlyh=0.1; // thickness of PML region
|
||||
|
||||
lpmlzl=0.1; // thickness of PML region
|
||||
lpmlzh=0.1; // thickness of PML region
|
||||
|
||||
xminic=lpmlxl; // x min of inner cube
|
||||
xmaxic=lx-lpmlxh; // x max of inner cube
|
||||
yminic=lpmlyl; // y min of inner cube
|
||||
ymaxic=ly-lpmlyh; // y max of inner cube
|
||||
zminic=lpmlzl; // z min of inner cube
|
||||
zmaxic=lz-lpmlzh; // z max of inner cube
|
||||
|
||||
// 1.2 Define physical material domains
|
||||
|
||||
vacuum=609; // physical entity vacuum
|
||||
air=709; // physical entity air
|
||||
pml=1301; // physical entity pml material
|
||||
icelens=4001; // physical entity icelens
|
||||
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
|
||||
interelement_bnd=12702; // interior boundary, separating different material domains
|
||||
|
||||
|
||||
|
||||
// 2 Define cubes
|
||||
// 2.1.1 Define points of outer cube
|
||||
|
||||
p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcpml};
|
||||
p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcpml};
|
||||
p2=newp; Point(p2) = { lx, ly, 0.0, lambda * lcpml};
|
||||
p3=newp; Point(p3) = {0.0, ly, 0.0, lambda * lcpml};
|
||||
p4=newp; Point(p4) = {0.0, 0.0, lz, lambda * lcpml};
|
||||
p5=newp; Point(p5) = { lx, 0.0, lz, lambda * lcpml};
|
||||
p6=newp; Point(p6) = { lx, ly, lz, lambda * lcpml};
|
||||
p7=newp; Point(p7) = {0.0, ly, lz, lambda * lcpml};
|
||||
|
||||
// 2.1.2 Define points of inner cube
|
||||
|
||||
p100=newp; Point(p100) = {xminic, yminic, zminic, lambda * lcair};
|
||||
p101=newp; Point(p101) = {xmaxic, yminic, zminic, lambda * lcair};
|
||||
p102=newp; Point(p102) = {xmaxic, ymaxic, zminic, lambda * lcair};
|
||||
p103=newp; Point(p103) = {xminic, ymaxic, zminic, lambda * lcair};
|
||||
|
||||
p104=newp; Point(p104) = {xminic, yminic, zmaxic, lambda * lcair};
|
||||
p105=newp; Point(p105) = {xmaxic, yminic, zmaxic, lambda * lcair};
|
||||
p106=newp; Point(p106) = {xmaxic, ymaxic, zmaxic, lambda * lcair};
|
||||
p107=newp; Point(p107) = {xminic, ymaxic, zmaxic, lambda * lcair};
|
||||
|
||||
|
||||
// 2.1.3 Define lines of outer cube
|
||||
|
||||
// lower xy plane
|
||||
li0=newl; Line(li0) = {p0,p1};
|
||||
li1=newl; Line(li1) = {p1,p2};
|
||||
li2=newl; Line(li2) = {p2,p3};
|
||||
li3=newl; Line(li3) = {p3,p0};
|
||||
|
||||
// upper xy plane
|
||||
li4=newl; Line(li4) = {p4,p5};
|
||||
li5=newl; Line(li5) = {p5,p6};
|
||||
li6=newl; Line(li6) = {p6,p7};
|
||||
li7=newl; Line(li7) = {p7,p4};
|
||||
|
||||
// vertical lines
|
||||
li8=newl; Line(li8) = {p0,p4};
|
||||
li9=newl; Line(li9) = {p1,p5};
|
||||
li10=newl; Line(li10) = {p2,p6};
|
||||
li11=newl; Line(li11) = {p3,p7};
|
||||
|
||||
// 2.1.4 Define lines of outer cube
|
||||
|
||||
// lower xy plane
|
||||
li100=newl; Line(li100) = {p100,p101};
|
||||
li101=newl; Line(li101) = {p101,p102};
|
||||
li102=newl; Line(li102) = {p102,p103};
|
||||
li103=newl; Line(li103) = {p103,p100};
|
||||
|
||||
// upper xy plane
|
||||
li104=newl; Line(li104) = {p104,p105};
|
||||
li105=newl; Line(li105) = {p105,p106};
|
||||
li106=newl; Line(li106) = {p106,p107};
|
||||
li107=newl; Line(li107) = {p107,p104};
|
||||
|
||||
// vertical lines
|
||||
li108=newl; Line(li108) = {p100,p104};
|
||||
li109=newl; Line(li109) = {p101,p105};
|
||||
li110=newl; Line(li110) = {p102,p106};
|
||||
li111=newl; Line(li111) = {p103,p107};
|
||||
|
||||
|
||||
// 2.1.5 Define line 6 line loops for the 6 faces of outer cube
|
||||
|
||||
lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
|
||||
lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
|
||||
|
||||
lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
|
||||
lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
|
||||
|
||||
lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
|
||||
lloop5= newreg; Line Loop(lloop5) = { li3, li8, -li7, -li11};
|
||||
|
||||
|
||||
// 2.1.6 Define line 6 line loops for the 6 faces of inner cube
|
||||
|
||||
lloop100= newreg; Line Loop(lloop100) = { li100, li101, li102, li103};
|
||||
lloop101= newreg; Line Loop(lloop101) = { li104, li105, li106, li107};
|
||||
|
||||
lloop102= newreg; Line Loop(lloop102) = { li100, li109, -li104, -li108 };
|
||||
lloop103= newreg; Line Loop(lloop103) = { li101, li110, -li105, -li109};
|
||||
|
||||
lloop104= newreg; Line Loop(lloop104) = { li102, li111, -li106, -li110};
|
||||
lloop105= newreg; Line Loop(lloop105) = { li103, li108, -li107, -li111};
|
||||
|
||||
|
||||
// 2.1.7 define plane surfaces for outer cube
|
||||
|
||||
s0=news; Plane Surface(s0) = {lloop0};
|
||||
s1=news; Plane Surface(s1) = {lloop1};
|
||||
s2=news; Plane Surface(s2) = {lloop2};
|
||||
s3=news; Plane Surface(s3) = {lloop3};
|
||||
s4=news; Plane Surface(s4) = {lloop4};
|
||||
s5=news; Plane Surface(s5) = {lloop5};
|
||||
|
||||
// 2.1.8 define plane surfaces for inner cube
|
||||
|
||||
s100=news; Plane Surface(s100) = {lloop100};
|
||||
s101=news; Plane Surface(s101) = {lloop101};
|
||||
s102=news; Plane Surface(s102) = {lloop102};
|
||||
s103=news; Plane Surface(s103) = {lloop103};
|
||||
s104=news; Plane Surface(s104) = {lloop104};
|
||||
s105=news; Plane Surface(s105) = {lloop105};
|
||||
|
||||
|
||||
// 2.1.9 Define surface loops required for volume definition of outer cube
|
||||
|
||||
sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
|
||||
|
||||
|
||||
// 2.1.9 Define surface loops required for volume definition of inner cube
|
||||
|
||||
sloop100=newreg; Surface Loop(sloop100) ={s100,s101,s102,s103,s104,s105};
|
||||
|
||||
|
||||
// 2.1.10 Define volume of outer cube
|
||||
|
||||
v0=newv; Volume(v0) = {sloop0,sloop100};
|
||||
|
||||
|
||||
// 2.1.11 Define volume of inner cube
|
||||
|
||||
v100=newv; Volume(v100) = {sloop100};
|
||||
|
||||
|
||||
// 3.0 define physical entitites
|
||||
|
||||
Physical Point(vacuum_background_bnd) = {p0,p1,p2,p3,p4,p5,p6,p7};
|
||||
Physical Line(vacuum_background_bnd) = {li0,li1,li2,li3,li4,li5,li6,li7,li8,li9,li10,li11};
|
||||
//Physical Line Loop(vacuum_background_bnd) = {lloop0,lloop1,lloop2,lloop3,lloop4,lloop5};
|
||||
Physical Surface(vacuum_background_bnd) = {s0,s1,s2,s3,s4,s5};
|
||||
//Physical Surface Loop(vacuum_background_bnd) = {sloop0};
|
||||
Physical Volume(pml) = {v0};
|
||||
|
||||
Physical Point(interelement_bnd) = {p100,p101,p102,p103,p104,p105,p106,p107};
|
||||
Physical Line(interelement_bnd) = {li100,li101,li102,li103,li104,li105,li106,li107,li108,li109,li110,li111};
|
||||
//Physical Line Loop(interelement_bnd) = {lloop100,lloop101,lloop102,lloop103,lloop104,lloop105};
|
||||
Physical Surface(interelement_bnd) = {s100,s101,s102,s103,s104,s105};
|
||||
//Physical Surface Loop(interelement_bnd) = {sloop100};
|
||||
Physical Volume(air) = {v100};
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,135 @@
|
||||
// rights - 2002-2005, benedikt oswald,
|
||||
// project - aq
|
||||
// file name - sphere.geo
|
||||
// file type - GMSH script file
|
||||
// objective - model cube in a cube, 2 spherical objects mesh to investigate sub lambda resolution capability
|
||||
// modified - 2005 jan 25, benedikt oswald, creation
|
||||
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
|
||||
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
|
||||
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
|
||||
// modified - 2005 mar 09, benedikt oswald, adapted to cube in cube and spherical particle configuration
|
||||
// modified - 2005 mar 11, benedikt oswald, adapted to investigation of sub-lambda resolution capability
|
||||
// modified - 2005 mar 22, benedikt oswald, adapted to be based on reference background medium subLambda310.geo
|
||||
// modified - 2005 mar 23, benedikt oswald, adapted to model a microresonator geometry
|
||||
// modified - 2005 mar 29, benedikt oswald, adapted to model a high quality sphere for a Hertzian dipole benchmark
|
||||
// modified - 2005
|
||||
// inheritance -
|
||||
// feature - models a microresonator geometry; a dielectric sphere within an air sphere; the dielectric
|
||||
// feature - sphere will be excited by a Hertzian dipole in the vicinity of the sphere;
|
||||
// feature -
|
||||
|
||||
|
||||
// 1 modeling constants
|
||||
|
||||
lcair=1.20; // characteristic length in fractions of lambda@1 GHz for air domain
|
||||
lcsubsurface=1.20; // characteristic length in fractions of lambda@1 GHz for subsurface domain
|
||||
lcil1=0.80; // characteristic length in fractions of lambda@1 GHz for icelens region
|
||||
lcil2=0.40; // characteristic length in fractions of lambda@1 GHz for icelens 2 region
|
||||
lambda=3.0e-1; // wavelength of electromagntic wave at a frequency of 1 GHz
|
||||
|
||||
lx=3.0; // x dim of computational domain
|
||||
ly=3.0; // y dim of computational domain
|
||||
lz=2.0; // z dim of computational domain
|
||||
|
||||
cx=0.5*lx; // calculate center of computational domain
|
||||
cy=0.5*ly; // calculate center of computational domain
|
||||
cz=0.5*lz; // calculate center of computational domain
|
||||
|
||||
dxl=0.3; // thickness of PML region
|
||||
dxh=0.3; // thickness of PML region
|
||||
|
||||
dyl=0.3; // thickness of PML region
|
||||
dyh=0.3; // thickness of PML region
|
||||
|
||||
dzl=0.30; // thickness of PML region
|
||||
dzh=0.60; // thickness of PML region
|
||||
|
||||
xminic=dxl; // x min of inner cube
|
||||
xmaxic=lx-dxh; // x max of inner cube
|
||||
yminic=dyl; // y min of inner cube
|
||||
ymaxic=ly-dyh; // y max of inner cube
|
||||
zminic=dzl; // z min of inner cube
|
||||
zmaxic=lz-dzh; // z max of inner cube
|
||||
|
||||
dsx=0.10; // x distance separating the two spherical scatterers
|
||||
dsy=0.00; // y distance separating the two spherical scatterers
|
||||
dsz=0.00; // z distance separating the two spherical scatterers
|
||||
|
||||
r1=1.0; // radius of air sphere
|
||||
ilcx=0.0; // x center of air sphere
|
||||
ilcy=0.0; // y center of
|
||||
ilcz=0.0; // z center of
|
||||
|
||||
r2=2.0e-6; // radius of dielectric sphere
|
||||
il2cx=0.0; // x center of dielectric sphere
|
||||
il2cy=0.0; // y center of dielectric sphere
|
||||
il2cz=0.0; // z center of dielectric sphere
|
||||
|
||||
|
||||
// 1.2 Define physical material domains
|
||||
|
||||
vacuum=609; // physical entity vacuum
|
||||
air=709; // physical entity air
|
||||
subsurface=809; // physical entity subsurface
|
||||
pml=1301; // physical entity pml material
|
||||
icelens1=4001; // physical entity icelens
|
||||
icelens2=4003; // physical entity icelens 2
|
||||
dielsphere=4005; // physical entity dielectric sphere
|
||||
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
|
||||
air_soil_bnd=12702; // interior boundary, separating air and subsurface material
|
||||
soil_icelens1_bnd=12703; // interior boundary, separating background subsurface from icelens particle
|
||||
soil_icelens2_bnd=12705; // interior boundary, separating background subsurface from icelens 2 particle
|
||||
dielectric_sphere_bnd=12707; // interior boundary, separting air background from dielectric sphere
|
||||
|
||||
|
||||
// 2.2.1 Define air sphere 1
|
||||
|
||||
ilp1 = newp; Point(ilp1) = {ilcx, ilcy, ilcz, lcil1 * lambda} ;
|
||||
ilp2 = newp; Point(ilp2) = {ilcx+r1, ilcy, ilcz, lcil1 * lambda} ;
|
||||
ilp3 = newp; Point(ilp3) = {ilcx, ilcy+r1, ilcz, lcil1 * lambda} ;
|
||||
ilp4 = newp; Point(ilp4) = {ilcx, ilcy, ilcz+r1, lcil1 * lambda} ;
|
||||
ilp5 = newp; Point(ilp5) = {ilcx-r1, ilcy, ilcz, lcil1 * lambda} ;
|
||||
ilp6 = newp; Point(ilp6) = {ilcx, ilcy-r1, ilcz, lcil1 * lambda} ;
|
||||
ilp7 = newp; Point(ilp7) = {ilcx, ilcy, ilcz-r1, lcil1 * lambda} ;
|
||||
|
||||
ilc1 = newreg; Circle(ilc1) = {ilp2,ilp1,ilp7};
|
||||
ilc2 = newreg; Circle(ilc2) = {ilp7,ilp1,ilp5};
|
||||
ilc3 = newreg; Circle(ilc3) = {ilp5,ilp1,ilp4};
|
||||
ilc4 = newreg; Circle(ilc4) = {ilp4,ilp1,ilp2};
|
||||
ilc5 = newreg; Circle(ilc5) = {ilp2,ilp1,ilp3};
|
||||
ilc6 = newreg; Circle(ilc6) = {ilp3,ilp1,ilp5};
|
||||
ilc7 = newreg; Circle(ilc7) = {ilp5,ilp1,ilp6};
|
||||
ilc8 = newreg; Circle(ilc8) = {ilp6,ilp1,ilp2};
|
||||
ilc9 = newreg; Circle(ilc9) = {ilp7,ilp1,ilp3};
|
||||
ilc10 = newreg; Circle(ilc10) = {ilp3,ilp1,ilp4};
|
||||
ilc11 = newreg; Circle(ilc11) = {ilp4,ilp1,ilp6};
|
||||
ilc12 = newreg; Circle(ilc12) = {ilp6,ilp1,ilp7};
|
||||
|
||||
// We need non-plane surfaces to define the spherical icelens:
|
||||
// here we use ruled surfaces, which can have 3 or 4
|
||||
// sides:
|
||||
|
||||
ill1 = newreg; Line Loop(ill1) = {ilc5,ilc10,ilc4}; ilruls1=newreg; Ruled Surface(ilruls1) = {ill1};
|
||||
ill2 = newreg; Line Loop(ill2) = {ilc9,-ilc5,ilc1}; ilruls2=newreg; Ruled Surface(ilruls2) = {ill2};
|
||||
ill3 = newreg; Line Loop(ill3) = {ilc12,-ilc8,-ilc1}; ilruls3=newreg; Ruled Surface(ilruls3) = {ill3};
|
||||
ill4 = newreg; Line Loop(ill4) = {ilc8,-ilc4,ilc11}; ilruls4=newreg; Ruled Surface(ilruls4) = {ill4};
|
||||
ill5 = newreg; Line Loop(ill5) = {-ilc10,ilc6,ilc3}; ilruls5=newreg; Ruled Surface(ilruls5) = {ill5};
|
||||
ill6 = newreg; Line Loop(ill6) = {-ilc11,-ilc3,ilc7}; ilruls6=newreg; Ruled Surface(ilruls6) = {ill6};
|
||||
ill7 = newreg; Line Loop(ill7) = {-ilc2,-ilc7,-ilc12};ilruls7=newreg; Ruled Surface(ilruls7) = {ill7};
|
||||
ill8 = newreg; Line Loop(ill8) = {-ilc6,-ilc9,ilc2}; ilruls8=newreg; Ruled Surface(ilruls8) = {ill8};
|
||||
|
||||
ilsloop0 = newreg;
|
||||
Surface Loop(ilsloop0) = {ill8+1,ill5+1,ill1+1,ill2+1,ill3+1,ill7+1,ill6+1,ill4+1};
|
||||
|
||||
|
||||
// 2.3.3 Define volume of air sphere
|
||||
|
||||
vil1=newv; Volume(vil1) = {ilsloop0};
|
||||
|
||||
|
||||
// 3.0 define physical entitites
|
||||
|
||||
Physical Point(vacuum_background_bnd) = {ilp1,ilp2,ilp3,ilp4,ilp5,ilp6,ilp7};
|
||||
Physical Surface(vacuum_background_bnd) = {ilruls1,ilruls2,ilruls3,ilruls4,ilruls5,ilruls6,ilruls7,ilruls8};
|
||||
Physical Volume(air) = {vil1};
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,375 @@
|
||||
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
|
||||
// all rights reserved
|
||||
// project - gmsh2h5fed
|
||||
// file name - gmsh.cc
|
||||
// file type - c++ implementation file
|
||||
// objective - implement class for readind gmsh data files
|
||||
// modified - 2006 aug 24, creation, patrick leidenberger
|
||||
// modified - 2006 aug 26, pl, Access to private members.
|
||||
|
||||
#include "gmsh.hh"
|
||||
|
||||
using namespace boost::spirit;
|
||||
using namespace gmshtohdf5fed;
|
||||
using namespace rlog;
|
||||
using namespace std;
|
||||
|
||||
#include <boost/spirit/core.hpp>
|
||||
#include <boost/spirit/iterator/file_iterator.hpp>
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
#include <fstream>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
#include "gmshgrammar.hh"
|
||||
#include "gmshsemanticaction.hh"
|
||||
|
||||
|
||||
gmsh::gmsh()
|
||||
{
|
||||
//rDebug("Enter vtk constructor.");
|
||||
// Clean the gmsh data structure.
|
||||
gmshNodes_.clear();
|
||||
gmshNodesNumber_.clear();
|
||||
gmshLine_.clear();
|
||||
gmshLineTag_.clear();
|
||||
gmshTriangle_.clear();
|
||||
gmshTriangleTag_.clear();
|
||||
gmshQuadrangle_.clear();
|
||||
gmshQuadrangleTag_.clear();
|
||||
gmshTetrahedron_.clear();
|
||||
gmshTetrahedronTag_.clear();
|
||||
gmshHexahedron_.clear();
|
||||
gmshHexahedronTag_.clear();
|
||||
gmshPrism_.clear();
|
||||
gmshPrismTag_.clear();
|
||||
gmshPyramid_.clear();
|
||||
gmshPyramidTag_.clear();
|
||||
gmsh2ndLineTag_.clear();
|
||||
gmsh2ndTriangle_.clear();
|
||||
gmsh2ndTriangleTag_.clear();
|
||||
gmsh2ndQuadrangle_.clear();
|
||||
gmsh2ndQuadrangleTag_.clear();
|
||||
gmsh2ndTetrahedron_.clear();
|
||||
gmsh2ndTetrahedronTag_.clear();
|
||||
gmsh2ndHexahedron_.clear();
|
||||
gmsh2ndHexahedronTag_.clear();
|
||||
gmsh2ndPrism_.clear();
|
||||
gmsh2ndPrismTag_.clear();
|
||||
gmsh2ndPyramid_.clear();
|
||||
gmsh2ndPyramidTag_.clear();
|
||||
gmshPoint_.clear();
|
||||
gmshPointTag_.clear();
|
||||
//rDebug("Leafe vtk constructor.");
|
||||
}
|
||||
|
||||
gmsh::~gmsh()
|
||||
{
|
||||
//rDebug("Enter vtk destructor.");
|
||||
//rDebug("Leafe vtk destructor.");
|
||||
}
|
||||
|
||||
|
||||
int gmsh::gmshFileName(char* fileName)
|
||||
{
|
||||
//rDebug("Enter fileName.");
|
||||
// Erase the fileName_.
|
||||
fileName_.erase();
|
||||
// Copy fileName in private string fileName_.
|
||||
gmshCpString(fileName, &fileName_);
|
||||
// rDebug("fileName_= %s",fileName_.c_str());
|
||||
//rDebug("Leafe fileName");
|
||||
return OKCODE;
|
||||
}
|
||||
int gmsh::gmshFileName(string fileName)
|
||||
{
|
||||
//rDebug("Enter fileName.");
|
||||
// Erase the fileName_.
|
||||
fileName_.erase();
|
||||
// Copy fileName in private string fileName_.
|
||||
fileName_ = fileName;
|
||||
// rDebug("fileName_= %s",fileName_.c_str());
|
||||
//rDebug("Leafe fileName");
|
||||
}
|
||||
|
||||
|
||||
int gmsh::gmshOpen(void)
|
||||
{
|
||||
//rDebug("Enter openVtk.");
|
||||
|
||||
// Open a stream to read the gmsh file in a string.
|
||||
ifstream inFile (fileName_.c_str());
|
||||
|
||||
// Check if file was opened corretly.
|
||||
if (! inFile)
|
||||
{
|
||||
rError("Cannot open file %s.", fileName_.c_str());
|
||||
return ERRORCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rInfo("Open file %s", fileName_.c_str());
|
||||
|
||||
// Read file content into a string
|
||||
fileContent.erase();
|
||||
char chr;
|
||||
while (inFile.get(chr))
|
||||
{
|
||||
fileContent.append(1,chr);
|
||||
}
|
||||
rInfo(" File has been read.");
|
||||
//rDebug("Input file:\n%s",fileContent.c_str());
|
||||
// Close input file.
|
||||
inFile.close();
|
||||
rInfo(" File Closed.");
|
||||
return OKCODE;
|
||||
}
|
||||
//rDebug("Leave openVtk.");
|
||||
}
|
||||
|
||||
|
||||
int gmsh::gmshParseFile(gmsh* gmshSelf)
|
||||
{
|
||||
//rDebug("Enter parseFile.");
|
||||
|
||||
// Provide an instance of the grammar describing the gmsh file format.
|
||||
stack<long> gmshStack;
|
||||
// Our vtk parser.
|
||||
// Give the parser a pointer to the instance of the gmsh class. So we can
|
||||
// call member functions as semantic action.
|
||||
gmsh_g gmsh_p(gmshSelf);
|
||||
|
||||
// Call the parser.
|
||||
parse_info <iterator_t> info = parse(fileContent.c_str(),gmsh_p,space_p);
|
||||
|
||||
// Feedback to user on parsing outcome.
|
||||
if (info.full)
|
||||
{
|
||||
rInfo("-------------------------");
|
||||
rInfo("parsing succeeded :-)");
|
||||
rInfo("-------------------------");
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
ostringstream temp;
|
||||
temp << info.stop ;
|
||||
rError("-------------------------");
|
||||
rError("parsing failed :-(");
|
||||
rError("stopped at line: %s", temp.str().c_str());
|
||||
rError("-------------------------");
|
||||
return ERRORCODE;
|
||||
}
|
||||
|
||||
//rDebug("Leave parseFile.");
|
||||
}
|
||||
|
||||
int gmsh::gmshPushNode(vector<double>* nodeCoords)
|
||||
{
|
||||
//rDebug("gmshPushNode(vector<double>* nodeCoords).");
|
||||
gmshNodes_.push_back(*nodeCoords);
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
int gmsh::gmshPushNodeNumber(unsigned int* nodeNumber)
|
||||
{
|
||||
gmshNodesNumber_.push_back(*nodeNumber);
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
int gmsh::gmshPushElem(unsigned short int elemType,
|
||||
vector<unsigned int>* nodeVector)
|
||||
{
|
||||
//rDebug("Inside gmshPushElem.");
|
||||
if (elemType == GMSH_LINE)
|
||||
gmshLine_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_TRIANGLE)
|
||||
gmshTriangle_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_QUADRANGLE)
|
||||
gmshQuadrangle_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_TETRAHEDRON)
|
||||
gmshTetrahedron_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_HEXAHEDRON)
|
||||
gmshHexahedron_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_PRISM)
|
||||
gmshPrism_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_PYRAMID)
|
||||
gmshPyramid_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_LINE)
|
||||
gmsh2ndLine_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_TRIANGLE)
|
||||
gmsh2ndTriangle_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_QUADRANGLE)
|
||||
gmsh2ndQuadrangle_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_TETRAHEDRON)
|
||||
gmsh2ndTetrahedron_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_HEXAHEDRON)
|
||||
gmsh2ndHexahedron_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_PRISM)
|
||||
gmsh2ndPrism_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_2ND_PYRAMID)
|
||||
gmsh2ndPyramid_.push_back(*nodeVector);
|
||||
else if (elemType == GMSH_POINT)
|
||||
gmshPoint_.push_back(*nodeVector);
|
||||
else
|
||||
{
|
||||
rError("A unknown element type found!");
|
||||
rError("Element type: %d", elemType);
|
||||
}
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
int gmsh::gmshPushTag(unsigned short int elemType,
|
||||
vector<unsigned int>* tagVector)
|
||||
{
|
||||
//rDebug("Inside gmshPushElem.");
|
||||
if (elemType == GMSH_LINE)
|
||||
{
|
||||
//rDebug(" Line pushedback");
|
||||
}
|
||||
else if (elemType == GMSH_TRIANGLE)
|
||||
{
|
||||
//rDebug(" Triangle pushedback");
|
||||
}
|
||||
else if (elemType == GMSH_QUADRANGLE)
|
||||
{
|
||||
//rDebug(" Quadrangle pushedback");
|
||||
}
|
||||
else if (elemType == GMSH_TETRAHEDRON)
|
||||
{
|
||||
//rDebug(" Tetrahedron pushedback");
|
||||
gmshTetrahedronTag_.push_back(*tagVector);
|
||||
}
|
||||
else
|
||||
{
|
||||
}
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
|
||||
int gmsh::gmshShowElemResult()
|
||||
{
|
||||
rInfo("Elements found in gmsh file:");
|
||||
rInfo(" lines: %d",gmshLine_.size());
|
||||
rInfo(" triangles: %d",gmshTriangle_.size());
|
||||
rInfo(" quadrangles: %d",gmshQuadrangle_.size());
|
||||
rInfo(" tetrahedrons: %d",gmshTetrahedron_.size());
|
||||
rInfo(" hexahedrons: %d",gmshHexahedron_.size());
|
||||
rInfo(" prisms: %d",gmshPrism_.size());
|
||||
rInfo(" pyramids: %d",gmshPyramid_.size());
|
||||
rInfo(" 2nd order lines: %d",gmsh2ndLine_.size());
|
||||
rInfo(" 2nd order Triangles: %d",gmsh2ndTriangle_.size());
|
||||
rInfo(" 2nd order Quadrangles: %d",gmsh2ndQuadrangle_.size());
|
||||
rInfo(" 2nd order Tetrahedrons: %d",gmsh2ndTetrahedron_.size());
|
||||
rInfo(" 2nd order Hexahedrons: %d",gmsh2ndHexahedron_.size());
|
||||
rInfo(" 2nd order Prisms: %d",gmsh2ndPrism_.size());
|
||||
rInfo(" 2nd order Pyramids: %d",gmsh2ndPyramid_.size());
|
||||
rInfo(" Points : %d",gmshPoint_.size());
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
void gmsh::cpString(char const* first,
|
||||
char const* last,
|
||||
string* str)
|
||||
{
|
||||
//rDebug("Enter cpString.");
|
||||
|
||||
// Erase the str content.
|
||||
str->erase();
|
||||
|
||||
// Copy version in str.
|
||||
for(unsigned int i = 0; i<strlen(first)-strlen(last); i++)
|
||||
{
|
||||
str->append(1,first[i]);
|
||||
}
|
||||
//rDebug("*str= %s",str->c_str());
|
||||
|
||||
//rDebug("Leafe cpString.");
|
||||
}
|
||||
string gmsh::cpString(char const* first,
|
||||
char const* last)
|
||||
{
|
||||
//rDebug("Enter cpString.");
|
||||
|
||||
// Create and erase a tempral string;
|
||||
string tempString;
|
||||
tempString.erase();
|
||||
|
||||
// Copy version in str.
|
||||
for(unsigned int i = 0; i<strlen(first)-strlen(last); i++)
|
||||
{
|
||||
tempString.append(1,first[i]);
|
||||
}
|
||||
//rDebug("tempString= %s",tempString.c_str());
|
||||
//rDebug("Leafe cpString.");
|
||||
return tempString;
|
||||
}
|
||||
|
||||
int gmsh::gmshCpString(char const* first,
|
||||
string*str)
|
||||
{
|
||||
// Create and erase a tempral string;
|
||||
std::string tempString;
|
||||
tempString.erase();
|
||||
// Copy the character sign for sign into the string.
|
||||
for(unsigned int i = 0; i<strlen(first); i++)
|
||||
{
|
||||
tempString.append(1,first[i]);
|
||||
}
|
||||
//rDebug("tempString= %s",tempString.c_str());
|
||||
//rDebug("Leafe cpString.");
|
||||
return OKCODE;
|
||||
}
|
||||
|
||||
int gmsh::gmshCheckVersion(int* version)
|
||||
{
|
||||
if ((int)(*version) == 2)
|
||||
{
|
||||
rInfo("Gmsh file has format 2.");
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("Gmsh file has format: %d.", (int)(*version));
|
||||
rError("But this program can only read format 2.");
|
||||
rError("Exit");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
}
|
||||
|
||||
int gmsh::gmshCheckFileType(int* fileType)
|
||||
{
|
||||
if ((int)(*fileType) == 0)
|
||||
{
|
||||
rInfo("Gmsh file has ascii format.");
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("Gmsh file has format: %d.", (int)(*fileType));
|
||||
rError("But this program can only read format 0 (ascii).");
|
||||
rError("Exit");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
}
|
||||
|
||||
std::vector< std::vector <double> > gmsh::gmshNode()
|
||||
{
|
||||
return gmshNodes_;
|
||||
}
|
||||
|
||||
std::vector<unsigned int> gmsh::gmshNodeNumber()
|
||||
{
|
||||
return gmshNodesNumber_;
|
||||
}
|
||||
|
||||
std::vector< std::vector<unsigned int> > gmsh::gmshTetrahedron()
|
||||
{
|
||||
return gmshTetrahedron_;
|
||||
}
|
||||
|
||||
std::vector< std::vector<unsigned int> > gmsh::gmshTetrahedronTag()
|
||||
{
|
||||
return gmshTetrahedronTag_;
|
||||
}
|
||||
@@ -0,0 +1,142 @@
|
||||
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
|
||||
// all rights reserved
|
||||
// project - gmsh2h5fed
|
||||
// file name - gmsh.hh
|
||||
// file type - c++ header file
|
||||
// objective - declare class for readind gmsh mesh files v2.0
|
||||
//
|
||||
// modified - 2006 aug 21, creation, Patrick Leidenberger
|
||||
// modified - 2006 aug 22, pl.
|
||||
// modified - 2006 aug 23, pl.
|
||||
// modified - 2006 aug 24, pl, delete old things.
|
||||
// modified - 2006 aug 26, pl, Access to private members.
|
||||
|
||||
#ifndef GMSH_HH_
|
||||
#define GMSH_HH_
|
||||
|
||||
#include <iostream>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
#include <boost/spirit/core.hpp>
|
||||
#include <boost/spirit/iterator/file_iterator.hpp>
|
||||
#include <boost/spirit/core.hpp>
|
||||
|
||||
/* 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>
|
||||
|
||||
#include <nonsciconst.h>
|
||||
|
||||
// Include gmsh specific constants.
|
||||
#include "gmshconst.hh"
|
||||
|
||||
using namespace std;
|
||||
using namespace nonsciconst;
|
||||
|
||||
namespace gmshtohdf5fed
|
||||
{
|
||||
class gmsh
|
||||
{
|
||||
public:
|
||||
// Constructor: Here we clear all private data vectors.
|
||||
gmsh();
|
||||
// Destructor.
|
||||
~gmsh();
|
||||
|
||||
int gmshFileName(char* fileName);
|
||||
int gmshFileName(string fileName);
|
||||
|
||||
int gmshOpen(void);
|
||||
|
||||
int gmshParseFile(gmsh* vtkSelf);
|
||||
|
||||
void cpString(char const* first,
|
||||
char const* last,
|
||||
string* str);
|
||||
string cpString(char const* first,
|
||||
char const* last);
|
||||
|
||||
int gmshCpString(char const* first,
|
||||
string*str);
|
||||
// Check if gmsh file is of version 2.
|
||||
int gmshCheckVersion(int* version);
|
||||
// Check if the gmsh file is in ascii format.
|
||||
int gmshCheckFileType(int* fileType);
|
||||
|
||||
// Pushes the three coordinates of a node in the gmshNodes_ vector.
|
||||
int gmshPushNode(vector<double>* nodeCoords);
|
||||
|
||||
// Pushes the number of a node in the gmshNodesNumber_ vector.
|
||||
int gmshPushNodeNumber(unsigned int * nodeNumber);
|
||||
|
||||
// Push the node vector nodeVector to the appropriate data structure
|
||||
// denoted by the string.
|
||||
int gmshPushElem(unsigned short int elemType,
|
||||
vector<unsigned int>* nodeVector);
|
||||
// Push the tag vector tagVector to the appropriate data structure
|
||||
// denoted by the string.
|
||||
int gmshPushTag(unsigned short int elemType,
|
||||
vector<unsigned int>* tagVector);
|
||||
// Show the size of the element vectors.
|
||||
int gmshShowElemResult();
|
||||
|
||||
//-------------------------------------//
|
||||
// Access to private stored gmsh data. //
|
||||
//-------------------------------------//
|
||||
|
||||
std::vector< std::vector <double> > gmshNode();
|
||||
std::vector<unsigned int> gmshNodeNumber();
|
||||
std::vector< std::vector<unsigned int> > gmshTetrahedron();
|
||||
std::vector< std::vector<unsigned int> > gmshTetrahedronTag();
|
||||
|
||||
private:
|
||||
string fileName_;
|
||||
string fileContent;
|
||||
|
||||
// Data structure for node coordinates from gmsh file.
|
||||
vector<vector<double> > gmshNodes_;
|
||||
// Data structure for gmsh node number.
|
||||
// A number belongs to the respective node coordinate in the gmshNodes_
|
||||
// vector.
|
||||
vector<unsigned int> gmshNodesNumber_;
|
||||
|
||||
// Data structure for the topological entities and their tags stored in
|
||||
// the gmsh file. The 'gmsh2nd..' denote second order Elements.
|
||||
vector<vector<unsigned int> > gmshLine_;
|
||||
vector<vector<unsigned int> > gmshLineTag_;
|
||||
vector<vector<unsigned int> > gmshTriangle_;
|
||||
vector<vector<unsigned int> > gmshTriangleTag_;
|
||||
vector<vector<unsigned int> > gmshQuadrangle_;
|
||||
vector<vector<unsigned int> > gmshQuadrangleTag_;
|
||||
vector<vector<unsigned int> > gmshTetrahedron_;
|
||||
vector<vector<unsigned int> > gmshTetrahedronTag_;
|
||||
vector<vector<unsigned int> > gmshHexahedron_;
|
||||
vector<vector<unsigned int> > gmshHexahedronTag_;
|
||||
vector<vector<unsigned int> > gmshPrism_;
|
||||
vector<vector<unsigned int> > gmshPrismTag_;
|
||||
vector<vector<unsigned int> > gmshPyramid_;
|
||||
vector<vector<unsigned int> > gmshPyramidTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndLine_;
|
||||
vector<vector<unsigned int> > gmsh2ndLineTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndTriangle_;
|
||||
vector<vector<unsigned int> > gmsh2ndTriangleTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndQuadrangle_;
|
||||
vector<vector<unsigned int> > gmsh2ndQuadrangleTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndTetrahedron_;
|
||||
vector<vector<unsigned int> > gmsh2ndTetrahedronTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndHexahedron_;
|
||||
vector<vector<unsigned int> > gmsh2ndHexahedronTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndPrism_;
|
||||
vector<vector<unsigned int> > gmsh2ndPrismTag_;
|
||||
vector<vector<unsigned int> > gmsh2ndPyramid_;
|
||||
vector<vector<unsigned int> > gmsh2ndPyramidTag_;
|
||||
vector<vector<unsigned int> > gmshPoint_;
|
||||
vector<vector<unsigned int> > gmshPointTag_;
|
||||
};
|
||||
}
|
||||
|
||||
#endif //GMSH_HH_
|
||||
@@ -0,0 +1,28 @@
|
||||
#ifndef GMSHCONST_HH_
|
||||
#define GMSHCONST_HH_
|
||||
|
||||
// Contants of gmsh element types.
|
||||
// See Gmsh Reference Manual (14 May 2006) page 147-148.
|
||||
const unsigned short int GMSH_LINE = 1;
|
||||
const unsigned short int GMSH_TRIANGLE = 2;
|
||||
const unsigned short int GMSH_QUADRANGLE = 3;
|
||||
const unsigned short int GMSH_TETRAHEDRON = 4;
|
||||
const unsigned short int GMSH_HEXAHEDRON = 5;
|
||||
const unsigned short int GMSH_PRISM = 6;
|
||||
const unsigned short int GMSH_PYRAMID = 7;
|
||||
const unsigned short int GMSH_2ND_LINE = 8;
|
||||
const unsigned short int GMSH_2ND_TRIANGLE = 9;
|
||||
const unsigned short int GMSH_2ND_QUADRANGLE = 10;
|
||||
const unsigned short int GMSH_2ND_TETRAHEDRON = 11;
|
||||
const unsigned short int GMSH_2ND_HEXAHEDRON = 12;
|
||||
const unsigned short int GMSH_2ND_PRISM = 13;
|
||||
const unsigned short int GMSH_2ND_PYRAMID = 14;
|
||||
const unsigned short int GMSH_POINT = 15;
|
||||
|
||||
// Every element has an spesific number of tags.
|
||||
// This is the list of the number. There is a leading zero, because there is
|
||||
// no element with the index 0.
|
||||
const unsigned short int GMSH_ELEM_N_NODES[] = { 0, 2, 3, 4, 4, 8, 6, 5, 3,
|
||||
6, 9, 10, 27, 18, 14, 1 };
|
||||
|
||||
#endif //GMSHCONST_HH_
|
||||
@@ -0,0 +1,242 @@
|
||||
/** \brief Definition of gmsh file format v2.0 parser data types and variables
|
||||
*
|
||||
* rights - patrick leidenberger and benedikt oswald
|
||||
* file name - gmshgrammar.hh
|
||||
* file type - include file
|
||||
* objective - define grammar of gmsh file format v2.0
|
||||
* author - patrick leidenberger and benedikt oswald
|
||||
* modified - 2006 jun 29, pl, creation
|
||||
* features - defines grammar of gmsh files v2.0
|
||||
*/
|
||||
|
||||
/* include standard header files */
|
||||
#include <boost/spirit/core.hpp>
|
||||
#include <boost/spirit/iterator/file_iterator.hpp>
|
||||
#include <boost/spirit/actor/assign_actor.hpp>
|
||||
#include <boost/spirit/utility/functor_parser.hpp>
|
||||
#include <boost/spirit/utility/escape_char.hpp>
|
||||
#include <boost/spirit/utility/loops.hpp>
|
||||
#include <boost/spirit/dynamic/if.hpp>
|
||||
#include <iostream>
|
||||
#include <functional>
|
||||
#include <map>
|
||||
#include <stack>
|
||||
#include <string>
|
||||
#include <boost/bind.hpp>
|
||||
#include <boost/ref.hpp>
|
||||
|
||||
/* include proprietary header files */
|
||||
#include "gmshsemanticaction.hh"
|
||||
#include "gmsh.hh"
|
||||
// Include gmsh specific constants.
|
||||
#include "gmshconst.hh"
|
||||
|
||||
#ifndef GMSHGRAMMAR_HH_
|
||||
#define GMSHGRAMMAR_HH_
|
||||
|
||||
/* activate namespaces */
|
||||
using namespace std;
|
||||
using namespace boost::spirit;
|
||||
using namespace gmshtohdf5fed;
|
||||
|
||||
/* type definitions */
|
||||
//typedef char char_t;
|
||||
//typedef file_iterator<char_t> iterator_t;
|
||||
//typedef scanner<iterator_t> scanner_t;
|
||||
//typedef rule<scanner_t> rule_t;
|
||||
|
||||
|
||||
////////////////////////////////////////////////////////////////////////////
|
||||
//
|
||||
// Our calculator grammar
|
||||
//
|
||||
////////////////////////////////////////////////////////////////////////////
|
||||
struct gmsh_g : public grammar<gmsh_g>
|
||||
{
|
||||
// vtk_g(/*stack<long>& eval_*/)
|
||||
// /*: eval(eval_)*/ {}
|
||||
gmsh_g(gmsh* gmshSelf)
|
||||
: gmshSelf_(gmshSelf)
|
||||
{
|
||||
}
|
||||
|
||||
template <typename ScannerT>
|
||||
struct definition
|
||||
{
|
||||
definition(gmsh_g const& self)
|
||||
{
|
||||
gmsh_import_r = gmsh_mesh_format_r
|
||||
>> gmsh_nodes_r
|
||||
>> gmsh_elements_r;
|
||||
|
||||
//////////////////////////////////////////////////////////////////////////
|
||||
// GENERAL NOTE: All tranport of numbers to gmshsemanticaction.hh must //
|
||||
// be done by reference, not by value. Transport by //
|
||||
// value fails! You have to debug long for it! //
|
||||
/////////////////////////////////////////////////////////////////////////
|
||||
|
||||
// Rules for the MeshFormat section.
|
||||
gmsh_mesh_format_r = str_p("$MeshFormat")
|
||||
>> int_p[assign_a(tempInt1_)]
|
||||
[gmsh_version_a(self.gmshSelf_, &tempInt1_)]
|
||||
>> int_p[assign_a(tempInt1_)]
|
||||
[gmsh_file_type_a(self.gmshSelf_, &tempInt1_)]
|
||||
>> int_p[assign_a(tempInt1_)]
|
||||
>> str_p("$EndMeshFormat");
|
||||
|
||||
// Rules for the Nodes section.
|
||||
gmsh_nodes_r = str_p("$Nodes")
|
||||
>> eps_p[gmsh_clear_map_a<unsigned int,
|
||||
vector<double> >(&tempCoordMap_)]
|
||||
>> int_p[assign_a(tempUnInt1_)]
|
||||
>> eps_p[gmsh_info_msg_a("Nodes in gmsh file: ",
|
||||
&tempUnInt1_)]
|
||||
>> repeat_p(boost::ref(tempUnInt1_))
|
||||
[
|
||||
eps_p[gmsh_clear_vec_a<double>(&tempVecDouble1_)]
|
||||
>> int_p[assign_a(tempUnInt2_)]
|
||||
>> repeat_p(3)
|
||||
[real_p[assign_a(tempDouble1_)]
|
||||
[gmsh_push_vec_a<double>(&tempVecDouble1_,
|
||||
&tempDouble1_)]
|
||||
]
|
||||
[gmsh_insert_map_a<unsigned int,
|
||||
vector<double> >
|
||||
(&tempCoordMap_, &tempUnInt2_,
|
||||
&tempVecDouble1_)
|
||||
]
|
||||
]
|
||||
>> str_p("$EndNodes")
|
||||
>> eps_p[gmsh_transport_nodes_a(self.gmshSelf_,
|
||||
&tempCoordMap_)];
|
||||
|
||||
// Rules for the Elements section.
|
||||
gmsh_elements_r = str_p("$Elements")
|
||||
>> int_p[assign_a(tempUnInt1_)]
|
||||
>> eps_p[gmsh_info_msg_a("Elements in gmsh file: ",
|
||||
&tempUnInt1_)]
|
||||
>> gmsh_element_r
|
||||
>> str_p("$EndElements");
|
||||
|
||||
gmsh_element_r = repeat_p(boost::ref(tempUnInt1_))
|
||||
[ // Parse one element
|
||||
// Clear the vectors for nodes and tags of an elem.
|
||||
eps_p[gmsh_clear_vec_a<unsigned int>
|
||||
(&tempElemNode_)]
|
||||
>> eps_p[gmsh_clear_vec_a<unsigned int>
|
||||
(&tempElemTag_)]
|
||||
// Parse the element number. We don't need it.
|
||||
>> int_p[assign_a(tempUnInt2_)]
|
||||
// Parse the element type.
|
||||
>> int_p[assign_a(tempUnShortInt1_)]
|
||||
// Parse the number of tags.
|
||||
>> int_p[assign_a(tempUnInt3_)]
|
||||
// Parse the tags.
|
||||
>> repeat_p(boost::ref(tempUnInt3_))
|
||||
[
|
||||
// Parse a single tag.
|
||||
int_p[assign_a(tempUnInt4_)]
|
||||
// Copy to vector.
|
||||
>> eps_p[gmsh_push_vec_a<unsigned int>
|
||||
(&tempElemTag_, &tempUnInt4_)]
|
||||
][gmsh_nothing_a()]
|
||||
// Copy the number of nodes of the actual element
|
||||
// type (in tempUnShortInt1_) from the
|
||||
// GMSH_ELEM_N_NODES array in gmshconst.hh in
|
||||
// tempUnShortInt2_.
|
||||
// Do this, because I don't get the direct array
|
||||
// access not work.
|
||||
>> eps_p[gmsh_array_access_a<unsigned short int>
|
||||
(&tempUnShortInt2_, &tempUnShortInt1_)]
|
||||
// Parse the respective number of nodes.
|
||||
>> repeat_p(boost::ref(tempUnShortInt2_))
|
||||
[
|
||||
// Parse a sigle node.
|
||||
int_p[assign_a(tempUnInt4_)]
|
||||
// Copy to vector.
|
||||
>> eps_p[gmsh_push_vec_a<unsigned int>
|
||||
(&tempElemNode_, &tempUnInt4_)]
|
||||
|
||||
]
|
||||
[
|
||||
// Transport the parsed element nodes in the
|
||||
// respective gmsh.hh data structure.
|
||||
gmsh_transport_elem_a(self.gmshSelf_,
|
||||
&tempUnShortInt1_, &tempElemNode_)
|
||||
]
|
||||
[
|
||||
// Transport the parsed element tags in the
|
||||
// respective gmsh.hh data structure.
|
||||
gmsh_transport_tag_a(self.gmshSelf_,
|
||||
&tempUnShortInt1_, &tempElemTag_)
|
||||
]
|
||||
// This short section demonstrates, like con-
|
||||
// ditional parsing can be used instead:
|
||||
//
|
||||
//>> if_p(gmsh_compare_a<unsigned short int>
|
||||
// (&tempUnShortInt1_,&(elemType_[0])))
|
||||
// [
|
||||
// // Element type 1 == line.
|
||||
// repeat_p(2)
|
||||
// [
|
||||
// int_p[assign_a(tempUnInt4_)]
|
||||
// ][gmsh_nothing_a()]
|
||||
// ]
|
||||
//
|
||||
]
|
||||
[
|
||||
// All elements are parsed.
|
||||
// Show what we have paresd.
|
||||
gmsh_show_elem_result_a(self.gmshSelf_)
|
||||
];
|
||||
|
||||
}
|
||||
|
||||
rule<ScannerT> expression, term, factor, integer;
|
||||
|
||||
|
||||
rule<ScannerT> vtk_import_r;
|
||||
|
||||
rule<ScannerT> gmsh_import_r;
|
||||
rule<ScannerT> gmsh_mesh_format_r;
|
||||
rule<ScannerT> gmsh_nodes_r;
|
||||
rule<ScannerT> gmsh_elements_r;
|
||||
rule<ScannerT> gmsh_element_r;
|
||||
|
||||
rule<ScannerT> const&
|
||||
start() const { return gmsh_import_r; }
|
||||
|
||||
// These are temporal variables used during the parsing process.
|
||||
// These variables are used at different places for different things,
|
||||
// they are only valid in small ranges.
|
||||
int tempInt1_;
|
||||
unsigned int tempUnInt1_;
|
||||
unsigned int tempUnInt2_;
|
||||
unsigned int tempUnInt3_;
|
||||
unsigned int tempUnInt4_;
|
||||
unsigned short int tempUnShortInt1_;
|
||||
unsigned short int tempUnShortInt2_;
|
||||
|
||||
double tempDouble1_;
|
||||
|
||||
vector<int> tempIntVec1_;
|
||||
vector<double> tempDoubleVec1_;
|
||||
vector<vector<double> > tempDoubleVec2_;
|
||||
|
||||
vector<double> tempVecDouble1_;
|
||||
|
||||
// Data structure for node coordinates.
|
||||
// The gmsh node coordinates are not stored and numbered consecutive. So we
|
||||
// have to sort and map them to a consecutive index set using this map.
|
||||
map<unsigned int, vector<double> > tempCoordMap_;
|
||||
// Data structure to store the nodes of an element.
|
||||
vector<unsigned int> tempElemNode_;
|
||||
// Data structure to store an elements tags.
|
||||
vector<unsigned int> tempElemTag_;
|
||||
|
||||
};
|
||||
|
||||
gmsh* gmshSelf_;
|
||||
};
|
||||
|
||||
#endif // GMSHGRAMMAR_HH_
|
||||
@@ -0,0 +1,344 @@
|
||||
// rights - 2006-, copyright benedikt oswald and patrick leidenberger,
|
||||
// all rights reserved
|
||||
/** \brief Definition of VTK ASCII file format parser
|
||||
* project - phidias3d
|
||||
* file name - vtksemanticaction.h
|
||||
* file type - c++ include file
|
||||
* objective - declare semantic action for the vtk file parser
|
||||
* modified - 2006 jul 03, creation, pl
|
||||
* modified - 2006 jul 05, insert fuctionality of calling member functions
|
||||
* of the vtk class, pl
|
||||
* modified - 2006 jul 06, Add actions for vtk file header and file format.
|
||||
* modified - 2006 jul 11, Add a lot of action to store the unstructured
|
||||
* grid dataset. This section is complete.
|
||||
* modified - 2006 jul 13, Make the action work well: it is not a good idea
|
||||
* to transport pointers or strings! Use pointers of
|
||||
* characters.
|
||||
* modified - 2006 aug 27, Correct error in pushNode function, pl.
|
||||
**/
|
||||
|
||||
|
||||
/* include standard header files */
|
||||
#include <boost/spirit/core.hpp>
|
||||
#include <boost/spirit/iterator/file_iterator.hpp>
|
||||
#include <iostream>
|
||||
//#include <iterator>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
#include <map>
|
||||
#include <functional>
|
||||
#include <stack>
|
||||
#include "gmsh.hh"
|
||||
|
||||
/* include proprietary header files */
|
||||
//#include "ansyscnx.h"
|
||||
|
||||
/* activate namespaces */
|
||||
using namespace std;
|
||||
using namespace boost;
|
||||
using namespace boost::spirit;
|
||||
//using namespace phidias3d;
|
||||
|
||||
using namespace gmshtohdf5fed;
|
||||
|
||||
|
||||
/* type definitions */
|
||||
typedef char char_t;
|
||||
typedef file_iterator<char_t> iterator_t;
|
||||
typedef scanner<iterator_t> scanner_t;
|
||||
typedef rule<scanner_t> rule_t;
|
||||
|
||||
#ifndef GMSHSEMANTICACTION_HH_
|
||||
#define GMSHSEMANTICACTION_HH_
|
||||
|
||||
/* semantic actions */
|
||||
|
||||
// Call version-check of gmsh file.
|
||||
struct gmsh_version_a
|
||||
{
|
||||
gmsh_version_a(gmsh* gmshSelf, int* tempInt)
|
||||
: gmshSelf_(gmshSelf), tempInt_(tempInt) {}
|
||||
void operator()(int value) const
|
||||
{
|
||||
//rDebug("Inside gmsh_version_a.");
|
||||
gmshSelf_->gmshCheckVersion(tempInt_);
|
||||
};
|
||||
gmsh* gmshSelf_;
|
||||
int* tempInt_;
|
||||
};
|
||||
|
||||
struct gmsh_file_type_a
|
||||
{
|
||||
gmsh_file_type_a(gmsh* gmshSelf, int* tempInt)
|
||||
: gmshSelf_(gmshSelf), tempInt_(tempInt) {}
|
||||
void operator()(int value) const
|
||||
{
|
||||
//rDebug("Inside gmsh_version_a.");
|
||||
gmshSelf_->gmshCheckFileType(tempInt_);
|
||||
};
|
||||
gmsh* gmshSelf_;
|
||||
int* tempInt_;
|
||||
};
|
||||
|
||||
template<typename Type>
|
||||
struct gmsh_clear_vec_a
|
||||
{
|
||||
gmsh_clear_vec_a(vector<Type>* vect)
|
||||
: vect_(vect) {}
|
||||
void operator()(char const* first, char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug("Clear temporal vector.");
|
||||
(*vect_).clear();
|
||||
};
|
||||
vector<Type>* vect_;
|
||||
};
|
||||
|
||||
template<typename type>
|
||||
struct gmsh_resize_vec_a
|
||||
{
|
||||
gmsh_resize_vec_a(vector<type>* vec, unsigned int size)
|
||||
: vec_(vec), size_(size) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug("Inside gmsh_resize_vec_a.");
|
||||
(*vec_).resize(size_);
|
||||
};
|
||||
void operator() (const int tempInt)
|
||||
const
|
||||
{
|
||||
//rDebug("Inside gmsh_resize_vec_a.");
|
||||
(*vec_).resize(size_);
|
||||
};
|
||||
unsigned int size_;
|
||||
vector<type> * vec_;
|
||||
};
|
||||
|
||||
template<typename type>
|
||||
struct gmsh_insert_vec_a
|
||||
{
|
||||
gmsh_insert_vec_a(vector<type>* vec, unsigned int const position,
|
||||
type* value)
|
||||
: vec_(vec), position_(position), value_(value) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
(*vec_)[position_]=*value_;
|
||||
}
|
||||
vector<type> * vec_;
|
||||
unsigned int position_;
|
||||
type* value_;
|
||||
};
|
||||
|
||||
|
||||
template<typename type>
|
||||
struct gmsh_push_vec_a
|
||||
{
|
||||
gmsh_push_vec_a(vector<type>* vec, type* value)
|
||||
: vec_(vec), value_(value){}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug(" Push value to vector.");
|
||||
(*vec_).push_back(*value_);
|
||||
};
|
||||
void operator() (const double tempDouble)
|
||||
const
|
||||
{
|
||||
//rDebug(" Push value to vector.");
|
||||
(*vec_).push_back(*value_);
|
||||
};
|
||||
type* value_;
|
||||
vector<type> * vec_;
|
||||
};
|
||||
|
||||
|
||||
template<typename type1, typename type2>
|
||||
struct gmsh_insert_map_a
|
||||
{
|
||||
gmsh_insert_map_a(map<type1, type2>* tempMap, type1* key,
|
||||
type2* value)
|
||||
: map_(tempMap), key_(key), value_(value) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
(*map_)[(*key_)]=*value_;
|
||||
};
|
||||
map<type1, type2> * map_;
|
||||
type1* key_;
|
||||
type2* value_;
|
||||
};
|
||||
|
||||
template<typename type1, typename type2>
|
||||
struct gmsh_clear_map_a
|
||||
{
|
||||
gmsh_clear_map_a(map<type1, type2>* tempMap)
|
||||
: map_(tempMap) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
(*map_).clear();
|
||||
};
|
||||
map<type1, type2> * map_;
|
||||
};
|
||||
|
||||
|
||||
struct gmsh_transport_nodes_a
|
||||
{
|
||||
gmsh_transport_nodes_a(gmsh* gmshSelf,
|
||||
map<unsigned int, vector<double> >* tempMap)
|
||||
: gmshSelf_(gmshSelf), map_(tempMap) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug("Copy nodes in data structure.");
|
||||
for (map<unsigned int, vector<double> >::iterator
|
||||
iter = (*map_).begin(); iter != (*map_).end(); iter++)
|
||||
{
|
||||
vector<double>* temp;
|
||||
unsigned int tempNumber;
|
||||
temp = &((*iter).second);
|
||||
tempNumber = ((*iter).first);
|
||||
gmshSelf_->gmshPushNode(temp);
|
||||
gmshSelf_->gmshPushNodeNumber(&tempNumber);
|
||||
//rDebug("%f %f %f", (*temp)[0], (*temp)[1], (*temp)[2]);
|
||||
}
|
||||
|
||||
};
|
||||
map<unsigned int, vector<double> >* map_;
|
||||
gmsh* gmshSelf_;
|
||||
};
|
||||
|
||||
|
||||
|
||||
struct gmsh_transport_elem_a
|
||||
{
|
||||
gmsh_transport_elem_a(gmsh* gmshSelf, unsigned short int* elemType,
|
||||
vector <unsigned int>* tempElemNode)
|
||||
: gmshSelf_(gmshSelf), elemType_(elemType), tempElemNode_(tempElemNode) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug("Copy element type %d in data structure.", *elemType_);
|
||||
gmshSelf_->gmshPushElem(*elemType_, tempElemNode_);
|
||||
};
|
||||
gmsh* gmshSelf_;
|
||||
unsigned short int* elemType_;
|
||||
vector <unsigned int>* tempElemNode_;
|
||||
};
|
||||
|
||||
|
||||
struct gmsh_transport_tag_a
|
||||
{
|
||||
gmsh_transport_tag_a(gmsh* gmshSelf, unsigned short int* elemType,
|
||||
vector <unsigned int>* tempElemTag)
|
||||
: gmshSelf_(gmshSelf), elemType_(elemType), tempElemTag_(tempElemTag) {}
|
||||
void operator() (char const* first,char const* last)
|
||||
const
|
||||
{
|
||||
//rDebug("Copy element tag list in data structure.");
|
||||
gmshSelf_->gmshPushTag(*elemType_, tempElemTag_);
|
||||
};
|
||||
gmsh* gmshSelf_;
|
||||
unsigned short int* elemType_;
|
||||
vector <unsigned int>* tempElemTag_;
|
||||
};
|
||||
|
||||
|
||||
// Print actions.
|
||||
struct gmshEMsg_a
|
||||
{
|
||||
gmshEMsg_a(string gmshEMsg, unsigned int* tempUnLongInt)
|
||||
: gmshEMsg_(gmshEMsg), tempUnLongInt_(tempUnLongInt) {}
|
||||
void operator()(char const* first, char const* last)
|
||||
const
|
||||
{
|
||||
rError("%s %d",gmshEMsg_.c_str(),(*tempUnLongInt_));
|
||||
};
|
||||
string gmshEMsg_;
|
||||
unsigned int* tempUnLongInt_;
|
||||
};
|
||||
|
||||
struct gmsh_info_msg_a
|
||||
{
|
||||
gmsh_info_msg_a(string gmsh_info_msg)
|
||||
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(NULL), tempUnShortInt_(NULL) {}
|
||||
gmsh_info_msg_a(string gmsh_info_msg, unsigned int* tempUnLongInt)
|
||||
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(tempUnLongInt), tempUnShortInt_(NULL) {}
|
||||
gmsh_info_msg_a(string gmsh_info_msg, unsigned short int* tempUnShortInt)
|
||||
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(NULL), tempUnShortInt_(tempUnShortInt) {}
|
||||
void operator()(char const* first, char const* last)
|
||||
const
|
||||
{
|
||||
if ((tempUnLongInt_ == NULL) && (tempUnShortInt_ == NULL))
|
||||
rInfo("%s",gmsh_info_msg_.c_str());
|
||||
else if ((tempUnLongInt_ != NULL) && (tempUnShortInt_ == NULL))
|
||||
rInfo("%s%d",gmsh_info_msg_.c_str(),(*tempUnLongInt_));
|
||||
else if ((tempUnLongInt_ == NULL) && (tempUnShortInt_ != NULL))
|
||||
rInfo("%s%d",gmsh_info_msg_.c_str(),(*tempUnShortInt_));
|
||||
};
|
||||
string gmsh_info_msg_;
|
||||
unsigned int* tempUnLongInt_;
|
||||
unsigned short int* tempUnShortInt_;
|
||||
};
|
||||
|
||||
struct gmsh_nothing_a
|
||||
{
|
||||
gmsh_nothing_a()
|
||||
{}
|
||||
void operator()(char const* first, char const* last)
|
||||
const
|
||||
{
|
||||
};
|
||||
};
|
||||
|
||||
template<typename type>
|
||||
struct gmsh_compare_a
|
||||
{
|
||||
gmsh_compare_a(type* a, type* b)
|
||||
: a_(a), b_(b) {}
|
||||
bool operator () () const
|
||||
{
|
||||
if (*a_ == *b_)
|
||||
{
|
||||
//rDebug("Return TRUE! a = %d b = %d", *a_, *b_);
|
||||
return true;
|
||||
}
|
||||
else
|
||||
{
|
||||
//rDebug("Return FALSE! a = %d b = %d", *a_, *b_);
|
||||
return false;
|
||||
}
|
||||
};
|
||||
type* a_;
|
||||
type* b_;
|
||||
};
|
||||
|
||||
template<typename type>
|
||||
struct gmsh_array_access_a
|
||||
{
|
||||
gmsh_array_access_a(type* a, type* b)
|
||||
: a_(a), b_(b) {}
|
||||
void operator()(char const* first, char const* last) const
|
||||
{
|
||||
*a_ = GMSH_ELEM_N_NODES[*b_];
|
||||
};
|
||||
type* a_;
|
||||
type* b_;
|
||||
};
|
||||
|
||||
|
||||
struct gmsh_show_elem_result_a
|
||||
{
|
||||
gmsh_show_elem_result_a(gmsh* gmshSelf)
|
||||
: gmshSelf_(gmshSelf) {}
|
||||
void operator()(char const* first, char const* last)
|
||||
const
|
||||
{
|
||||
gmshSelf_->gmshShowElemResult();
|
||||
};
|
||||
gmsh* gmshSelf_;
|
||||
};
|
||||
|
||||
#endif // GMSHSEMANTICACTION_HH_
|
||||
@@ -0,0 +1,18 @@
|
||||
## Makefile.am -- process this file with automake to produce Makefile.in
|
||||
##
|
||||
## authors - benedikt oswald and patrick leidenberger
|
||||
## modified - 2006 aug 21, patrick leidenberger, creation
|
||||
## modified - 2006 aug 23, pl, adaped to new directory structure.
|
||||
#
|
||||
## objective - automake input file for the gmsh directory
|
||||
## project - gmshtohdf5fed
|
||||
|
||||
noinst_LTLIBRARIES = libgmsh.la
|
||||
gmshdir = $(topleveldir)/libsrc/gmsh
|
||||
gmsh_HEADERS = gmsh.hh
|
||||
libgmsh_la_SOURCES = gmsh.cc \
|
||||
gmsh.hh \
|
||||
gmshconst.hh \
|
||||
gmshgrammer.hh \
|
||||
gmshsemanticaction.hh
|
||||
AM_CPPFLAGS = @AM_CPPFLAGS@
|
||||
@@ -0,0 +1,37 @@
|
||||
// rights - 2006-, copyright benedikt, all rights reserved
|
||||
// project - phidias3d
|
||||
// file name - hdf5em.h
|
||||
// file type - c++ implementation file
|
||||
// objective - implement class for HDF5/ELECTROMAGNETIC file format access
|
||||
// modified - 2006 jun 26, creation, benedikt oswald
|
||||
// modified - 2006
|
||||
// inheritance -
|
||||
// feature - implements the base class for HDF5/ELECTROMAGNETIC file format access.
|
||||
// feature -
|
||||
// required software -
|
||||
|
||||
|
||||
/* include standard header files */
|
||||
//#include <h5.h>
|
||||
|
||||
|
||||
|
||||
/* include proprietary files */
|
||||
#include "h5fed.hh"
|
||||
#ifdef HAVE_HDF5
|
||||
|
||||
namespace hdf5em
|
||||
{
|
||||
//
|
||||
// hdf5em::hdf5em()
|
||||
// {
|
||||
// ;
|
||||
// }
|
||||
//
|
||||
// hdf5em::~hdf5em()
|
||||
// {
|
||||
// ;
|
||||
// }
|
||||
//
|
||||
}
|
||||
#endif // HAVE_HDF5
|
||||
@@ -0,0 +1,658 @@
|
||||
// rights - 2006-, copyright benedikt, all rights reserved
|
||||
// project - phidias3d
|
||||
// file name - hdf5em.h
|
||||
// file type - c++ header file
|
||||
// objective - declare class for HDF5/ELECTROMAGNETIC file format access
|
||||
// modified - 2006 jun 26, creation, benedikt oswald
|
||||
// modified - 2006 aug 26, pl, integrate automatic index mapping.
|
||||
// inheritance -
|
||||
// feature - declares the base class for HDF5/ELECTROMAGNETIC file format access;
|
||||
// feature - this class is completely self contained, i.e. it does not need anything
|
||||
// feature - external, except the STL and the HDF5 header files and the corresponding
|
||||
// feature - library.
|
||||
// required software -
|
||||
|
||||
#ifndef H5FED_HH_
|
||||
#define H5FED_HH_
|
||||
|
||||
#ifdef HAVE_HDF5
|
||||
|
||||
/* include standard header files */
|
||||
#include <cmath>
|
||||
#include <iostream>
|
||||
#include <complex>
|
||||
#include <string>
|
||||
#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>
|
||||
|
||||
// Include HDF5 headers.
|
||||
#include <hdf5.h>
|
||||
|
||||
// Include h5fed specific constants.
|
||||
#include "h5fedconst.hh"
|
||||
|
||||
/* include standard proprietary header files */
|
||||
#include "nonsciconst.h"
|
||||
#include "physicomath.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace physicomath;
|
||||
using namespace nonsciconst;
|
||||
|
||||
namespace H5Fed
|
||||
{
|
||||
|
||||
class H5Fed {
|
||||
public:
|
||||
/** \brief constructor and destructor */
|
||||
H5Fed()
|
||||
{
|
||||
doIndexMapping_ = false;
|
||||
indexMap_.clear();
|
||||
positionMap_.clear();
|
||||
|
||||
// Deactivate the HDF5 error output.
|
||||
H5Eset_auto (0, NULL );
|
||||
};
|
||||
|
||||
// The Destructor.
|
||||
~H5Fed(){};
|
||||
|
||||
|
||||
//! Open an hdf5 finite element data file with appropriate access.
|
||||
int open(string fileName, string fileAccess)
|
||||
{
|
||||
// Store filename and file access in private variable.
|
||||
fileName_ = fileName;
|
||||
fileAccess_ = fileAccess;
|
||||
// Open file with respective rights via HDF5 API.
|
||||
if (!fileAccess_.compare(FILE_READ))
|
||||
{
|
||||
hdf5FileIdent_ = H5Fopen(fileName_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
|
||||
return OKCODE;
|
||||
}
|
||||
else if (!fileAccess_.compare(FILE_READ_WRITE))
|
||||
{
|
||||
hdf5FileIdent_ = H5Fopen(fileName_.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
|
||||
return OKCODE;
|
||||
}
|
||||
else if (!fileAccess_.compare(FILE_CREATE))
|
||||
{
|
||||
hdf5FileIdent_ = H5Fcreate(fileName_.c_str(), H5F_ACC_EXCL,
|
||||
H5P_DEFAULT, H5P_DEFAULT);
|
||||
if (hdf5FileIdent_ < 0)
|
||||
{
|
||||
rError("The file %s already exist.",fileName_.c_str());
|
||||
rError("To overwrite use the --force option.");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
else
|
||||
return OKCODE;
|
||||
}
|
||||
else if (!fileAccess_.compare(FILE_CREATE_FORCE))
|
||||
{
|
||||
hdf5FileIdent_ = H5Fcreate(fileName_.c_str(), H5F_ACC_TRUNC,
|
||||
H5P_DEFAULT, H5P_DEFAULT);
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("Unknown file-open-attribute for hdf5 file.");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
};
|
||||
|
||||
// Close an open hdf5 file.
|
||||
int close(void)
|
||||
{
|
||||
if (hdf5FileIdent_ >= 0)
|
||||
{
|
||||
hdf5Status_ = H5Fclose(hdf5FileIdent_);
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("You cannot close a file that is not opened.");
|
||||
return ERRORCODE;
|
||||
}
|
||||
};
|
||||
|
||||
// Create the empty HDF5 Finite Element Stardart group hierarchy.
|
||||
int createGroupHierarchie()
|
||||
{
|
||||
// Hdf5 group identifier for group access, localy valid (this method).
|
||||
hid_t hdf5GroupIdent_;
|
||||
// Create the groups. All group-name strings are defined in h5fedconst.hh.
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_ROOT.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_COORD.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_VOLUME_MESH.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_BOUNDARY_MESH.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_MATERIAL.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_ELECTROMAGNETIC.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_DISCRETE.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_PHYSICAL.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_DEBYE.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_LORENTZ.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_DRUDE.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_DOF.c_str(),H5P_DEFAULT);
|
||||
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
|
||||
H5FED_G_FIELD.c_str(),H5P_DEFAULT);
|
||||
return OKCODE;
|
||||
};
|
||||
|
||||
// This function activate the automatic index mapping to create a gapfree
|
||||
// and consecutive index set for the hdf5fed file.
|
||||
// The indexVec holdes the numbers of the nodes in the same way, as the
|
||||
// nodes are in the node vector.
|
||||
int beginIndexMapping(std::vector<unsigned int>* indexVec)
|
||||
{
|
||||
rDebug("Begin automatic index mapping.");
|
||||
doIndexMapping_ = true;
|
||||
indexMap_.clear();
|
||||
positionMap_.clear();
|
||||
|
||||
// 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));
|
||||
}
|
||||
// Number all elements in the map consecutive, starting with zero, that
|
||||
// is the new index set.
|
||||
unsigned int tempUnInt = 0;
|
||||
for(std::map<unsigned int, unsigned int>::iterator
|
||||
iter = indexMap_.begin();
|
||||
iter != indexMap_.end(); iter ++)
|
||||
{
|
||||
iter->second = tempUnInt;
|
||||
tempUnInt++;
|
||||
}
|
||||
// The first column contains the new index, the second the old position
|
||||
// of the coordinate in the vector.
|
||||
for(unsigned int varI = 0; varI < indexVec->size(); varI++)
|
||||
{
|
||||
positionMap_.insert(make_pair(
|
||||
(indexMap_.find((*indexVec)[varI]))->second,varI));
|
||||
}
|
||||
return OKCODE;
|
||||
};
|
||||
|
||||
// This function deactivate the automatic index mapping.
|
||||
// The uses index sets must be consecutive and gapfree.
|
||||
int endIndexMapping()
|
||||
{
|
||||
rDebug("End automatic index mapping.");
|
||||
doIndexMapping_ = false;
|
||||
indexMap_.clear();
|
||||
return OKCODE;
|
||||
};
|
||||
|
||||
// Write 3dim coordinates to h5fed file.
|
||||
int coord3d (std::vector<std::vector<double> >* coord)
|
||||
{
|
||||
// All these operations are only allowed, if there is a valid file
|
||||
// identifier.
|
||||
if (hdf5FileIdent_ >= 0)
|
||||
{
|
||||
// Define the rank of the different dataspaces.
|
||||
const int rank = 2;
|
||||
// Hdf5 error handling variable for Hdf5 actions.
|
||||
herr_t hdf5Status;
|
||||
// Hdf5 dataspace identifier.
|
||||
hid_t hdf5DataspaceId;
|
||||
// Hdf5 dataset identifier.
|
||||
hid_t hdf5DatasetId;
|
||||
// Define the dimension of the data array.
|
||||
// Number of rows: as much as coordinates.
|
||||
// Number of colums: 3, one for each dimension.
|
||||
hsize_t dim[2];
|
||||
dim[0] = coord->size();
|
||||
dim[1] = 3;
|
||||
|
||||
// We copy the coordinates from coord in an standart array, so that
|
||||
// hdf5 can handle it.
|
||||
// We do this in portions, so we save memory.
|
||||
|
||||
// Subdimension of hyperslab in memory: 1 line, 3 columns.
|
||||
hsize_t dim_sub_mem[2];
|
||||
dim_sub_mem[0] = 1;
|
||||
dim_sub_mem[1] = 3;
|
||||
// Subdimension of hyperslab in file: 1 line, 3 columns.
|
||||
hsize_t dim_sub_file[2];
|
||||
dim_sub_file[0] = 1;
|
||||
dim_sub_file[1] = 3;
|
||||
// Define the offset for reading from the memory.
|
||||
// Always fixed.
|
||||
hsize_t offset_mem[2];
|
||||
offset_mem[0] = 0;
|
||||
offset_mem[1] = 0;
|
||||
// Define the offset for writing into the file.
|
||||
hsize_t offset_file[2];
|
||||
offset_file[0] = 0; // Row only at the beginning. We iterate over it.
|
||||
offset_file[1] = 0; // We have no offset respective to the column.
|
||||
|
||||
// Array for x, y and z component of one coordinate.
|
||||
double coordinate[3];
|
||||
|
||||
// Dimesion and datatype of the file dataset, read out form file.
|
||||
// This is not the fastest, but the most robust way.
|
||||
hsize_t dim_out[2];
|
||||
hid_t dataType;
|
||||
|
||||
|
||||
// Create dataspace of full size.
|
||||
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
|
||||
|
||||
// Create dataset of full size.
|
||||
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, H5FED_D_COORD3D.c_str(),
|
||||
H5T_IEEE_F64LE, hdf5DataspaceId, H5P_DEFAULT);
|
||||
|
||||
|
||||
|
||||
// Loop over all rows of the dataset (file) and copy the coord vector
|
||||
// element wise.
|
||||
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out, H5P_DEFAULT);
|
||||
dataType = H5Dget_type(hdf5DatasetId);
|
||||
// If we use automatic mapping we need an interator to the map.
|
||||
std::map<unsigned int, unsigned int>::iterator
|
||||
iter = positionMap_.begin();
|
||||
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
|
||||
{
|
||||
// Iterate over the rows in file dataspace.
|
||||
offset_file[0] = varI;
|
||||
|
||||
// Copy every element of a coordinate.
|
||||
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
|
||||
{
|
||||
// Here is the only special case for automated mapping:
|
||||
// Do not copy the next in the input vector, copy the coord
|
||||
// with the next following number.
|
||||
if (doIndexMapping_ == true)
|
||||
coordinate[varJ] = (*coord)[iter->second][varJ];
|
||||
else
|
||||
coordinate[varJ] = (*coord)[varI][varJ];
|
||||
}
|
||||
|
||||
// Select hyperslab ('region') in file dataspace.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
|
||||
offset_file, H5P_DEFAULT,
|
||||
dim_sub_file, H5P_DEFAULT);
|
||||
|
||||
// Define memory Dataspace.
|
||||
hid_t hdf5MemspaceId;
|
||||
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
|
||||
// Select hyperslab ('region') in memory.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
|
||||
offset_mem, H5P_DEFAULT,
|
||||
dim_sub_mem, H5P_DEFAULT);
|
||||
|
||||
// Copy dataset to dataset from memory to file.
|
||||
hdf5Status = H5Dwrite(hdf5DatasetId, H5T_NATIVE_DOUBLE,
|
||||
hdf5MemspaceId, hdf5DataspaceId,
|
||||
H5P_DEFAULT, coordinate);
|
||||
|
||||
H5Sclose(hdf5MemspaceId);
|
||||
// Increment the map iterator if we make automatic mapping.
|
||||
if (doIndexMapping_)
|
||||
iter++;
|
||||
}
|
||||
|
||||
// Close hdf5 identifier.
|
||||
hdf5Status = H5Dclose(hdf5DatasetId);
|
||||
hdf5Status = H5Sclose(hdf5DataspaceId);
|
||||
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("You cannot operate to dataset COORD3D.");
|
||||
rError("There is no valid file identifier.");
|
||||
return ERRORCODE;
|
||||
}
|
||||
};
|
||||
|
||||
// Read and return tetrahedron on of the given level.
|
||||
std::vector<std::vector<unsigned int> > tetrahedron(unsigned int level)
|
||||
{
|
||||
rError("The function: tetrahedron(unsigned int level) is not implemented.");
|
||||
};
|
||||
// Copy the tetrahedon elements to the h5fed file.
|
||||
int tetrahedron(unsigned int level,
|
||||
std::vector< std::vector<unsigned int> >* elem)
|
||||
{
|
||||
// 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 + stringify(level);
|
||||
// This function does the real work for all elements.
|
||||
element_(level, elem, datasetName, elemDim);
|
||||
return OKCODE;
|
||||
|
||||
}
|
||||
|
||||
int element_(unsigned int level,
|
||||
std::vector< std::vector<unsigned int> >* elem,
|
||||
std::string datasetName,
|
||||
unsigned int elemDim )
|
||||
{
|
||||
// All these operations are only allowed, if there is a valid file
|
||||
// identifier.
|
||||
if (hdf5FileIdent_ >= 0)
|
||||
{
|
||||
rDebug("Insert a check, if the selected level exits,");
|
||||
rDebug("and if it is consecutive.");
|
||||
// Define the rank of the different dataspaces.
|
||||
const int rank = 2;
|
||||
// Hdf5 error handling variable for Hdf5 actions.
|
||||
herr_t hdf5Status;
|
||||
// Hdf5 dataspace identifier.
|
||||
hid_t hdf5DataspaceId;
|
||||
// Hdf5 dataset identifier.
|
||||
hid_t hdf5DatasetId;
|
||||
// Define the dimension of the data array.
|
||||
hsize_t dim[2];
|
||||
// Number of rows: as much as elements.
|
||||
dim[0] = elem->size();
|
||||
// Number of colums: dimenstion of an elements vector.
|
||||
dim[1] = elemDim;
|
||||
|
||||
// We copy the element nodes from a element in an standart array,
|
||||
// so that hdf5 can handle it.
|
||||
// We do this for every element separate, so we save memory.
|
||||
|
||||
// Subdimension of hyperslab in memory: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_mem[2];
|
||||
dim_sub_mem[0] = 1;
|
||||
dim_sub_mem[1] = elemDim;
|
||||
// Subdimension of hyperslab in file: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_file[2];
|
||||
dim_sub_file[0] = 1;
|
||||
dim_sub_file[1] = elemDim;
|
||||
// Define the offset for reading from the memory.
|
||||
// Always fixed, because memory has exactly the same size.
|
||||
hsize_t offset_mem[2];
|
||||
offset_mem[0] = 0;
|
||||
offset_mem[1] = 0;
|
||||
// Define the offset for writing into the file.
|
||||
hsize_t offset_file[2];
|
||||
offset_file[0] = 0; // Row ofsett zero only at the beginning.
|
||||
offset_file[1] = 0; // We have no offset respective to the column.
|
||||
|
||||
// Array for single elements of an element vector.
|
||||
unsigned int element[elemDim];
|
||||
|
||||
// Dimesion and datatype of the file dataset, read out form file.
|
||||
// This is not the fastest, but the most robust way.
|
||||
hsize_t dim_out[2];
|
||||
hid_t dataType;
|
||||
|
||||
// Create dataspace of full size.
|
||||
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
|
||||
|
||||
// Create dataset of full size.
|
||||
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, datasetName.c_str(),
|
||||
H5T_STD_U32LE, hdf5DataspaceId, H5P_DEFAULT);
|
||||
|
||||
// Loop over all rows of the dataset (file) and copy the elem vector
|
||||
// row wise.
|
||||
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out,
|
||||
H5P_DEFAULT);
|
||||
// Get the datatype of the datas we want to write.
|
||||
dataType = H5Dget_type(hdf5DatasetId);
|
||||
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
|
||||
{
|
||||
// Iterate over the rows in file dataspace.
|
||||
offset_file[0] = varI;
|
||||
|
||||
// Copy every element of a coordinate.
|
||||
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
|
||||
{
|
||||
// Here is the only special case for automated mapping:
|
||||
// Do not copy the next in the input vector, copy the coord
|
||||
// with the next following number.
|
||||
if (doIndexMapping_ == true)
|
||||
{
|
||||
std::map<unsigned int, unsigned int>::iterator iter;
|
||||
iter = indexMap_.find((*elem)[varI][varJ]);
|
||||
element[varJ] = iter->second;
|
||||
}
|
||||
else
|
||||
element[varJ] = (*elem)[varI][varJ];
|
||||
}
|
||||
|
||||
// Select hyperslab ('region') in file dataspace.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
|
||||
offset_file, H5P_DEFAULT,
|
||||
dim_sub_file, H5P_DEFAULT);
|
||||
// Define memory Dataspace.
|
||||
hid_t hdf5MemspaceId;
|
||||
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
|
||||
// Select hyperslab ('region') in memory.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
|
||||
offset_mem, H5P_DEFAULT,
|
||||
dim_sub_mem, H5P_DEFAULT);
|
||||
// Copy dataset to dataset from memory to file.
|
||||
hdf5Status = H5Dwrite(hdf5DatasetId, dataType,
|
||||
hdf5MemspaceId, hdf5DataspaceId,
|
||||
H5P_DEFAULT, element);
|
||||
// Close the memory space identifier.
|
||||
H5Sclose(hdf5MemspaceId);
|
||||
}
|
||||
|
||||
// Close hdf5 identifier.
|
||||
hdf5Status = H5Dclose(hdf5DatasetId);
|
||||
hdf5Status = H5Sclose(hdf5DataspaceId);
|
||||
|
||||
return OKCODE;
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("You cannot operate to a dataset.");
|
||||
rError("There is no valid file identifier.");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/** \brief Inquire existence of HDF5 groups */
|
||||
// existsVolumeMesh()
|
||||
// existsCoord()
|
||||
// virtual bool existsMesh(){ return(false); }
|
||||
// virtual bool existsVertices(){ return(false); }
|
||||
// virtual bool existsEdges(){ return(false); }
|
||||
// virtual bool existsTriangles(){ return(false); }
|
||||
// virtual bool existsBoundaryTriangles(){ return(false); }
|
||||
|
||||
// /** \brief Data access both reading and writing */
|
||||
// virtual unsigned int nDim(){ return(ndim_); } /* retrieve number of mesh dimension */
|
||||
// virtual unsigned int nLevel(){ return(nlevel_); } /* retrieve number of mesh levels */
|
||||
// virtual unsigned int nCoord(){ return(nvertex_); } /* retrieve total number of all vertices */
|
||||
// virtual unsigned int nCoord(unsigned int level){ return(nvertex_); } /* retrieve total number of vertices used for defining the mesh */
|
||||
// Überladen greifen auf nelem zu
|
||||
// virtual std::vector<unsigned int> nTet(){ return(ntet_); } /* retrieve vector containing number of tetrahedra present in levels of the mesh */
|
||||
// virtual std::vector<unsigned int> nBoundary(){ return(nboundary_); } /* retrieve vector containing number of boundary meshes present on a level of the mesh */
|
||||
// Pism, ...
|
||||
// nBoundaryTriangle
|
||||
// Quad..
|
||||
// Edge
|
||||
|
||||
|
||||
/** \brief HDF5EM data access routines */
|
||||
|
||||
/** \brief Electromagnetic boundary conditions */
|
||||
//_______________________________
|
||||
// virtual int triangleBC(unsigned int level, unsigned int triangle, unsigned int bc){} /* set electromagnetic boundary condition for triangle on level */
|
||||
// virtual unsigned int triangleBC(unsigned int level, unsigned int triangle){} /* retrieve electromagnetic boundary condition type */
|
||||
//
|
||||
// virtual int rhoSurfaceImpedance(unsigned int level, unsigned int triangle, double rho){} /* store resistance of surface impedance for triangle on level */
|
||||
// virtual double rhoSurfaceImpedance(unsigned int level, unsigned int triangle){} /* retrieve resistance of surface impedance boundary condition */
|
||||
//
|
||||
// /** \brief Mesh */
|
||||
// stl vectoren
|
||||
// virtual unsigned int** tetrahedron(unsigned int level){} /* read tetrahedra on level l stored in hdf5 file and return them in simple form */
|
||||
// virtual int tetrahedron(unsigned int level, unsigned int ntetrahedron, unsigned int** tetrahedron){}
|
||||
// virtual unsigned int* vertexId(){} /* read identification tag of vertices */
|
||||
//
|
||||
// virtual double** vertex(unsigned int level){} /* read vertices */
|
||||
// virtual int vertex(unsigned int nvertex, double** vertex){} /* write vertices */
|
||||
//
|
||||
// virtual unsigned int** boundary(unsigned int level, unsigned int wboundary){} /* read boundary meshes stored in the hdf5 file on level and return number of them */
|
||||
// virtual int boundary(unsigned int level, unsigned int** boundary, unsigned int wboundary){} /* write whichboundary boundary mesh into file */
|
||||
//
|
||||
// virtual unsigned int** edge(unsigned int level, aqmedge* &edge){} /* read edges on level and return number of them */
|
||||
// virtual int edge(unsigned int level, unsigned int* edge){} /* write edges on level and return number of them */
|
||||
//
|
||||
// virtual unsigned int** triangle(unsigned int level){} /* read Triangular faces on level */
|
||||
// virtual int triangle(unsigned int level, unsigned int** triangle){} /* write Triangular faces on level */
|
||||
//
|
||||
// /** \brief Materials */
|
||||
// bool existsMaterials() /* find out if there are materials parameters at discrete frequencies, energies or wavelength */
|
||||
//
|
||||
// vector<double> frequency(){} /* read a vector of discrete frequencies stored in the file */
|
||||
// int frequency(vector<double> f){} /* store a vector of discrete frequencies into the file */
|
||||
//
|
||||
// vector<double> energy(){} /* read a vector of discrete energies stored in the file */
|
||||
// int energy(vector<double> e){} /* store a vector of discrete wavelengths into the file */
|
||||
//
|
||||
// vector<double> wavelength(){} /* read a vector of discrete wavelengths stored in the file */
|
||||
// int wavelength(vector<double> lambda){} /* store a vector of discrete wavelengths into the file */
|
||||
//
|
||||
// vector< complex<double> > permittivity(){} /* read a vector of complex valued relative permittivities from the file */
|
||||
// int permittivity( vector< complex<double> > epsilonr){} /* store a vector of complex valued relative permittivities into the file */
|
||||
//
|
||||
// vector< complex<double> > permeability(){} /* read a vector of complex valued relative permittivities from the file */
|
||||
// int permeability( vector< complex<double> > mur){} /* store a vector of complex valued relative permittivities into the file */
|
||||
//
|
||||
// vector< complex<double> > conductivity(){} /* read a vector of complex valued relative permittivities from the file */
|
||||
// int conductivity( vector< complex<double> sigma>){} /* store a vector of complex valued relative permittivities into the file */
|
||||
//
|
||||
// /** \brief Materials */
|
||||
// bool existsDebyeMaterial(){} /* are the Debye material model paramters */
|
||||
// bool existsLorentz(){} /* are there Lorentz material model parameters */
|
||||
// bool existsDrudeMaterial(){} /* are there Drude material model parameters */
|
||||
//
|
||||
// /* Debye dielectric material model parameters, cf. Taflove et al. pp. 354 */
|
||||
// std<double> weightsDebye(){} /* retrieve vector of Debye material model weights */
|
||||
// int weightsDebye(vector<double> weightsdebye){} /* store vector of Debye material model weights */
|
||||
//
|
||||
// std<double> relaxationFrequencyDebye(){} /* retrieve vector of Debye material model relaxation frequencies */
|
||||
// int relaxationFrequencyDebye(vector<double> relaxfreq){} /* retrieve vector of Debye material model relaxation frequencies */
|
||||
//
|
||||
// double epsilonStaticDebye(){} /* retrieve static limit of relative permittivitiye */
|
||||
// int epsilonStaticDebye(double epsilonstaticr){} /* store static limit of relative permittivitiye */
|
||||
//
|
||||
// double epsilonInfinityDebye(){} /* retrieve infinite limit of relative permittivity */
|
||||
// int epsilonInfinityDebye(double epsiloninftyr){} /* store infinite limit of relative permittivity */
|
||||
//
|
||||
// /* Lorentz dielectric material model parameters, cf. Taflove et al. pp. 354 */
|
||||
// std<double> weightsLorentz(){} /* retrieve vector of Debye material model weights */
|
||||
// int weightsLorentz(vector<double> weightsdebye){} /* store vector of Debye material model weights */
|
||||
//
|
||||
// std<double> poleFrequencyLorentz(){} /* retrieve vector of Lorentz material model relaxation frequencies */
|
||||
// int poleFrequencyDebye(vector<double> polefreq){} /* retrieve vector of Lorentz material model relaxation frequencies */
|
||||
//
|
||||
// std<double> dampingCoefficientLorentz(){} /* retrieve vector of Lorentz material model damping coefficients */
|
||||
// int dampingCoefficientLorentz(vector<double> dampingcoeff){} /* retrieve vector of Lorentz material model damping coefficients */
|
||||
//
|
||||
// double epsilonStaticLorentz(){} /* retrieve static limit of relative permittivitiye */
|
||||
// int epsilonStaticLorentz(double epsilonstaticr){} /* store static limit of relative permittivitiye */
|
||||
//
|
||||
// double epsilonInfinityLorentz(){} /* retrieve infinite limit of relative permittivity */
|
||||
// int epsilonInfinityLorentz(double epsiloninftyr){} /* store infinite limit of relative permittivity */
|
||||
//
|
||||
// /* Drude dielectric material model parameters, cf. Taflove et al. pp. 354 */
|
||||
// std<double> weightsDrude(){} /* retrieve vector of Drude material model weights */
|
||||
// int weightsDrude(vector<double> weightsdebye){} /* store vector of Drude material model weights */
|
||||
//
|
||||
// std<double> poleFrequencyDrude(){} /* retrieve vector of Drude material model pole frequencies */
|
||||
// int poleFrequencyDrude(vector<double> relaxfreq){} /* retrieve vector of Drude material model pole frequencies */
|
||||
//
|
||||
// std<double> inversePoleRelaxationTimeDrude(){} /* retrieve vector of Lorentz material model inverse pole relaxation time */
|
||||
// int inversePoleRelaxationTimeDrude(vector<double> inversepolerelaxtime){} /* retrieve vector of Lorentz material model inverse pole relaxation time */
|
||||
//
|
||||
// double epsilonStaticDrude(){} /* retrieve static limit of relative permittivitiye */
|
||||
// int epsilonStaticDrude(double epsilonstaticr){} /* store static limit of relative permittivitiye */
|
||||
//
|
||||
// double epsilonInfinityDrude(){} /* retrieve infinite limit of relative permittivity */
|
||||
// int epsilonInfinityDRude(double epsiloninftyr){} /* store infinite limit of relative permittivity */
|
||||
//________________________________________________________________
|
||||
// protected:
|
||||
//
|
||||
|
||||
private:
|
||||
//-----------------------------------------------------------------------//
|
||||
// Private data structure. //
|
||||
//-----------------------------------------------------------------------//
|
||||
// Store the filename of the H5Fed here.
|
||||
string fileName_;
|
||||
// Store the file access rights of the H5Fed here.
|
||||
string fileAccess_;
|
||||
|
||||
// Hdf5 error variable stores the success of an Hdf5 action.
|
||||
herr_t hdf5Status_;
|
||||
// Hdf5 file identifier for file access. If a file access fails, the
|
||||
// identifyer is negetive.
|
||||
hid_t hdf5FileIdent_;
|
||||
|
||||
// If the elements we want to write to the h5fed file are not consecutive
|
||||
// and with gaps numbered, this API shoud be able to map this to an gapfree
|
||||
// and consecutive index set.
|
||||
// To activate this function we have the following variable.
|
||||
bool doIndexMapping_;
|
||||
// The first entry in indexMap_ is the old index of a coordinate, the
|
||||
// second is the new index usend in the h5fed file.
|
||||
std::map<unsigned int, unsigned int> indexMap_;
|
||||
// The first entry in positionMap_ is the new index usend in the h5fed
|
||||
// file, the second is the old postion in the coordinate vector.
|
||||
std::map<unsigned int, unsigned int> positionMap_;
|
||||
|
||||
//-----------------------------------------------------------------------//
|
||||
// Private helper functions. //
|
||||
//-----------------------------------------------------------------------//
|
||||
// This function converts a number to a string.
|
||||
template<typename type>
|
||||
inline std::string stringify(type value)
|
||||
{
|
||||
std::ostringstream oStream;
|
||||
try
|
||||
{
|
||||
oStream << value;
|
||||
}
|
||||
catch(exception& error)
|
||||
{
|
||||
rError("Cannot convert this variable to a string.");
|
||||
rError("Error: %d",error.what());
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
return oStream.str();
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
} // End of namespace H5Fed
|
||||
|
||||
|
||||
#endif // HAVE_HDF5
|
||||
#endif //H5FED_HH_
|
||||
@@ -0,0 +1,50 @@
|
||||
#ifndef H5FEDCONST_HH_
|
||||
#define H5FEDCONST_HH_
|
||||
|
||||
#include<string>
|
||||
using namespace std;
|
||||
|
||||
//! 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");
|
||||
|
||||
// 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");
|
||||
|
||||
// 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");
|
||||
|
||||
// How much nodes have a geometric figure.
|
||||
const unsigned short int H5FED_TET_N_NODE = 4;
|
||||
const unsigned short int H5FED_HEX_N_NODE = 8;
|
||||
const unsigned short int H5FED_PRISMATIC_N_NODE = 6;
|
||||
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;
|
||||
|
||||
|
||||
#endif /*H5FEDCONST_HH_*/
|
||||
@@ -0,0 +1,14 @@
|
||||
## Makefile.am -- process this file with automake to produce Makefile.in
|
||||
##
|
||||
## authors - benedikt oswald and patrick leidenberger
|
||||
## modified - 2006 aug 24, patrick leidenberger, creation
|
||||
#
|
||||
## objective - automake input file for the h5fed directory
|
||||
## project - gmsh2h5fed
|
||||
|
||||
noinst_LTLIBRARIES = libh5fed.la
|
||||
h5feddir = $(topleveldir)/libsrc/h5fed
|
||||
h5fed_HEADERS = h5fed.hh
|
||||
libh5fed_la_SOURCES = h5fed.cc \
|
||||
h5fed.hh
|
||||
AM_CPPFLAGS = @AM_CPPFLAGS@
|
||||
@@ -0,0 +1,11 @@
|
||||
## Makefile.am -- process this file with automake to produce Makefile.in
|
||||
##
|
||||
## authors - benedikt oswald and patrick leidenberger
|
||||
## modified - 2006 aug 21, patrick leidenberger, creation
|
||||
## modified - 2006 aug 24, pl, add h5fed path.
|
||||
#
|
||||
## objective - automake input file for the libsrc directory
|
||||
## project - gmsh2h5fed
|
||||
|
||||
SUBDIRS = gmsh h5fed
|
||||
AM_CPPFLAGS = @AM_CPPFLAGS@
|
||||
@@ -0,0 +1,143 @@
|
||||
// rights - copyright by benedikt oswald, 2002-2006, all rights reserved
|
||||
// project - phidias3d
|
||||
// file name - nonsciconst.h
|
||||
// file type - c++ include file
|
||||
// author - benedikt oswald
|
||||
// modified - 2004 may 21, creation, benedikt oswald
|
||||
// modified - 2004 jun 11, added font definitions, benedikt oswald
|
||||
// modified - 2006 jun 26, transferred to project phidias3d, benedikt oswald
|
||||
// modified - 2006 jun 28, correction of RIGHTANGLE_DEG from int to double,
|
||||
// patrick leidenberger
|
||||
// modified - 2006 jul 11, add vtk cell type constants,
|
||||
// patrick leidenberger
|
||||
// objective - define technical, non-scientific constants, e.g. plot paper
|
||||
// dimensions etc.
|
||||
|
||||
|
||||
/* include standard libraries */
|
||||
#include <cmath>
|
||||
#include <complex>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
|
||||
#ifndef _NONSCICONST_
|
||||
#define _NONSCICONST_
|
||||
|
||||
using namespace std;
|
||||
|
||||
namespace nonsciconst
|
||||
{
|
||||
|
||||
const double A4WIDTH = 210.0;
|
||||
const double A4HEIGHT = 297.0;
|
||||
|
||||
const double A5WIDHT = 105.0;
|
||||
const double A5HEIGHT = 148.5;
|
||||
|
||||
const unsigned int FRAMED = 1;
|
||||
const unsigned int NOTFRAMED = 0;
|
||||
const unsigned int BELOW = 1;
|
||||
const unsigned int ABOVE = 0;
|
||||
const unsigned int ATLEFT = 1;
|
||||
const unsigned int ATRIGHT = 0;
|
||||
const unsigned int FILLED = 1;
|
||||
const unsigned int NOTFILLED = 0;
|
||||
const unsigned int OUTERFACES = 1;
|
||||
const unsigned int INNERFACES = 0;
|
||||
|
||||
const double RIGHTANGLE_DEG = 90.0;
|
||||
|
||||
const unsigned int DRAW_GRID_NODES_FLAG = 1;
|
||||
const unsigned int DRAW_GRID_LINES_FLAG = 1;
|
||||
|
||||
const double MAXHUE = 0.7;
|
||||
const double MAXSAT = 1.0;
|
||||
const double MAXBRG = 1.0;
|
||||
|
||||
const unsigned int GRAY_COLORSPACE = 0;
|
||||
const unsigned int RGB_COLORSPACE = 2;
|
||||
const unsigned int HSB_COLORSPACE = 4;
|
||||
const unsigned int CMYK_COLORSPACE = 8;
|
||||
|
||||
const double HSB_H_BLUE = 0.7;
|
||||
const double HSB_H_RED = 1.0;
|
||||
const double HSB_H_BLACK = 0.1;
|
||||
|
||||
const unsigned int LEGEND_HORIZONTAL = 1;
|
||||
const unsigned int LEGEND_VERTICAL = 0;
|
||||
|
||||
const unsigned int NUMCHARPLTFLNM = 256;
|
||||
const unsigned int NUMCHARSTRINGPLOTPROD = 256;
|
||||
const unsigned int DSPLYSTRLE = 512;
|
||||
const unsigned int MAXFILENAMSTRLEN = 512;
|
||||
const unsigned int DSPSTRLEN = 256;
|
||||
|
||||
const double MINIMUM_DB_VAL = -60.0;
|
||||
|
||||
const string HELVETICA_OBLIQUE_FNT("Helvetica-Oblique");
|
||||
const string HELVETICA_FNT("Helvetica");
|
||||
const string TIMES_FNT("Times-Roman");
|
||||
const string ARIAL_FNT("Arial");
|
||||
const string SYMBOL_FNT("Symbol");
|
||||
|
||||
const double INCHINPT = 72.0; /* define an inch in points, a typographic unit */
|
||||
const double INCHINMM = 25.4; /* define an inch in millimeter */
|
||||
|
||||
const string ELECTRIC_FIELD_UNIT_STRING("[V/m]");
|
||||
const string ELECTRIC_FIELD_UNIT_STRING_DB("[norm. dB]");
|
||||
|
||||
const double TEXT_DOWN_DIR_DEG = 270.0;
|
||||
const double TEXT_RIGHT_DIR_DEG = 0.0;
|
||||
|
||||
const unsigned int COLRSPCDIM = 3;
|
||||
|
||||
const double PSGRAF3_SYMBOL_RADIUS_PCOORD=0.3;
|
||||
|
||||
const int PSGRAF3_SYMBOL_CIRCLE = 0;
|
||||
const int PSGRAF3_SYMBOL_SQUARE = 1;
|
||||
const int PSGRAF3_SYMBOL_RHOMBUS = 2;
|
||||
const int PSGRAF3_SYMBOL_TRIANGLE_TIPUP = 3;
|
||||
const int PSGRAF3_SYMBOL_TRIANGLE_TIPDOWN = 4;
|
||||
|
||||
const int OKCODE = 0;
|
||||
const int ERRORCODE = 1;
|
||||
const int ERROR_SINGULAR_MATRIX = 2;
|
||||
const int ERROR_PSGRAF3_NOT_AVAILABLE = 3;
|
||||
const int ERROR_NNZ_IS_ZERO = 100;
|
||||
|
||||
|
||||
const string VTK_LFF_EXTENSION(".vtk");
|
||||
const string HDF5_EXTENSION(".h5");
|
||||
|
||||
const string TAB_STRING("\t");
|
||||
const string SINGLE_SPACE(" ");
|
||||
|
||||
|
||||
const int DEFAULT_FLOAT_PRECISION=6;
|
||||
|
||||
// Define constants for vtk cell types.
|
||||
const unsigned int VTK_VERTEX = 1;
|
||||
const unsigned int VTK_POLY_VERTEX = 2;
|
||||
const unsigned int VTK_LINE = 3;
|
||||
const unsigned int VTK_POLY_LINE = 4;
|
||||
const unsigned int VTK_TRIANGLE = 5;
|
||||
const unsigned int VTK_TRIANGEL_STRIP = 6;
|
||||
const unsigned int VTK_POLYGON = 7;
|
||||
const unsigned int VTK_PIXEL = 8;
|
||||
const unsigned int VTK_QUAD = 9;
|
||||
const unsigned int VTK_TETRA = 10;
|
||||
const unsigned int VTK_VOXEL = 11;
|
||||
const unsigned int VTK_HEXAHEDRON = 12;
|
||||
const unsigned int VTK_WEDGE = 13;
|
||||
const unsigned int VTK_PYRAMID = 14;
|
||||
const unsigned int VTK_QUADRATIC_EDGE = 21;
|
||||
const unsigned int VTK_QUADRATIC_TRIANGLE = 22;
|
||||
const unsigned int VTK_QUADRATIC_QUAD = 23;
|
||||
const unsigned int VTK_QUADRATIC_TETRA = 24;
|
||||
const unsigned int VTK_QUATRATIC_HEXAHEDRON = 25;
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@@ -0,0 +1,72 @@
|
||||
// rights - copyright by benedikt oswald, 2002-2006, all rights reserved
|
||||
// project - phidias3d
|
||||
// file name - physicomath.h
|
||||
// file type - c++ include file
|
||||
// author - benedikt oswald
|
||||
// modified - 2003 jan 30, creation -
|
||||
// modified - 2006 jun 26, transferred to project phidias3d, benedikt oswald
|
||||
// objective - physical and mathematical quantities, constansts etc.
|
||||
|
||||
#include <cmath>
|
||||
#include <complex>
|
||||
|
||||
#ifndef _PHYSICO_MATH_
|
||||
#define _PHYSICO_MATH_
|
||||
|
||||
using namespace std;
|
||||
|
||||
namespace physicomath
|
||||
{
|
||||
const double ZERO = 0;
|
||||
const int INT_ZERO = 0;
|
||||
const unsigned int UNSIGNED_INT_ZERO = 0;
|
||||
const double DOUBLE_ZERO = 0.0;
|
||||
const int INT_ONE = 1;
|
||||
const unsigned int UNSIGNED_INT_ONE = 1;
|
||||
const int INT_TWO = 2;
|
||||
const double DOUBLE_ONE = 1.0;
|
||||
const double DOUBLE_TWO = 2.0;
|
||||
|
||||
#ifndef IMAGINARY_UNIT_
|
||||
#define IMAGINARY_UNIT_
|
||||
const complex<double> IU(0.0,1.0);
|
||||
#endif
|
||||
|
||||
const double PI = 3.1415926535;
|
||||
const double EPSILON_ZERO = 8.85418782e-12;
|
||||
|
||||
const double MU_ZERO = 4.0 * PI * 1.0e-7;
|
||||
|
||||
const double SPEED_OF_LIGHT = (1.0/(sqrt(EPSILON_ZERO*MU_ZERO)));
|
||||
|
||||
const double Z0 = sqrt(MU_ZERO/EPSILON_ZERO);
|
||||
|
||||
const double TERAHERTZ = 1.0e12;
|
||||
const double GIGAHERTZ = 1.0e9;
|
||||
const double MEGAHERTZ = 1.0e6;
|
||||
const double KILOHERTZ = 1.0e3;
|
||||
|
||||
const double SECOND = 1.0e0;
|
||||
const double MILLISECOND = 1.0e-3;
|
||||
const double MICROSECOND = 1.0e-6;
|
||||
const double NANOSECOND = 1.0e-9;
|
||||
const double PICOSECOND = 1.0e-12;
|
||||
const double FEMTOSECOND = 1.0e-15;
|
||||
|
||||
|
||||
const double L_BAND_CENTER_FREQUENCY=1.414e9;
|
||||
|
||||
const double DOUBLE_REL_ZERO_LIMIT=1.0e-100;
|
||||
|
||||
|
||||
const double METER = 1.0; /* define a meter, the standard */
|
||||
const double DECIMETER = 0.1; /* define a tenth of a meter */
|
||||
const double CENTIMETER = 1.0e-2; /* define a centimeter */
|
||||
const double MICROMETER = 1.0e-6; /* define a micrometer */
|
||||
const double NANOMETER = 1.0e-9; /* define a nanomenter */
|
||||
const double ANGSTROM = 1.0e-10; /* define an angstrom */
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@@ -0,0 +1,10 @@
|
||||
## Makefile.am -- process this file with automake to produce Makefile.in
|
||||
##
|
||||
## authors - patrick leidenberger
|
||||
## modified - 2006 aug 21, patrick leidenberger, creation
|
||||
## objective - top level automake file for H5Fed
|
||||
## project - H5Fed
|
||||
|
||||
SUBDIRS = libsrc applications
|
||||
|
||||
AM_CPPFLAGS = @AM_CPPFLAGS@
|
||||
+11
-18
@@ -1,21 +1,14 @@
|
||||
ACLOCAL_AMFLAGS = -I m4
|
||||
EXTRA_DIST = \
|
||||
autogen.sh \
|
||||
ax_pkg_swig.m4
|
||||
# Trial by Antino Kim
|
||||
# Top level Makefile.am
|
||||
|
||||
SUBDIRS = \
|
||||
src \
|
||||
test \
|
||||
tools \
|
||||
doc \
|
||||
examples/H5 \
|
||||
examples/H5Part \
|
||||
examples/H5Block \
|
||||
examples/H5Fed
|
||||
SUBDIRS = \
|
||||
src \
|
||||
test \
|
||||
tools
|
||||
|
||||
MAINTAINERCLEANFILES = \
|
||||
config.h \
|
||||
config.log \
|
||||
config.status \
|
||||
stamp-h.in \
|
||||
MAINTAINERCLEANFILES = \
|
||||
config.h \
|
||||
config.log \
|
||||
config.status \
|
||||
stamp-h.in \
|
||||
stamp-h1
|
||||
|
||||
Executable
+59
@@ -0,0 +1,59 @@
|
||||
|
||||
# This is a very rudimentary multiarchitecture makefile
|
||||
# You need to uncomment the default block of make variables you need
|
||||
# Some key things to watch for are the following defines
|
||||
# -DREGRESSIONTEST : enables a main(){} inside of
|
||||
# the H5Part.cc file that does simple regression testing.
|
||||
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
|
||||
# enable this. Otherwise, you get only the serial
|
||||
# implementation of the library.
|
||||
|
||||
# MacOS-X Serial
|
||||
#CXX = c++
|
||||
#CC = cc
|
||||
#F90 = xlf
|
||||
#H5HOME = /usr/local
|
||||
#CFLAGS = -O -g -I$(H5HOME)/include
|
||||
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
|
||||
# AIX/SP-2 Parallel : Seaborg
|
||||
#CXX = mpCC_r
|
||||
#CC = mpcc_r
|
||||
#F90 = mpxlf
|
||||
#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
|
||||
#H4HOME = /usr/common/usg/hdf/default
|
||||
#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
|
||||
#CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
|
||||
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
|
||||
|
||||
# Linux Serial
|
||||
#CXX = g++
|
||||
#CC = gcc
|
||||
#F90 = g77 # or could be pgif90
|
||||
#CFLAGS = -O -g -I$(H5HOME)/include
|
||||
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
|
||||
# Linux Jacquard
|
||||
CC = mpicc
|
||||
CXX = mpicxx
|
||||
F90 = mpif90
|
||||
H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
|
||||
CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
|
||||
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
|
||||
|
||||
# Linux Parallel
|
||||
#CC = gcc
|
||||
#CXX = g++
|
||||
#F90 = g77
|
||||
#H5HOME = /usr/local
|
||||
# /usr/common/usg/hdf5/1.6.3/parallel
|
||||
#MPIHOME = /usr/local
|
||||
#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
|
||||
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
|
||||
|
||||
all: H5PartTest H5PartTest.o H5Part.o
|
||||
parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
|
||||
fortran: H5PartF.o # fortran bindings
|
||||
|
||||
include rules.make
|
||||
|
||||
@@ -1,257 +1,3 @@
|
||||
#### H5PART trunk ############################################################
|
||||
|
||||
* h5_file_t is now uintptr_t
|
||||
* experimental version of parallel H5Fed
|
||||
* new API function for file open using properties (similiar to hdf5 properties)
|
||||
|
||||
#### H5PART 1.99.10 ############################################################
|
||||
|
||||
* C99 compiler required
|
||||
* C API with inline functions
|
||||
|
||||
|
||||
#### H5PART 1.99.0 ############################################################
|
||||
|
||||
rudimental implementation of a grid manager
|
||||
|
||||
Important changes from version 1.6 to 1.99.0
|
||||
|
||||
Renamed type:
|
||||
H5PartFile -> h5_file_t
|
||||
h5part_int64_t -> h5_int64_t
|
||||
h5part_float64_t -> h5_float_t
|
||||
|
||||
Renamed functions:
|
||||
All function not related to a specific data model have been renamed from
|
||||
H5PartFunction() to H5Function().
|
||||
|
||||
Example:
|
||||
H5PartOpenFile() -> H5OpenFile()
|
||||
|
||||
Removed functions:
|
||||
To simplify the API, there is just one function to open a file. It's the
|
||||
same function for serial and parallel code.
|
||||
|
||||
#### H5PART 1.6.6 ############################################################
|
||||
|
||||
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
|
||||
interface.
|
||||
|
||||
Added missing type normalization for int32 type.
|
||||
|
||||
Rewrite of h5pAttrib tool.
|
||||
|
||||
#### H5PART 1.6.5 ############################################################
|
||||
|
||||
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
|
||||
|
||||
#### H5PART 1.6.4 ############################################################
|
||||
|
||||
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
|
||||
number of elements is 0.
|
||||
|
||||
Set a threshold on the HDF5 alignment parameter so that small metadata writes
|
||||
are not aligned, which causes large gaps in the file.
|
||||
|
||||
#### H5PART 1.6.3 ############################################################
|
||||
|
||||
New build system uses libtool and can build shared libraries.
|
||||
|
||||
Fixed a bug that incorrectly identifies the number of selected points in a view
|
||||
when using H5PartSetViewIndices.
|
||||
|
||||
Fixed bug in Fortran test reported by several people, as well as several
|
||||
incorrect views set in the C test that were causing segfaults.
|
||||
|
||||
Fixed name mismatches in the Fortran interface, and an off-by-one indexing
|
||||
problem.
|
||||
|
||||
#### H5PART 1.6.2 ############################################################
|
||||
|
||||
Removed H5PartSetViewEmpty
|
||||
--------------------------
|
||||
|
||||
An empty view can now be selected with:
|
||||
H5PartSetNumParticles(file, 0);
|
||||
|
||||
Bug Fixes to Attribute Calls in Fortran API
|
||||
-------------------------------------------
|
||||
|
||||
Fixed a problem where attribute values were reverting to zero.
|
||||
|
||||
#### H5PART 1.6.1 ############################################################
|
||||
|
||||
Chunking in the H5Part API
|
||||
--------------------------
|
||||
|
||||
There is now an H5Part equivalent H5PartSetChunkSize to the existing
|
||||
H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
|
||||
mechanism in the underlying HDF5 layer. Chunking is used in combination
|
||||
with the aligned open calls to pad datasets to alignment multiples
|
||||
on disk.
|
||||
|
||||
All Steps Available on Write
|
||||
----------------------------
|
||||
|
||||
Previously, existing steps in a file were only accessible in read-only mode.
|
||||
Now, all steps are available in all modes, including write-truncate and
|
||||
write-append. Thus, it is now possible to overwrite existing data in write
|
||||
mode. To help alert the user to this possibility, a warning is issued every
|
||||
time an existing dataset is written to. Warnings can be printed by setting
|
||||
the verbosity to H5PART_VERB_WARN or higher.
|
||||
|
||||
New Throttling Routine
|
||||
----------------------
|
||||
|
||||
Previously, a throttle factor of N meant that for P processors, the total
|
||||
number of P writes were divided into N batches of P/N writes.
|
||||
|
||||
To better accommodate round-robin lustre striping, the new policy is to
|
||||
execute P/N batches of N writes. Thus, matching N to the number of stripes
|
||||
results in the desirable 1-1 matching of writers to stripes.
|
||||
|
||||
Other Fixes
|
||||
-----------
|
||||
|
||||
* The configure script should correctly detect PGI compilers now.
|
||||
* There was a small memory leak in the Fortran file open calls.
|
||||
* There was a compile error with HDF5 1.6.x due to a missing assignment.
|
||||
|
||||
#### H5PART 1.6 ##############################################################
|
||||
|
||||
Updated Documentation
|
||||
---------------------
|
||||
|
||||
The Fortran API has been added to the doxygen documentation. Most entries have
|
||||
a reference to their respective C API call.
|
||||
|
||||
Regression Test Suite
|
||||
---------------------
|
||||
|
||||
The test subdirectory has been reorganized to include a systematic series
|
||||
of regression tests of common use cases for the API. The goal is to have both
|
||||
complete coverage of the API (every call is exercised) and testing of some
|
||||
unlikely or unsuspected values and cases.
|
||||
|
||||
Currently, the C test covers the entire H5Part API and the Fortran test is
|
||||
still in development.
|
||||
|
||||
Benchmark Utilities
|
||||
-------------------
|
||||
|
||||
Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
|
||||
the tools collection. Both require the parallel library and have functionality
|
||||
and syntax similar to the IOR benchmark:
|
||||
|
||||
http://sourceforge.net/projects/ior-sio/
|
||||
|
||||
File Mode Flags
|
||||
---------------
|
||||
|
||||
Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
|
||||
H5PART_APPEND, and these were mutually exclusive. Additional flags have been
|
||||
added to select the underlying virtual file driver (VFD) that HDF5 uses in
|
||||
parallel mode and to accommodate the lustre filesystem:
|
||||
|
||||
H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
|
||||
H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
|
||||
H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
|
||||
|
||||
These flags can be specified using the typical bitwise OR method, e.g.
|
||||
|
||||
char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
|
||||
|
||||
will select write mode with these two additional options.
|
||||
|
||||
The parallel library now defaults to using the MPI-IO collective mode driver
|
||||
(previously it used independent mode). The collective buffering algorithm in
|
||||
the Cray XT4/5 environment has been substantially improved in the last year,
|
||||
and defaulting to collective mode allows us to take advantage of these
|
||||
improvements automatically.
|
||||
|
||||
There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
|
||||
take an additional 'alignment' value. This value is passed to HDF5 and used to
|
||||
pad out objects so that they align to filesystem boundaries. For instance, it
|
||||
would make sense to use the stripe size as the alignment value when writing to
|
||||
a lustre filesystem.
|
||||
|
||||
Unified 'View' Model
|
||||
--------------------
|
||||
|
||||
Views are now supported in both read and write mode (previously only supported
|
||||
in read mode). It is possible to specify non-sensical views: you could for
|
||||
instance specify a read view that is larger than the dataset on disk. Or you
|
||||
could create a write view that is larger than the data in memory. In those
|
||||
cases, you will encounter an error when you try to perform a read or write
|
||||
operation on a dataset.
|
||||
|
||||
There are two new methods for selecting views. H5PartSetNumParticlesStrided
|
||||
selects a view with $n$ particles per processor, but such that the data in
|
||||
memory is expected to have a 'stride' factor. For instance, if you have
|
||||
particle data with fields $x$ and $y$ and a single array with entries
|
||||
$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
|
||||
and writes and only affects the view of memory: individual fields are still
|
||||
stored as individual arrays on disk.
|
||||
|
||||
The second new method is H5PartSetViewIndices, which allows for point
|
||||
selections of datasets. You can pass a list of indices for the points you
|
||||
want to select. This is useful, for instance, when interfacing with FastBit
|
||||
to perform queries that select a small subset of non-contiguous particles.
|
||||
|
||||
Because views are now supported on write, it is possible to write a dataset
|
||||
using multiple 'passes' or to leave some values unwritten.
|
||||
|
||||
Also, all views are now *inclusive*, so that a view of (0,9) corresponds
|
||||
to the 10 items 0, 1, 2, ... 9.
|
||||
|
||||
Internal Handling of Dataspaces
|
||||
-------------------------------
|
||||
|
||||
H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
|
||||
HDF5 dataspace state in the H5PartFile struct with the calls that modify
|
||||
the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
|
||||
were regenerated from the view on every read access, which was unnecessary.
|
||||
|
||||
Autogeneration of API Calls
|
||||
---------------------------
|
||||
|
||||
Python scripts have been added to automatically generate read/write call
|
||||
variants for different data types.
|
||||
|
||||
Renamed Fortran Include
|
||||
-----------------------
|
||||
|
||||
The automake system no longer greps the *F90.inc files to generate an include
|
||||
called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
|
||||
and awk is used to generate an 'H5PartF.h' file (the same naming convention
|
||||
as in MPI's 'mpif.h').
|
||||
|
||||
The change to *.f90 was necessary to facilitate integration of the Fortran
|
||||
API into doxygen. Note that the *.f90 files will not compile, nor can they
|
||||
be included directly. Simply use
|
||||
|
||||
include 'H5PartF.h'
|
||||
|
||||
in your Fortran code to include all the definitions for Fortran H5Part/H5Block
|
||||
calls.
|
||||
|
||||
64 Char Limit on Dataset Names
|
||||
------------------------------
|
||||
|
||||
Previously, a user could overrun internal buffers for dataset names. Now, a
|
||||
fixed limit of 64 chars is imposed. Dataset names that are longer than this are
|
||||
truncated and a warning is printed. We expect that most users are using
|
||||
short canonical names like x, px, id, etc.
|
||||
|
||||
Changes to Existing API
|
||||
-----------------------
|
||||
|
||||
The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
|
||||
a parameter for the 'type' of the field.
|
||||
|
||||
|
||||
#### H5PART 1.4 ##############################################################
|
||||
|
||||
Error Handling
|
||||
--------------
|
||||
Now all functions, in which an error could occure, are returning a
|
||||
|
||||
@@ -0,0 +1,393 @@
|
||||
==============================================================================
|
||||
README file for H5Part configure
|
||||
==============================================================================
|
||||
|
||||
+ 0. HDF5 library
|
||||
-----------------
|
||||
|
||||
Make sure you have a working version of the HDF5 library in your computer. If you plan
|
||||
to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
|
||||
library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
|
||||
|
||||
+ 1. Quick start (If you feel lucky...)
|
||||
----------------------------------------
|
||||
|
||||
For many platforms, where compilers are installed in the "default" location
|
||||
and all the environment variables are set correctly, it should be sufficient
|
||||
to type:
|
||||
|
||||
./configure [OPTIONS] && make [install]
|
||||
|
||||
to have the libraries and test program compiled.
|
||||
|
||||
|
||||
==============================================================================
|
||||
|
||||
|
||||
+ 2. configure line options
|
||||
----------------------------
|
||||
|
||||
(1) Enable options
|
||||
--enable-fortran
|
||||
--enable-parallel
|
||||
--enable-tools
|
||||
--enable-python
|
||||
--enable-64 (only for AIX and Irix)
|
||||
|
||||
(2) Setting compilers related variables manually
|
||||
To assign environment variables (e.g., CC, CFLAGS...), specify them as
|
||||
VAR=VALUE. See below for descriptions of some of the useful variables.
|
||||
|
||||
Compiler environment variables:
|
||||
CC C compiler command
|
||||
CXX C++ compiler command
|
||||
FC Fortran compiler command
|
||||
|
||||
(3) Setting prefix for installation manually
|
||||
--prefix=PREFIX install files in PREFIX
|
||||
|
||||
|
||||
For more information, type:
|
||||
|
||||
./configure --help
|
||||
|
||||
|
||||
==============================================================================
|
||||
|
||||
|
||||
+ 3. Platform specific settings for compiling libraries & test programs
|
||||
------------------------------------------------------------------------
|
||||
|
||||
Building
|
||||
make : builds the libraries and test programs
|
||||
make install: builds and installs
|
||||
make clean : removes extraneous object files
|
||||
make distclean : returns configuration to unconfigured state
|
||||
|
||||
As tested on hosts:
|
||||
|
||||
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
|
||||
---------------------------------------------------
|
||||
FIRST THING FIRST!! Type:
|
||||
|
||||
module load intel
|
||||
to have the proper compilers set up for use.
|
||||
|
||||
module load hdf5_par
|
||||
|
||||
[NOTE: module load hdf5 does not work at this moment.
|
||||
Possible installation error of HDF5 on Davinci.]
|
||||
|
||||
|
||||
Brief profile:
|
||||
CC = icc
|
||||
CXX = icc
|
||||
FC = ifort
|
||||
MPICC = icc
|
||||
MPICXX = icc
|
||||
MPIFC = ifort
|
||||
|
||||
If default doesn't work, try:
|
||||
|
||||
For C shell:
|
||||
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
|
||||
|
||||
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
|
||||
|
||||
|
||||
On this host, executing:
|
||||
|
||||
For C shell:
|
||||
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
has functioned correctly.
|
||||
|
||||
|
||||
To run test program, go to test directory:
|
||||
|
||||
(i) Serial test
|
||||
run:
|
||||
./H5testF
|
||||
./H5PartTest
|
||||
|
||||
(ii) Parallel test
|
||||
run:
|
||||
mpirun 2 H5testFpar
|
||||
mpirun 2 H5PartTestP
|
||||
|
||||
NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
|
||||
-------------------------------------------------------
|
||||
Brief profile:
|
||||
CC = pathcc
|
||||
CXX = pathCC
|
||||
FC = pathf90
|
||||
MPICC = mpicc
|
||||
MPICXX = mpicxx
|
||||
MPIFC = mpif90
|
||||
|
||||
|
||||
|
||||
If default doesn't work, try:
|
||||
|
||||
For C shell:
|
||||
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
|
||||
|
||||
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
|
||||
|
||||
|
||||
|
||||
On this host, executing:
|
||||
|
||||
For C shell:
|
||||
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
has functioned correctly.
|
||||
|
||||
|
||||
|
||||
To run test program, go to test directory:
|
||||
|
||||
(i) Serial test
|
||||
run:
|
||||
./H5testF
|
||||
./H5PartTest
|
||||
|
||||
(ii) Parallel test
|
||||
In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
|
||||
|
||||
+++++++++++++++++++++++++++++++++++++++
|
||||
#!/bin/csh
|
||||
#PBS -l nodes=1:ppn=2,walltime=00:05:00
|
||||
#PBS -N H5testFpar
|
||||
#PBS -o H5testFpar.out
|
||||
#PBS -e H5testFpar.err
|
||||
#PBS -q debug
|
||||
#PBS -A mpccc
|
||||
#PBS -V
|
||||
|
||||
setenv PBS_OWORKDIR /home/H5Part/test
|
||||
|
||||
cd $PBS_O_WORKDIR
|
||||
mpirun -np 2 ./H5testFpar
|
||||
+++++++++++++++++++++++++++++++++++++++
|
||||
|
||||
Then, we need to submit the task to a queue by running:
|
||||
|
||||
qsub run_H5testFpar.scr
|
||||
|
||||
After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
|
||||
-------------------------------------------------
|
||||
FIRST THING FIRST!! Type:
|
||||
|
||||
module load gcc
|
||||
|
||||
to have the proper compilers set up for use.
|
||||
|
||||
Brief profile:
|
||||
CC = cc_r
|
||||
CXX = cc_r
|
||||
FC = xlf_r
|
||||
MPICC = mpcc_r
|
||||
MPICXX = mpcc_r
|
||||
MPIFC = mpxlf_r
|
||||
|
||||
|
||||
|
||||
If default doesn't work, try:
|
||||
|
||||
For C shell:
|
||||
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
|
||||
|
||||
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
|
||||
|
||||
|
||||
|
||||
On this host, executing:
|
||||
|
||||
For C shell:
|
||||
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
|
||||
|
||||
has functioned correctly.
|
||||
|
||||
|
||||
|
||||
To run test program, go to test directory:
|
||||
|
||||
(i) Serial test
|
||||
run:
|
||||
./H5testF
|
||||
./H5PartTest
|
||||
|
||||
(ii) Parallel test
|
||||
run:
|
||||
unsetenv MP_SINGLE_THREAD
|
||||
poe ./H5PartTestP -procs 2 -nodes 1
|
||||
poe ./H5testFpar -procs 2 -nodes 1
|
||||
|
||||
For more details on how to run parallel programs on Bassi, go to:
|
||||
|
||||
http://www.nersc.gov/nusers/resources/bassi/running_jobs/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
|
||||
----------------------------------------------------
|
||||
FIRST THING FIRST!! Set environment variables: (in tcsh)
|
||||
|
||||
setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
|
||||
setenv PATH ${PATH}:/usr/local/g95/bin
|
||||
|
||||
NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
|
||||
|
||||
Brief profile:
|
||||
CC = gcc
|
||||
CXX = g++
|
||||
FC = g95
|
||||
|
||||
|
||||
|
||||
If default doesn't work, try:
|
||||
|
||||
For C shell:
|
||||
env CC=gcc CXX=g++ FC=g95 ./configure && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=gcc CXX=g++ FC=g95 ./configure && make install
|
||||
|
||||
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
|
||||
|
||||
|
||||
|
||||
On this host, executing:
|
||||
|
||||
For C shell:
|
||||
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
|
||||
|
||||
has functioned correctly.
|
||||
|
||||
|
||||
|
||||
To run test program, go to test directory:
|
||||
|
||||
(i) Serial test
|
||||
run:
|
||||
./H5testF
|
||||
./H5PartTest
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
|
||||
---------------------------------------------------------
|
||||
Brief profile:
|
||||
CC = gcc
|
||||
CXX = g++
|
||||
FC = g95
|
||||
|
||||
|
||||
|
||||
If default doesn't work, try:
|
||||
|
||||
For C shell:
|
||||
env CC=gcc CXX=g++ FC=g95 ./configure && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=gcc CXX=g++ FC=g95 ./configure && make install
|
||||
|
||||
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
|
||||
|
||||
|
||||
|
||||
On this host, executing:
|
||||
|
||||
For C shell:
|
||||
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
|
||||
|
||||
For Korn or Bourne shell:
|
||||
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
|
||||
|
||||
has functioned correctly.
|
||||
|
||||
|
||||
|
||||
To run test program, go to test directory:
|
||||
|
||||
(i) Serial test
|
||||
run:
|
||||
./H5testF
|
||||
./H5PartTest
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
==============================================================================
|
||||
|
||||
|
||||
+ 4. Trouble shooting (Things to check for...)
|
||||
--------------------------------------------
|
||||
(0) Have you set the LD_LIBRARY_PATH?
|
||||
---Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
|
||||
|
||||
set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
|
||||
|
||||
For Korn or Bourne shell:
|
||||
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
|
||||
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
|
||||
|
||||
For C shell:
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
|
||||
|
||||
Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
|
||||
|
||||
Not properly set LD_LIBRARY_PATH value may result in a runtime error:
|
||||
|
||||
./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
|
||||
|
||||
(1) Are the compilers set correctly?
|
||||
---Check with: which COMPILER
|
||||
|
||||
(2) Have you installed HDF5?
|
||||
---You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
|
||||
|
||||
(3) Have you loaded the proper modules?
|
||||
---It is necessary in Davinci & Bassi, and configure && make install may not work without it.
|
||||
|
||||
|
||||
|
||||
+24
-26
@@ -1,48 +1,46 @@
|
||||
#!/bin/sh
|
||||
# Run this to generate all the initial makefiles, etc.
|
||||
|
||||
ACLOCAL_FLAGS="-I m4 -I . $ACLOCAL_FLAGS"
|
||||
LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
|
||||
AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
|
||||
|
||||
LIBTOOLIZE=`which libtoolize`
|
||||
if [ "$LIBTOOLIZE" = "" ]; then
|
||||
LIBTOOLIZE=`which glibtoolize`
|
||||
fi
|
||||
if [ "$LIBTOOLIZE" = "" ]; then
|
||||
echo "libtoolize not found" 1>&2
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "+ making misc files ..."
|
||||
touch NEWS README AUTHORS ChangeLog
|
||||
echo
|
||||
$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
|
||||
echo "libtoolize failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo
|
||||
echo "+ running aclocal ..."
|
||||
aclocal $ACLOCAL_FLAGS || {
|
||||
echo "aclocal failed - check that all needed development files are present on system"
|
||||
exit 1
|
||||
echo
|
||||
echo "aclocal failed - check that all needed development files are present on system"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo
|
||||
echo
|
||||
echo
|
||||
echo "+ running autoheader ... "
|
||||
autoheader || {
|
||||
echo "autoheader failed"
|
||||
exit 1
|
||||
echo
|
||||
echo "autoheader failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo
|
||||
echo
|
||||
echo "+ running autoconf ... "
|
||||
autoconf || {
|
||||
echo "autoconf failed"
|
||||
exit 1
|
||||
echo
|
||||
echo "autoconf failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo
|
||||
echo
|
||||
echo "+ running automake ... "
|
||||
automake $AUTOMAKE_FLAGS || {
|
||||
echo "automake failed"
|
||||
exit 1
|
||||
automake -a -c --foreign || {
|
||||
echo
|
||||
echo "automake failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo
|
||||
echo
|
||||
|
||||
|
||||
@@ -1,982 +0,0 @@
|
||||
# ===========================================================================
|
||||
# https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx.html
|
||||
# ===========================================================================
|
||||
#
|
||||
# SYNOPSIS
|
||||
#
|
||||
# AX_CXX_COMPILE_STDCXX(VERSION, [ext|noext], [mandatory|optional])
|
||||
#
|
||||
# DESCRIPTION
|
||||
#
|
||||
# Check for baseline language coverage in the compiler for the specified
|
||||
# version of the C++ standard. If necessary, add switches to CXX and
|
||||
# CXXCPP to enable support. VERSION may be '11' (for the C++11 standard)
|
||||
# or '14' (for the C++14 standard).
|
||||
#
|
||||
# The second argument, if specified, indicates whether you insist on an
|
||||
# extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
|
||||
# -std=c++11). If neither is specified, you get whatever works, with
|
||||
# preference for an extended mode.
|
||||
#
|
||||
# The third argument, if specified 'mandatory' or if left unspecified,
|
||||
# indicates that baseline support for the specified C++ standard is
|
||||
# required and that the macro should error out if no mode with that
|
||||
# support is found. If specified 'optional', then configuration proceeds
|
||||
# regardless, after defining HAVE_CXX${VERSION} if and only if a
|
||||
# supporting mode is found.
|
||||
#
|
||||
# LICENSE
|
||||
#
|
||||
# Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
|
||||
# Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
|
||||
# Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
|
||||
# Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
|
||||
# Copyright (c) 2015 Paul Norman <penorman@mac.com>
|
||||
# Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
|
||||
# Copyright (c) 2016 Krzesimir Nowak <qdlacz@gmail.com>
|
||||
#
|
||||
# Copying and distribution of this file, with or without modification, are
|
||||
# permitted in any medium without royalty provided the copyright notice
|
||||
# and this notice are preserved. This file is offered as-is, without any
|
||||
# warranty.
|
||||
|
||||
#serial 7
|
||||
|
||||
dnl This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro
|
||||
dnl (serial version number 13).
|
||||
|
||||
AX_REQUIRE_DEFINED([AC_MSG_WARN])
|
||||
AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
|
||||
m4_if([$1], [11], [ax_cxx_compile_alternatives="11 0x"],
|
||||
[$1], [14], [ax_cxx_compile_alternatives="14 1y"],
|
||||
[$1], [17], [ax_cxx_compile_alternatives="17 1z"],
|
||||
[m4_fatal([invalid first argument `$1' to AX_CXX_COMPILE_STDCXX])])dnl
|
||||
m4_if([$2], [], [],
|
||||
[$2], [ext], [],
|
||||
[$2], [noext], [],
|
||||
[m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX])])dnl
|
||||
m4_if([$3], [], [ax_cxx_compile_cxx$1_required=true],
|
||||
[$3], [mandatory], [ax_cxx_compile_cxx$1_required=true],
|
||||
[$3], [optional], [ax_cxx_compile_cxx$1_required=false],
|
||||
[m4_fatal([invalid third argument `$3' to AX_CXX_COMPILE_STDCXX])])
|
||||
AC_LANG_PUSH([C++])dnl
|
||||
ac_success=no
|
||||
AC_CACHE_CHECK(whether $CXX supports C++$1 features by default,
|
||||
ax_cv_cxx_compile_cxx$1,
|
||||
[AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
|
||||
[ax_cv_cxx_compile_cxx$1=yes],
|
||||
[ax_cv_cxx_compile_cxx$1=no])])
|
||||
if test x$ax_cv_cxx_compile_cxx$1 = xyes; then
|
||||
ac_success=yes
|
||||
fi
|
||||
|
||||
m4_if([$2], [noext], [], [dnl
|
||||
if test x$ac_success = xno; then
|
||||
for alternative in ${ax_cxx_compile_alternatives}; do
|
||||
switch="-std=gnu++${alternative}"
|
||||
cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
|
||||
AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
|
||||
$cachevar,
|
||||
[ac_save_CXX="$CXX"
|
||||
CXX="$CXX $switch"
|
||||
AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
|
||||
[eval $cachevar=yes],
|
||||
[eval $cachevar=no])
|
||||
CXX="$ac_save_CXX"])
|
||||
if eval test x\$$cachevar = xyes; then
|
||||
CXX="$CXX $switch"
|
||||
if test -n "$CXXCPP" ; then
|
||||
CXXCPP="$CXXCPP $switch"
|
||||
fi
|
||||
ac_success=yes
|
||||
break
|
||||
fi
|
||||
done
|
||||
fi])
|
||||
|
||||
m4_if([$2], [ext], [], [dnl
|
||||
if test x$ac_success = xno; then
|
||||
dnl HP's aCC needs +std=c++11 according to:
|
||||
dnl http://h21007.www2.hp.com/portal/download/files/unprot/aCxx/PDF_Release_Notes/769149-001.pdf
|
||||
dnl Cray's crayCC needs "-h std=c++11"
|
||||
for alternative in ${ax_cxx_compile_alternatives}; do
|
||||
for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do
|
||||
cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
|
||||
AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
|
||||
$cachevar,
|
||||
[ac_save_CXX="$CXX"
|
||||
CXX="$CXX $switch"
|
||||
AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
|
||||
[eval $cachevar=yes],
|
||||
[eval $cachevar=no])
|
||||
CXX="$ac_save_CXX"])
|
||||
if eval test x\$$cachevar = xyes; then
|
||||
CXX="$CXX $switch"
|
||||
if test -n "$CXXCPP" ; then
|
||||
CXXCPP="$CXXCPP $switch"
|
||||
fi
|
||||
ac_success=yes
|
||||
break
|
||||
fi
|
||||
done
|
||||
if test x$ac_success = xyes; then
|
||||
break
|
||||
fi
|
||||
done
|
||||
fi])
|
||||
AC_LANG_POP([C++])
|
||||
if test x$ax_cxx_compile_cxx$1_required = xtrue; then
|
||||
if test x$ac_success = xno; then
|
||||
AC_MSG_ERROR([*** A compiler with support for C++$1 language features is required.])
|
||||
fi
|
||||
fi
|
||||
if test x$ac_success = xno; then
|
||||
HAVE_CXX$1=0
|
||||
AC_MSG_NOTICE([No compiler with C++$1 support was found])
|
||||
else
|
||||
HAVE_CXX$1=1
|
||||
AC_DEFINE(HAVE_CXX$1,1,
|
||||
[define if the compiler supports basic C++$1 syntax])
|
||||
fi
|
||||
AC_SUBST(HAVE_CXX$1)
|
||||
m4_if([$1], [17], [AC_MSG_WARN([C++17 is not yet standardized, so the checks may change in incompatible ways anytime])])
|
||||
])
|
||||
|
||||
|
||||
dnl Test body for checking C++11 support
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_11],
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
|
||||
)
|
||||
|
||||
|
||||
dnl Test body for checking C++14 support
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_14],
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_14
|
||||
)
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_17],
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_14
|
||||
_AX_CXX_COMPILE_STDCXX_testbody_new_in_17
|
||||
)
|
||||
|
||||
dnl Tests for new features in C++11
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[
|
||||
|
||||
// If the compiler admits that it is not ready for C++11, why torture it?
|
||||
// Hopefully, this will speed up the test.
|
||||
|
||||
#ifndef __cplusplus
|
||||
|
||||
#error "This is not a C++ compiler"
|
||||
|
||||
#elif __cplusplus < 201103L
|
||||
|
||||
#error "This is not a C++11 compiler"
|
||||
|
||||
#else
|
||||
|
||||
namespace cxx11
|
||||
{
|
||||
|
||||
namespace test_static_assert
|
||||
{
|
||||
|
||||
template <typename T>
|
||||
struct check
|
||||
{
|
||||
static_assert(sizeof(int) <= sizeof(T), "not big enough");
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
namespace test_final_override
|
||||
{
|
||||
|
||||
struct Base
|
||||
{
|
||||
virtual void f() {}
|
||||
};
|
||||
|
||||
struct Derived : public Base
|
||||
{
|
||||
virtual void f() override {}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
namespace test_double_right_angle_brackets
|
||||
{
|
||||
|
||||
template < typename T >
|
||||
struct check {};
|
||||
|
||||
typedef check<void> single_type;
|
||||
typedef check<check<void>> double_type;
|
||||
typedef check<check<check<void>>> triple_type;
|
||||
typedef check<check<check<check<void>>>> quadruple_type;
|
||||
|
||||
}
|
||||
|
||||
namespace test_decltype
|
||||
{
|
||||
|
||||
int
|
||||
f()
|
||||
{
|
||||
int a = 1;
|
||||
decltype(a) b = 2;
|
||||
return a + b;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_type_deduction
|
||||
{
|
||||
|
||||
template < typename T1, typename T2 >
|
||||
struct is_same
|
||||
{
|
||||
static const bool value = false;
|
||||
};
|
||||
|
||||
template < typename T >
|
||||
struct is_same<T, T>
|
||||
{
|
||||
static const bool value = true;
|
||||
};
|
||||
|
||||
template < typename T1, typename T2 >
|
||||
auto
|
||||
add(T1 a1, T2 a2) -> decltype(a1 + a2)
|
||||
{
|
||||
return a1 + a2;
|
||||
}
|
||||
|
||||
int
|
||||
test(const int c, volatile int v)
|
||||
{
|
||||
static_assert(is_same<int, decltype(0)>::value == true, "");
|
||||
static_assert(is_same<int, decltype(c)>::value == false, "");
|
||||
static_assert(is_same<int, decltype(v)>::value == false, "");
|
||||
auto ac = c;
|
||||
auto av = v;
|
||||
auto sumi = ac + av + 'x';
|
||||
auto sumf = ac + av + 1.0;
|
||||
static_assert(is_same<int, decltype(ac)>::value == true, "");
|
||||
static_assert(is_same<int, decltype(av)>::value == true, "");
|
||||
static_assert(is_same<int, decltype(sumi)>::value == true, "");
|
||||
static_assert(is_same<int, decltype(sumf)>::value == false, "");
|
||||
static_assert(is_same<int, decltype(add(c, v))>::value == true, "");
|
||||
return (sumf > 0.0) ? sumi : add(c, v);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_noexcept
|
||||
{
|
||||
|
||||
int f() { return 0; }
|
||||
int g() noexcept { return 0; }
|
||||
|
||||
static_assert(noexcept(f()) == false, "");
|
||||
static_assert(noexcept(g()) == true, "");
|
||||
|
||||
}
|
||||
|
||||
namespace test_constexpr
|
||||
{
|
||||
|
||||
template < typename CharT >
|
||||
unsigned long constexpr
|
||||
strlen_c_r(const CharT *const s, const unsigned long acc) noexcept
|
||||
{
|
||||
return *s ? strlen_c_r(s + 1, acc + 1) : acc;
|
||||
}
|
||||
|
||||
template < typename CharT >
|
||||
unsigned long constexpr
|
||||
strlen_c(const CharT *const s) noexcept
|
||||
{
|
||||
return strlen_c_r(s, 0UL);
|
||||
}
|
||||
|
||||
static_assert(strlen_c("") == 0UL, "");
|
||||
static_assert(strlen_c("1") == 1UL, "");
|
||||
static_assert(strlen_c("example") == 7UL, "");
|
||||
static_assert(strlen_c("another\0example") == 7UL, "");
|
||||
|
||||
}
|
||||
|
||||
namespace test_rvalue_references
|
||||
{
|
||||
|
||||
template < int N >
|
||||
struct answer
|
||||
{
|
||||
static constexpr int value = N;
|
||||
};
|
||||
|
||||
answer<1> f(int&) { return answer<1>(); }
|
||||
answer<2> f(const int&) { return answer<2>(); }
|
||||
answer<3> f(int&&) { return answer<3>(); }
|
||||
|
||||
void
|
||||
test()
|
||||
{
|
||||
int i = 0;
|
||||
const int c = 0;
|
||||
static_assert(decltype(f(i))::value == 1, "");
|
||||
static_assert(decltype(f(c))::value == 2, "");
|
||||
static_assert(decltype(f(0))::value == 3, "");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_uniform_initialization
|
||||
{
|
||||
|
||||
struct test
|
||||
{
|
||||
static const int zero {};
|
||||
static const int one {1};
|
||||
};
|
||||
|
||||
static_assert(test::zero == 0, "");
|
||||
static_assert(test::one == 1, "");
|
||||
|
||||
}
|
||||
|
||||
namespace test_lambdas
|
||||
{
|
||||
|
||||
void
|
||||
test1()
|
||||
{
|
||||
auto lambda1 = [](){};
|
||||
auto lambda2 = lambda1;
|
||||
lambda1();
|
||||
lambda2();
|
||||
}
|
||||
|
||||
int
|
||||
test2()
|
||||
{
|
||||
auto a = [](int i, int j){ return i + j; }(1, 2);
|
||||
auto b = []() -> int { return '0'; }();
|
||||
auto c = [=](){ return a + b; }();
|
||||
auto d = [&](){ return c; }();
|
||||
auto e = [a, &b](int x) mutable {
|
||||
const auto identity = [](int y){ return y; };
|
||||
for (auto i = 0; i < a; ++i)
|
||||
a += b--;
|
||||
return x + identity(a + b);
|
||||
}(0);
|
||||
return a + b + c + d + e;
|
||||
}
|
||||
|
||||
int
|
||||
test3()
|
||||
{
|
||||
const auto nullary = [](){ return 0; };
|
||||
const auto unary = [](int x){ return x; };
|
||||
using nullary_t = decltype(nullary);
|
||||
using unary_t = decltype(unary);
|
||||
const auto higher1st = [](nullary_t f){ return f(); };
|
||||
const auto higher2nd = [unary](nullary_t f1){
|
||||
return [unary, f1](unary_t f2){ return f2(unary(f1())); };
|
||||
};
|
||||
return higher1st(nullary) + higher2nd(nullary)(unary);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_variadic_templates
|
||||
{
|
||||
|
||||
template <int...>
|
||||
struct sum;
|
||||
|
||||
template <int N0, int... N1toN>
|
||||
struct sum<N0, N1toN...>
|
||||
{
|
||||
static constexpr auto value = N0 + sum<N1toN...>::value;
|
||||
};
|
||||
|
||||
template <>
|
||||
struct sum<>
|
||||
{
|
||||
static constexpr auto value = 0;
|
||||
};
|
||||
|
||||
static_assert(sum<>::value == 0, "");
|
||||
static_assert(sum<1>::value == 1, "");
|
||||
static_assert(sum<23>::value == 23, "");
|
||||
static_assert(sum<1, 2>::value == 3, "");
|
||||
static_assert(sum<5, 5, 11>::value == 21, "");
|
||||
static_assert(sum<2, 3, 5, 7, 11, 13>::value == 41, "");
|
||||
|
||||
}
|
||||
|
||||
// http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
|
||||
// Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function
|
||||
// because of this.
|
||||
namespace test_template_alias_sfinae
|
||||
{
|
||||
|
||||
struct foo {};
|
||||
|
||||
template<typename T>
|
||||
using member = typename T::member_type;
|
||||
|
||||
template<typename T>
|
||||
void func(...) {}
|
||||
|
||||
template<typename T>
|
||||
void func(member<T>*) {}
|
||||
|
||||
void test();
|
||||
|
||||
void test() { func<foo>(0); }
|
||||
|
||||
}
|
||||
|
||||
} // namespace cxx11
|
||||
|
||||
#endif // __cplusplus >= 201103L
|
||||
|
||||
]])
|
||||
|
||||
|
||||
dnl Tests for new features in C++14
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_14], [[
|
||||
|
||||
// If the compiler admits that it is not ready for C++14, why torture it?
|
||||
// Hopefully, this will speed up the test.
|
||||
|
||||
#ifndef __cplusplus
|
||||
|
||||
#error "This is not a C++ compiler"
|
||||
|
||||
#elif __cplusplus < 201402L
|
||||
|
||||
#error "This is not a C++14 compiler"
|
||||
|
||||
#else
|
||||
|
||||
namespace cxx14
|
||||
{
|
||||
|
||||
namespace test_polymorphic_lambdas
|
||||
{
|
||||
|
||||
int
|
||||
test()
|
||||
{
|
||||
const auto lambda = [](auto&&... args){
|
||||
const auto istiny = [](auto x){
|
||||
return (sizeof(x) == 1UL) ? 1 : 0;
|
||||
};
|
||||
const int aretiny[] = { istiny(args)... };
|
||||
return aretiny[0];
|
||||
};
|
||||
return lambda(1, 1L, 1.0f, '1');
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_binary_literals
|
||||
{
|
||||
|
||||
constexpr auto ivii = 0b0000000000101010;
|
||||
static_assert(ivii == 42, "wrong value");
|
||||
|
||||
}
|
||||
|
||||
namespace test_generalized_constexpr
|
||||
{
|
||||
|
||||
template < typename CharT >
|
||||
constexpr unsigned long
|
||||
strlen_c(const CharT *const s) noexcept
|
||||
{
|
||||
auto length = 0UL;
|
||||
for (auto p = s; *p; ++p)
|
||||
++length;
|
||||
return length;
|
||||
}
|
||||
|
||||
static_assert(strlen_c("") == 0UL, "");
|
||||
static_assert(strlen_c("x") == 1UL, "");
|
||||
static_assert(strlen_c("test") == 4UL, "");
|
||||
static_assert(strlen_c("another\0test") == 7UL, "");
|
||||
|
||||
}
|
||||
|
||||
namespace test_lambda_init_capture
|
||||
{
|
||||
|
||||
int
|
||||
test()
|
||||
{
|
||||
auto x = 0;
|
||||
const auto lambda1 = [a = x](int b){ return a + b; };
|
||||
const auto lambda2 = [a = lambda1(x)](){ return a; };
|
||||
return lambda2();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_digit_separators
|
||||
{
|
||||
|
||||
constexpr auto ten_million = 100'000'000;
|
||||
static_assert(ten_million == 100000000, "");
|
||||
|
||||
}
|
||||
|
||||
namespace test_return_type_deduction
|
||||
{
|
||||
|
||||
auto f(int& x) { return x; }
|
||||
decltype(auto) g(int& x) { return x; }
|
||||
|
||||
template < typename T1, typename T2 >
|
||||
struct is_same
|
||||
{
|
||||
static constexpr auto value = false;
|
||||
};
|
||||
|
||||
template < typename T >
|
||||
struct is_same<T, T>
|
||||
{
|
||||
static constexpr auto value = true;
|
||||
};
|
||||
|
||||
int
|
||||
test()
|
||||
{
|
||||
auto x = 0;
|
||||
static_assert(is_same<int, decltype(f(x))>::value, "");
|
||||
static_assert(is_same<int&, decltype(g(x))>::value, "");
|
||||
return x;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
} // namespace cxx14
|
||||
|
||||
#endif // __cplusplus >= 201402L
|
||||
|
||||
]])
|
||||
|
||||
|
||||
dnl Tests for new features in C++17
|
||||
|
||||
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_17], [[
|
||||
|
||||
// If the compiler admits that it is not ready for C++17, why torture it?
|
||||
// Hopefully, this will speed up the test.
|
||||
|
||||
#ifndef __cplusplus
|
||||
|
||||
#error "This is not a C++ compiler"
|
||||
|
||||
#elif __cplusplus <= 201402L
|
||||
|
||||
#error "This is not a C++17 compiler"
|
||||
|
||||
#else
|
||||
|
||||
#if defined(__clang__)
|
||||
#define REALLY_CLANG
|
||||
#else
|
||||
#if defined(__GNUC__)
|
||||
#define REALLY_GCC
|
||||
#endif
|
||||
#endif
|
||||
|
||||
#include <initializer_list>
|
||||
#include <utility>
|
||||
#include <type_traits>
|
||||
|
||||
namespace cxx17
|
||||
{
|
||||
|
||||
#if !defined(REALLY_CLANG)
|
||||
namespace test_constexpr_lambdas
|
||||
{
|
||||
|
||||
// TODO: test it with clang++ from git
|
||||
|
||||
constexpr int foo = [](){return 42;}();
|
||||
|
||||
}
|
||||
#endif // !defined(REALLY_CLANG)
|
||||
|
||||
namespace test::nested_namespace::definitions
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
namespace test_fold_expression
|
||||
{
|
||||
|
||||
template<typename... Args>
|
||||
int multiply(Args... args)
|
||||
{
|
||||
return (args * ... * 1);
|
||||
}
|
||||
|
||||
template<typename... Args>
|
||||
bool all(Args... args)
|
||||
{
|
||||
return (args && ...);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_extended_static_assert
|
||||
{
|
||||
|
||||
static_assert (true);
|
||||
|
||||
}
|
||||
|
||||
namespace test_auto_brace_init_list
|
||||
{
|
||||
|
||||
auto foo = {5};
|
||||
auto bar {5};
|
||||
|
||||
static_assert(std::is_same<std::initializer_list<int>, decltype(foo)>::value);
|
||||
static_assert(std::is_same<int, decltype(bar)>::value);
|
||||
}
|
||||
|
||||
namespace test_typename_in_template_template_parameter
|
||||
{
|
||||
|
||||
template<template<typename> typename X> struct D;
|
||||
|
||||
}
|
||||
|
||||
namespace test_fallthrough_nodiscard_maybe_unused_attributes
|
||||
{
|
||||
|
||||
int f1()
|
||||
{
|
||||
return 42;
|
||||
}
|
||||
|
||||
[[nodiscard]] int f2()
|
||||
{
|
||||
[[maybe_unused]] auto unused = f1();
|
||||
|
||||
switch (f1())
|
||||
{
|
||||
case 17:
|
||||
f1();
|
||||
[[fallthrough]];
|
||||
case 42:
|
||||
f1();
|
||||
}
|
||||
return f1();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_extended_aggregate_initialization
|
||||
{
|
||||
|
||||
struct base1
|
||||
{
|
||||
int b1, b2 = 42;
|
||||
};
|
||||
|
||||
struct base2
|
||||
{
|
||||
base2() {
|
||||
b3 = 42;
|
||||
}
|
||||
int b3;
|
||||
};
|
||||
|
||||
struct derived : base1, base2
|
||||
{
|
||||
int d;
|
||||
};
|
||||
|
||||
derived d1 {{1, 2}, {}, 4}; // full initialization
|
||||
derived d2 {{}, {}, 4}; // value-initialized bases
|
||||
|
||||
}
|
||||
|
||||
namespace test_general_range_based_for_loop
|
||||
{
|
||||
|
||||
struct iter
|
||||
{
|
||||
int i;
|
||||
|
||||
int& operator* ()
|
||||
{
|
||||
return i;
|
||||
}
|
||||
|
||||
const int& operator* () const
|
||||
{
|
||||
return i;
|
||||
}
|
||||
|
||||
iter& operator++()
|
||||
{
|
||||
++i;
|
||||
return *this;
|
||||
}
|
||||
};
|
||||
|
||||
struct sentinel
|
||||
{
|
||||
int i;
|
||||
};
|
||||
|
||||
bool operator== (const iter& i, const sentinel& s)
|
||||
{
|
||||
return i.i == s.i;
|
||||
}
|
||||
|
||||
bool operator!= (const iter& i, const sentinel& s)
|
||||
{
|
||||
return !(i == s);
|
||||
}
|
||||
|
||||
struct range
|
||||
{
|
||||
iter begin() const
|
||||
{
|
||||
return {0};
|
||||
}
|
||||
|
||||
sentinel end() const
|
||||
{
|
||||
return {5};
|
||||
}
|
||||
};
|
||||
|
||||
void f()
|
||||
{
|
||||
range r {};
|
||||
|
||||
for (auto i : r)
|
||||
{
|
||||
[[maybe_unused]] auto v = i;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_lambda_capture_asterisk_this_by_value
|
||||
{
|
||||
|
||||
struct t
|
||||
{
|
||||
int i;
|
||||
int foo()
|
||||
{
|
||||
return [*this]()
|
||||
{
|
||||
return i;
|
||||
}();
|
||||
}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
namespace test_enum_class_construction
|
||||
{
|
||||
|
||||
enum class byte : unsigned char
|
||||
{};
|
||||
|
||||
byte foo {42};
|
||||
|
||||
}
|
||||
|
||||
namespace test_constexpr_if
|
||||
{
|
||||
|
||||
template <bool cond>
|
||||
int f ()
|
||||
{
|
||||
if constexpr(cond)
|
||||
{
|
||||
return 13;
|
||||
}
|
||||
else
|
||||
{
|
||||
return 42;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace test_selection_statement_with_initializer
|
||||
{
|
||||
|
||||
int f()
|
||||
{
|
||||
return 13;
|
||||
}
|
||||
|
||||
int f2()
|
||||
{
|
||||
if (auto i = f(); i > 0)
|
||||
{
|
||||
return 3;
|
||||
}
|
||||
|
||||
switch (auto i = f(); i + 4)
|
||||
{
|
||||
case 17:
|
||||
return 2;
|
||||
|
||||
default:
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
#if !defined(REALLY_CLANG)
|
||||
namespace test_template_argument_deduction_for_class_templates
|
||||
{
|
||||
|
||||
// TODO: test it with clang++ from git
|
||||
|
||||
template <typename T1, typename T2>
|
||||
struct pair
|
||||
{
|
||||
pair (T1 p1, T2 p2)
|
||||
: m1 {p1},
|
||||
m2 {p2}
|
||||
{}
|
||||
|
||||
T1 m1;
|
||||
T2 m2;
|
||||
};
|
||||
|
||||
void f()
|
||||
{
|
||||
[[maybe_unused]] auto p = pair{13, 42u};
|
||||
}
|
||||
|
||||
}
|
||||
#endif // !defined(REALLY_CLANG)
|
||||
|
||||
namespace test_non_type_auto_template_parameters
|
||||
{
|
||||
|
||||
template <auto n>
|
||||
struct B
|
||||
{};
|
||||
|
||||
B<5> b1;
|
||||
B<'a'> b2;
|
||||
|
||||
}
|
||||
|
||||
#if !defined(REALLY_CLANG)
|
||||
namespace test_structured_bindings
|
||||
{
|
||||
|
||||
// TODO: test it with clang++ from git
|
||||
|
||||
int arr[2] = { 1, 2 };
|
||||
std::pair<int, int> pr = { 1, 2 };
|
||||
|
||||
auto f1() -> int(&)[2]
|
||||
{
|
||||
return arr;
|
||||
}
|
||||
|
||||
auto f2() -> std::pair<int, int>&
|
||||
{
|
||||
return pr;
|
||||
}
|
||||
|
||||
struct S
|
||||
{
|
||||
int x1 : 2;
|
||||
volatile double y1;
|
||||
};
|
||||
|
||||
S f3()
|
||||
{
|
||||
return {};
|
||||
}
|
||||
|
||||
auto [ x1, y1 ] = f1();
|
||||
auto& [ xr1, yr1 ] = f1();
|
||||
auto [ x2, y2 ] = f2();
|
||||
auto& [ xr2, yr2 ] = f2();
|
||||
const auto [ x3, y3 ] = f3();
|
||||
|
||||
}
|
||||
#endif // !defined(REALLY_CLANG)
|
||||
|
||||
#if !defined(REALLY_CLANG)
|
||||
namespace test_exception_spec_type_system
|
||||
{
|
||||
|
||||
// TODO: test it with clang++ from git
|
||||
|
||||
struct Good {};
|
||||
struct Bad {};
|
||||
|
||||
void g1() noexcept;
|
||||
void g2();
|
||||
|
||||
template<typename T>
|
||||
Bad
|
||||
f(T*, T*);
|
||||
|
||||
template<typename T1, typename T2>
|
||||
Good
|
||||
f(T1*, T2*);
|
||||
|
||||
static_assert (std::is_same_v<Good, decltype(f(g1, g2))>);
|
||||
|
||||
}
|
||||
#endif // !defined(REALLY_CLANG)
|
||||
|
||||
namespace test_inline_variables
|
||||
{
|
||||
|
||||
template<class T> void f(T)
|
||||
{}
|
||||
|
||||
template<class T> inline T g(T)
|
||||
{
|
||||
return T{};
|
||||
}
|
||||
|
||||
template<> inline void f<>(int)
|
||||
{}
|
||||
|
||||
template<> int g<>(int)
|
||||
{
|
||||
return 5;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
} // namespace cxx17
|
||||
|
||||
#endif // __cplusplus <= 201402L
|
||||
|
||||
]])
|
||||
@@ -1,39 +0,0 @@
|
||||
# =============================================================================
|
||||
# https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html
|
||||
# =============================================================================
|
||||
#
|
||||
# SYNOPSIS
|
||||
#
|
||||
# AX_CXX_COMPILE_STDCXX_11([ext|noext], [mandatory|optional])
|
||||
#
|
||||
# DESCRIPTION
|
||||
#
|
||||
# Check for baseline language coverage in the compiler for the C++11
|
||||
# standard; if necessary, add switches to CXX and CXXCPP to enable
|
||||
# support.
|
||||
#
|
||||
# This macro is a convenience alias for calling the AX_CXX_COMPILE_STDCXX
|
||||
# macro with the version set to C++11. The two optional arguments are
|
||||
# forwarded literally as the second and third argument respectively.
|
||||
# Please see the documentation for the AX_CXX_COMPILE_STDCXX macro for
|
||||
# more information. If you want to use this macro, you also need to
|
||||
# download the ax_cxx_compile_stdcxx.m4 file.
|
||||
#
|
||||
# LICENSE
|
||||
#
|
||||
# Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
|
||||
# Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
|
||||
# Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
|
||||
# Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
|
||||
# Copyright (c) 2015 Paul Norman <penorman@mac.com>
|
||||
# Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
|
||||
#
|
||||
# Copying and distribution of this file, with or without modification, are
|
||||
# permitted in any medium without royalty provided the copyright notice
|
||||
# and this notice are preserved. This file is offered as-is, without any
|
||||
# warranty.
|
||||
|
||||
#serial 18
|
||||
|
||||
AX_REQUIRE_DEFINED([AX_CXX_COMPILE_STDCXX])
|
||||
AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [AX_CXX_COMPILE_STDCXX([11], [$1], [$2])])
|
||||
-135
@@ -1,135 +0,0 @@
|
||||
# ===========================================================================
|
||||
# http://www.gnu.org/software/autoconf-archive/ax_pkg_swig.html
|
||||
# ===========================================================================
|
||||
#
|
||||
# SYNOPSIS
|
||||
#
|
||||
# AX_PKG_SWIG([major.minor.micro], [action-if-found], [action-if-not-found])
|
||||
#
|
||||
# DESCRIPTION
|
||||
#
|
||||
# This macro searches for a SWIG installation on your system. If found,
|
||||
# then SWIG is AC_SUBST'd; if not found, then $SWIG is empty. If SWIG is
|
||||
# found, then SWIG_LIB is set to the SWIG library path, and AC_SUBST'd.
|
||||
#
|
||||
# You can use the optional first argument to check if the version of the
|
||||
# available SWIG is greater than or equal to the value of the argument. It
|
||||
# should have the format: N[.N[.N]] (N is a number between 0 and 999. Only
|
||||
# the first N is mandatory.) If the version argument is given (e.g.
|
||||
# 1.3.17), AX_PKG_SWIG checks that the swig package is this version number
|
||||
# or higher.
|
||||
#
|
||||
# As usual, action-if-found is executed if SWIG is found, otherwise
|
||||
# action-if-not-found is executed.
|
||||
#
|
||||
# In configure.in, use as:
|
||||
#
|
||||
# AX_PKG_SWIG(1.3.17, [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
|
||||
# AX_SWIG_ENABLE_CXX
|
||||
# AX_SWIG_MULTI_MODULE_SUPPORT
|
||||
# AX_SWIG_PYTHON
|
||||
#
|
||||
# LICENSE
|
||||
#
|
||||
# Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
|
||||
# Copyright (c) 2008 Alan W. Irwin
|
||||
# Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
|
||||
# Copyright (c) 2008 Andrew Collier
|
||||
# Copyright (c) 2011 Murray Cumming <murrayc@openismus.com>
|
||||
#
|
||||
# This program is free software; you can redistribute it and/or modify it
|
||||
# under the terms of the GNU General Public License as published by the
|
||||
# Free Software Foundation; either version 2 of the License, or (at your
|
||||
# option) any later version.
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful, but
|
||||
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
||||
# Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License along
|
||||
# with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
# As a special exception, the respective Autoconf Macro's copyright owner
|
||||
# gives unlimited permission to copy, distribute and modify the configure
|
||||
# scripts that are the output of Autoconf when processing the Macro. You
|
||||
# need not follow the terms of the GNU General Public License when using
|
||||
# or distributing such scripts, even though portions of the text of the
|
||||
# Macro appear in them. The GNU General Public License (GPL) does govern
|
||||
# all other use of the material that constitutes the Autoconf Macro.
|
||||
#
|
||||
# This special exception to the GPL applies to versions of the Autoconf
|
||||
# Macro released by the Autoconf Archive. When you make and distribute a
|
||||
# modified version of the Autoconf Macro, you may extend this special
|
||||
# exception to the GPL to apply to your modified version as well.
|
||||
|
||||
#serial 11
|
||||
|
||||
AC_DEFUN([AX_PKG_SWIG],[
|
||||
# Ubuntu has swig 2.0 as /usr/bin/swig2.0
|
||||
AC_PATH_PROGS([SWIG],[swig swig2.0])
|
||||
if test -z "$SWIG" ; then
|
||||
m4_ifval([$3],[$3],[:])
|
||||
elif test -n "$1" ; then
|
||||
AC_MSG_CHECKING([SWIG version])
|
||||
[swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
|
||||
AC_MSG_RESULT([$swig_version])
|
||||
if test -n "$swig_version" ; then
|
||||
# Calculate the required version number components
|
||||
[required=$1]
|
||||
[required_major=`echo $required | sed 's/[^0-9].*//'`]
|
||||
if test -z "$required_major" ; then
|
||||
[required_major=0]
|
||||
fi
|
||||
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
|
||||
[required_minor=`echo $required | sed 's/[^0-9].*//'`]
|
||||
if test -z "$required_minor" ; then
|
||||
[required_minor=0]
|
||||
fi
|
||||
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
|
||||
[required_patch=`echo $required | sed 's/[^0-9].*//'`]
|
||||
if test -z "$required_patch" ; then
|
||||
[required_patch=0]
|
||||
fi
|
||||
# Calculate the available version number components
|
||||
[available=$swig_version]
|
||||
[available_major=`echo $available | sed 's/[^0-9].*//'`]
|
||||
if test -z "$available_major" ; then
|
||||
[available_major=0]
|
||||
fi
|
||||
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
|
||||
[available_minor=`echo $available | sed 's/[^0-9].*//'`]
|
||||
if test -z "$available_minor" ; then
|
||||
[available_minor=0]
|
||||
fi
|
||||
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
|
||||
[available_patch=`echo $available | sed 's/[^0-9].*//'`]
|
||||
if test -z "$available_patch" ; then
|
||||
[available_patch=0]
|
||||
fi
|
||||
# Convert the version tuple into a single number for easier comparison.
|
||||
# Using base 100 should be safe since SWIG internally uses BCD values
|
||||
# to encode its version number.
|
||||
required_swig_vernum=`expr $required_major \* 10000 \
|
||||
\+ $required_minor \* 100 \+ $required_patch`
|
||||
available_swig_vernum=`expr $available_major \* 10000 \
|
||||
\+ $available_minor \* 100 \+ $available_patch`
|
||||
|
||||
if test $available_swig_vernum -lt $required_swig_vernum; then
|
||||
AC_MSG_WARN([SWIG version >= $1 is required. You have $swig_version.])
|
||||
SWIG=''
|
||||
m4_ifval([$3],[$3],[])
|
||||
else
|
||||
AC_MSG_CHECKING([for SWIG library])
|
||||
SWIG_LIB=`$SWIG -swiglib`
|
||||
AC_MSG_RESULT([$SWIG_LIB])
|
||||
m4_ifval([$2],[$2],[])
|
||||
fi
|
||||
else
|
||||
AC_MSG_WARN([cannot determine SWIG version])
|
||||
SWIG=''
|
||||
m4_ifval([$3],[$3],[])
|
||||
fi
|
||||
fi
|
||||
AC_SUBST([SWIG_LIB])
|
||||
])
|
||||
+1469
File diff suppressed because it is too large
Load Diff
Executable
+44
@@ -0,0 +1,44 @@
|
||||
/* config.h.in. Generated from configure.ac by autoheader. */
|
||||
|
||||
/* "" */
|
||||
#undef MY_BUILD_CPU
|
||||
|
||||
/* "" */
|
||||
#undef MY_BUILD_OS
|
||||
|
||||
/* "" */
|
||||
#undef MY_BUILD_VENDOR
|
||||
|
||||
/* "" */
|
||||
#undef MY_GNUNAME
|
||||
|
||||
/* "" */
|
||||
#undef MY_UNAME
|
||||
|
||||
/* Name of package */
|
||||
#undef PACKAGE
|
||||
|
||||
/* Define to the address where bug reports for this package should be sent. */
|
||||
#undef PACKAGE_BUGREPORT
|
||||
|
||||
/* Define to the full name of this package. */
|
||||
#undef PACKAGE_NAME
|
||||
|
||||
/* Define to the full name and version of this package. */
|
||||
#undef PACKAGE_STRING
|
||||
|
||||
/* Define to the one symbol short name of this package. */
|
||||
#undef PACKAGE_TARNAME
|
||||
|
||||
/* Define to the version of this package. */
|
||||
#undef PACKAGE_VERSION
|
||||
|
||||
/* Version number of package */
|
||||
#undef VERSION
|
||||
|
||||
/* Define to 1 if on AIX 3.
|
||||
System headers sometimes define this.
|
||||
We just want to avoid a redefinition error message. */
|
||||
#ifndef _ALL_SOURCE
|
||||
# undef _ALL_SOURCE
|
||||
#endif
|
||||
+1563
File diff suppressed because it is too large
Load Diff
+548
-495
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,529 @@
|
||||
#! /bin/sh
|
||||
# depcomp - compile a program generating dependencies as side-effects
|
||||
|
||||
scriptversion=2005-02-09.22
|
||||
|
||||
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
|
||||
|
||||
# This program is free software; you can redistribute it and/or modify
|
||||
# it under the terms of the GNU General Public License as published by
|
||||
# the Free Software Foundation; either version 2, or (at your option)
|
||||
# any later version.
|
||||
|
||||
# This program is distributed in the hope that it will be useful,
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
# GNU General Public License for more details.
|
||||
|
||||
# You should have received a copy of the GNU General Public License
|
||||
# along with this program; if not, write to the Free Software
|
||||
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
|
||||
# 02111-1307, USA.
|
||||
|
||||
# As a special exception to the GNU General Public License, if you
|
||||
# distribute this file as part of a program that contains a
|
||||
# configuration script generated by Autoconf, you may include it under
|
||||
# the same distribution terms that you use for the rest of that program.
|
||||
|
||||
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
|
||||
|
||||
case $1 in
|
||||
'')
|
||||
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
|
||||
exit 1;
|
||||
;;
|
||||
-h | --h*)
|
||||
cat <<\EOF
|
||||
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
|
||||
|
||||
Run PROGRAMS ARGS to compile a file, generating dependencies
|
||||
as side-effects.
|
||||
|
||||
Environment variables:
|
||||
depmode Dependency tracking mode.
|
||||
source Source file read by `PROGRAMS ARGS'.
|
||||
object Object file output by `PROGRAMS ARGS'.
|
||||
DEPDIR directory where to store dependencies.
|
||||
depfile Dependency file to output.
|
||||
tmpdepfile Temporary file to use when outputing dependencies.
|
||||
libtool Whether libtool is used (yes/no).
|
||||
|
||||
Report bugs to <bug-automake@gnu.org>.
|
||||
EOF
|
||||
exit $?
|
||||
;;
|
||||
-v | --v*)
|
||||
echo "depcomp $scriptversion"
|
||||
exit $?
|
||||
;;
|
||||
esac
|
||||
|
||||
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
|
||||
echo "depcomp: Variables source, object and depmode must be set" 1>&2
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
|
||||
depfile=${depfile-`echo "$object" |
|
||||
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
|
||||
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
|
||||
|
||||
rm -f "$tmpdepfile"
|
||||
|
||||
# Some modes work just like other modes, but use different flags. We
|
||||
# parameterize here, but still list the modes in the big case below,
|
||||
# to make depend.m4 easier to write. Note that we *cannot* use a case
|
||||
# here, because this file can only contain one case statement.
|
||||
if test "$depmode" = hp; then
|
||||
# HP compiler uses -M and no extra arg.
|
||||
gccflag=-M
|
||||
depmode=gcc
|
||||
fi
|
||||
|
||||
if test "$depmode" = dashXmstdout; then
|
||||
# This is just like dashmstdout with a different argument.
|
||||
dashmflag=-xM
|
||||
depmode=dashmstdout
|
||||
fi
|
||||
|
||||
case "$depmode" in
|
||||
gcc3)
|
||||
## gcc 3 implements dependency tracking that does exactly what
|
||||
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
|
||||
## it if -MD -MP comes after the -MF stuff. Hmm.
|
||||
"$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
|
||||
stat=$?
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile"
|
||||
exit $stat
|
||||
fi
|
||||
mv "$tmpdepfile" "$depfile"
|
||||
;;
|
||||
|
||||
gcc)
|
||||
## There are various ways to get dependency output from gcc. Here's
|
||||
## why we pick this rather obscure method:
|
||||
## - Don't want to use -MD because we'd like the dependencies to end
|
||||
## up in a subdir. Having to rename by hand is ugly.
|
||||
## (We might end up doing this anyway to support other compilers.)
|
||||
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
|
||||
## -MM, not -M (despite what the docs say).
|
||||
## - Using -M directly means running the compiler twice (even worse
|
||||
## than renaming).
|
||||
if test -z "$gccflag"; then
|
||||
gccflag=-MD,
|
||||
fi
|
||||
"$@" -Wp,"$gccflag$tmpdepfile"
|
||||
stat=$?
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile"
|
||||
exit $stat
|
||||
fi
|
||||
rm -f "$depfile"
|
||||
echo "$object : \\" > "$depfile"
|
||||
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
|
||||
## The second -e expression handles DOS-style file names with drive letters.
|
||||
sed -e 's/^[^:]*: / /' \
|
||||
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
|
||||
## This next piece of magic avoids the `deleted header file' problem.
|
||||
## The problem is that when a header file which appears in a .P file
|
||||
## is deleted, the dependency causes make to die (because there is
|
||||
## typically no way to rebuild the header). We avoid this by adding
|
||||
## dummy dependencies for each header file. Too bad gcc doesn't do
|
||||
## this for us directly.
|
||||
tr ' ' '
|
||||
' < "$tmpdepfile" |
|
||||
## Some versions of gcc put a space before the `:'. On the theory
|
||||
## that the space means something, we add a space to the output as
|
||||
## well.
|
||||
## Some versions of the HPUX 10.20 sed can't process this invocation
|
||||
## correctly. Breaking it into two sed invocations is a workaround.
|
||||
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
hp)
|
||||
# This case exists only to let depend.m4 do its work. It works by
|
||||
# looking at the text of this script. This case will never be run,
|
||||
# since it is checked for above.
|
||||
exit 1
|
||||
;;
|
||||
|
||||
sgi)
|
||||
if test "$libtool" = yes; then
|
||||
"$@" "-Wp,-MDupdate,$tmpdepfile"
|
||||
else
|
||||
"$@" -MDupdate "$tmpdepfile"
|
||||
fi
|
||||
stat=$?
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile"
|
||||
exit $stat
|
||||
fi
|
||||
rm -f "$depfile"
|
||||
|
||||
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
|
||||
echo "$object : \\" > "$depfile"
|
||||
|
||||
# Clip off the initial element (the dependent). Don't try to be
|
||||
# clever and replace this with sed code, as IRIX sed won't handle
|
||||
# lines with more than a fixed number of characters (4096 in
|
||||
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
|
||||
# the IRIX cc adds comments like `#:fec' to the end of the
|
||||
# dependency line.
|
||||
tr ' ' '
|
||||
' < "$tmpdepfile" \
|
||||
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
|
||||
tr '
|
||||
' ' ' >> $depfile
|
||||
echo >> $depfile
|
||||
|
||||
# The second pass generates a dummy entry for each header file.
|
||||
tr ' ' '
|
||||
' < "$tmpdepfile" \
|
||||
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
|
||||
>> $depfile
|
||||
else
|
||||
# The sourcefile does not contain any dependencies, so just
|
||||
# store a dummy comment line, to avoid errors with the Makefile
|
||||
# "include basename.Plo" scheme.
|
||||
echo "#dummy" > "$depfile"
|
||||
fi
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
aix)
|
||||
# The C for AIX Compiler uses -M and outputs the dependencies
|
||||
# in a .u file. In older versions, this file always lives in the
|
||||
# current directory. Also, the AIX compiler puts `$object:' at the
|
||||
# start of each line; $object doesn't have directory information.
|
||||
# Version 6 uses the directory in both cases.
|
||||
stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
|
||||
tmpdepfile="$stripped.u"
|
||||
if test "$libtool" = yes; then
|
||||
"$@" -Wc,-M
|
||||
else
|
||||
"$@" -M
|
||||
fi
|
||||
stat=$?
|
||||
|
||||
if test -f "$tmpdepfile"; then :
|
||||
else
|
||||
stripped=`echo "$stripped" | sed 's,^.*/,,'`
|
||||
tmpdepfile="$stripped.u"
|
||||
fi
|
||||
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile"
|
||||
exit $stat
|
||||
fi
|
||||
|
||||
if test -f "$tmpdepfile"; then
|
||||
outname="$stripped.o"
|
||||
# Each line is of the form `foo.o: dependent.h'.
|
||||
# Do two passes, one to just change these to
|
||||
# `$object: dependent.h' and one to simply `dependent.h:'.
|
||||
sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
|
||||
sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
|
||||
else
|
||||
# The sourcefile does not contain any dependencies, so just
|
||||
# store a dummy comment line, to avoid errors with the Makefile
|
||||
# "include basename.Plo" scheme.
|
||||
echo "#dummy" > "$depfile"
|
||||
fi
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
icc)
|
||||
# Intel's C compiler understands `-MD -MF file'. However on
|
||||
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
|
||||
# ICC 7.0 will fill foo.d with something like
|
||||
# foo.o: sub/foo.c
|
||||
# foo.o: sub/foo.h
|
||||
# which is wrong. We want:
|
||||
# sub/foo.o: sub/foo.c
|
||||
# sub/foo.o: sub/foo.h
|
||||
# sub/foo.c:
|
||||
# sub/foo.h:
|
||||
# ICC 7.1 will output
|
||||
# foo.o: sub/foo.c sub/foo.h
|
||||
# and will wrap long lines using \ :
|
||||
# foo.o: sub/foo.c ... \
|
||||
# sub/foo.h ... \
|
||||
# ...
|
||||
|
||||
"$@" -MD -MF "$tmpdepfile"
|
||||
stat=$?
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile"
|
||||
exit $stat
|
||||
fi
|
||||
rm -f "$depfile"
|
||||
# Each line is of the form `foo.o: dependent.h',
|
||||
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
|
||||
# Do two passes, one to just change these to
|
||||
# `$object: dependent.h' and one to simply `dependent.h:'.
|
||||
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
|
||||
# Some versions of the HPUX 10.20 sed can't process this invocation
|
||||
# correctly. Breaking it into two sed invocations is a workaround.
|
||||
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
|
||||
sed -e 's/$/ :/' >> "$depfile"
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
tru64)
|
||||
# The Tru64 compiler uses -MD to generate dependencies as a side
|
||||
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
|
||||
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
|
||||
# dependencies in `foo.d' instead, so we check for that too.
|
||||
# Subdirectories are respected.
|
||||
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
|
||||
test "x$dir" = "x$object" && dir=
|
||||
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
|
||||
|
||||
if test "$libtool" = yes; then
|
||||
# With Tru64 cc, shared objects can also be used to make a
|
||||
# static library. This mecanism is used in libtool 1.4 series to
|
||||
# handle both shared and static libraries in a single compilation.
|
||||
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
|
||||
#
|
||||
# With libtool 1.5 this exception was removed, and libtool now
|
||||
# generates 2 separate objects for the 2 libraries. These two
|
||||
# compilations output dependencies in in $dir.libs/$base.o.d and
|
||||
# in $dir$base.o.d. We have to check for both files, because
|
||||
# one of the two compilations can be disabled. We should prefer
|
||||
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
|
||||
# automatically cleaned when .libs/ is deleted, while ignoring
|
||||
# the former would cause a distcleancheck panic.
|
||||
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
|
||||
tmpdepfile2=$dir$base.o.d # libtool 1.5
|
||||
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
|
||||
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
|
||||
"$@" -Wc,-MD
|
||||
else
|
||||
tmpdepfile1=$dir$base.o.d
|
||||
tmpdepfile2=$dir$base.d
|
||||
tmpdepfile3=$dir$base.d
|
||||
tmpdepfile4=$dir$base.d
|
||||
"$@" -MD
|
||||
fi
|
||||
|
||||
stat=$?
|
||||
if test $stat -eq 0; then :
|
||||
else
|
||||
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
|
||||
exit $stat
|
||||
fi
|
||||
|
||||
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
|
||||
do
|
||||
test -f "$tmpdepfile" && break
|
||||
done
|
||||
if test -f "$tmpdepfile"; then
|
||||
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
|
||||
# That's a tab and a space in the [].
|
||||
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
|
||||
else
|
||||
echo "#dummy" > "$depfile"
|
||||
fi
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
#nosideeffect)
|
||||
# This comment above is used by automake to tell side-effect
|
||||
# dependency tracking mechanisms from slower ones.
|
||||
|
||||
dashmstdout)
|
||||
# Important note: in order to support this mode, a compiler *must*
|
||||
# always write the preprocessed file to stdout, regardless of -o.
|
||||
"$@" || exit $?
|
||||
|
||||
# Remove the call to Libtool.
|
||||
if test "$libtool" = yes; then
|
||||
while test $1 != '--mode=compile'; do
|
||||
shift
|
||||
done
|
||||
shift
|
||||
fi
|
||||
|
||||
# Remove `-o $object'.
|
||||
IFS=" "
|
||||
for arg
|
||||
do
|
||||
case $arg in
|
||||
-o)
|
||||
shift
|
||||
;;
|
||||
$object)
|
||||
shift
|
||||
;;
|
||||
*)
|
||||
set fnord "$@" "$arg"
|
||||
shift # fnord
|
||||
shift # $arg
|
||||
;;
|
||||
esac
|
||||
done
|
||||
|
||||
test -z "$dashmflag" && dashmflag=-M
|
||||
# Require at least two characters before searching for `:'
|
||||
# in the target name. This is to cope with DOS-style filenames:
|
||||
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
|
||||
"$@" $dashmflag |
|
||||
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
|
||||
rm -f "$depfile"
|
||||
cat < "$tmpdepfile" > "$depfile"
|
||||
tr ' ' '
|
||||
' < "$tmpdepfile" | \
|
||||
## Some versions of the HPUX 10.20 sed can't process this invocation
|
||||
## correctly. Breaking it into two sed invocations is a workaround.
|
||||
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
dashXmstdout)
|
||||
# This case only exists to satisfy depend.m4. It is never actually
|
||||
# run, as this mode is specially recognized in the preamble.
|
||||
exit 1
|
||||
;;
|
||||
|
||||
makedepend)
|
||||
"$@" || exit $?
|
||||
# Remove any Libtool call
|
||||
if test "$libtool" = yes; then
|
||||
while test $1 != '--mode=compile'; do
|
||||
shift
|
||||
done
|
||||
shift
|
||||
fi
|
||||
# X makedepend
|
||||
shift
|
||||
cleared=no
|
||||
for arg in "$@"; do
|
||||
case $cleared in
|
||||
no)
|
||||
set ""; shift
|
||||
cleared=yes ;;
|
||||
esac
|
||||
case "$arg" in
|
||||
-D*|-I*)
|
||||
set fnord "$@" "$arg"; shift ;;
|
||||
# Strip any option that makedepend may not understand. Remove
|
||||
# the object too, otherwise makedepend will parse it as a source file.
|
||||
-*|$object)
|
||||
;;
|
||||
*)
|
||||
set fnord "$@" "$arg"; shift ;;
|
||||
esac
|
||||
done
|
||||
obj_suffix="`echo $object | sed 's/^.*\././'`"
|
||||
touch "$tmpdepfile"
|
||||
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
|
||||
rm -f "$depfile"
|
||||
cat < "$tmpdepfile" > "$depfile"
|
||||
sed '1,2d' "$tmpdepfile" | tr ' ' '
|
||||
' | \
|
||||
## Some versions of the HPUX 10.20 sed can't process this invocation
|
||||
## correctly. Breaking it into two sed invocations is a workaround.
|
||||
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
|
||||
rm -f "$tmpdepfile" "$tmpdepfile".bak
|
||||
;;
|
||||
|
||||
cpp)
|
||||
# Important note: in order to support this mode, a compiler *must*
|
||||
# always write the preprocessed file to stdout.
|
||||
"$@" || exit $?
|
||||
|
||||
# Remove the call to Libtool.
|
||||
if test "$libtool" = yes; then
|
||||
while test $1 != '--mode=compile'; do
|
||||
shift
|
||||
done
|
||||
shift
|
||||
fi
|
||||
|
||||
# Remove `-o $object'.
|
||||
IFS=" "
|
||||
for arg
|
||||
do
|
||||
case $arg in
|
||||
-o)
|
||||
shift
|
||||
;;
|
||||
$object)
|
||||
shift
|
||||
;;
|
||||
*)
|
||||
set fnord "$@" "$arg"
|
||||
shift # fnord
|
||||
shift # $arg
|
||||
;;
|
||||
esac
|
||||
done
|
||||
|
||||
"$@" -E |
|
||||
sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
|
||||
sed '$ s: \\$::' > "$tmpdepfile"
|
||||
rm -f "$depfile"
|
||||
echo "$object : \\" > "$depfile"
|
||||
cat < "$tmpdepfile" >> "$depfile"
|
||||
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
msvisualcpp)
|
||||
# Important note: in order to support this mode, a compiler *must*
|
||||
# always write the preprocessed file to stdout, regardless of -o,
|
||||
# because we must use -o when running libtool.
|
||||
"$@" || exit $?
|
||||
IFS=" "
|
||||
for arg
|
||||
do
|
||||
case "$arg" in
|
||||
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
|
||||
set fnord "$@"
|
||||
shift
|
||||
shift
|
||||
;;
|
||||
*)
|
||||
set fnord "$@" "$arg"
|
||||
shift
|
||||
shift
|
||||
;;
|
||||
esac
|
||||
done
|
||||
"$@" -E |
|
||||
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
|
||||
rm -f "$depfile"
|
||||
echo "$object : \\" > "$depfile"
|
||||
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
|
||||
echo " " >> "$depfile"
|
||||
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
|
||||
rm -f "$tmpdepfile"
|
||||
;;
|
||||
|
||||
none)
|
||||
exec "$@"
|
||||
;;
|
||||
|
||||
*)
|
||||
echo "Unknown depmode $depmode" 1>&2
|
||||
exit 1
|
||||
;;
|
||||
esac
|
||||
|
||||
exit 0
|
||||
|
||||
# Local Variables:
|
||||
# mode: shell-script
|
||||
# sh-indentation: 2
|
||||
# eval: (add-hook 'write-file-hooks 'time-stamp)
|
||||
# time-stamp-start: "scriptversion="
|
||||
# time-stamp-format: "%:y-%02m-%02d.%02H"
|
||||
# time-stamp-end: "$"
|
||||
# End:
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
@@ -0,0 +1,294 @@
|
||||
#FIG 3.2
|
||||
Landscape
|
||||
Center
|
||||
Inches
|
||||
Letter
|
||||
100.00
|
||||
Single
|
||||
-2
|
||||
1200 2
|
||||
0 32 #c6b797
|
||||
0 33 #eff8ff
|
||||
0 34 #dccba6
|
||||
0 35 #404040
|
||||
0 36 #808080
|
||||
0 37 #c0c0c0
|
||||
0 38 #e0e0e0
|
||||
0 39 #8e8f8e
|
||||
0 40 #aaaaaa
|
||||
0 41 #555555
|
||||
0 42 #bebebe
|
||||
0 43 #515151
|
||||
0 44 #e7e3e7
|
||||
0 45 #000049
|
||||
0 46 #797979
|
||||
0 47 #303430
|
||||
0 48 #414141
|
||||
0 49 #c7b696
|
||||
0 50 #8e8e8e
|
||||
0 51 #414541
|
||||
0 52 #8e8e8e
|
||||
0 53 #000079
|
||||
0 54 #ff8200
|
||||
0 55 #007d00
|
||||
0 56 #0000be
|
||||
# Desktop computer
|
||||
6 375 2400 2025 4050
|
||||
6 1575 3825 2025 4050
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 8
|
||||
1615 3916 1719 3874 1908 3874 1950 3853 1972 3853 1846 3937
|
||||
1615 3937 1615 3916
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
|
||||
1888 3853 1846 3874 1908 3874 1950 3853 1908 3853 1888 3853
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
|
||||
1846 3874 1888 3853 1846 3853 1803 3874 1846 3874
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
|
||||
1803 3874 1740 3874 1803 3853 1824 3853 1803 3874
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
|
||||
1846 3958 1866 3916 1972 3853 1992 3895 1846 3979 1846 3958
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
|
||||
1615 3937 1866 3937 1846 3958 1615 3958 1615 3937
|
||||
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 9
|
||||
1615 3958 1594 4000 1719 4000 1846 4000 1866 4000 1992 3916
|
||||
1992 3895 1846 3958 1615 3958
|
||||
-6
|
||||
6 600 2400 1950 3675
|
||||
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
|
||||
669 2530 648 3307 1594 3307 1615 2468 1594 2468 669 2530
|
||||
2 3 0 1 -1 7 0 0 10 0.000 0 0 -1 0 0 5
|
||||
1615 2468 1594 3307 1719 3307 1719 2509 1615 2468
|
||||
2 3 0 1 -1 7 0 0 15 0.000 0 0 -1 0 0 5
|
||||
1762 2677 1908 2719 1908 3139 1762 3203 1762 2677
|
||||
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
|
||||
732 3349 732 3412 1594 3454 1594 3371 753 3349 732 3349
|
||||
2 3 0 1 -1 7 1 0 15 0.000 0 0 -1 0 0 5
|
||||
1594 3371 1846 3280 1846 3348 1594 3454 1594 3371
|
||||
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 5
|
||||
732 3433 732 3559 1594 3601 1594 3454 732 3433
|
||||
2 3 0 1 -1 0 2 0 20 0.000 0 0 -1 0 0 5
|
||||
1594 3454 732 3412 753 3433 1572 3454 1594 3454
|
||||
2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
|
||||
1594 3454 1594 3601 1635 3580 1635 3433 1594 3454
|
||||
2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
|
||||
1719 3538 1846 3475 1846 3349 1719 3391 1719 3538
|
||||
2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
|
||||
1635 3496 1719 3454 1719 3391 1635 3433 1635 3496
|
||||
2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
|
||||
1635 3580 1719 3538 1719 3475 1635 3517 1635 3580
|
||||
2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
|
||||
1635 3496 1719 3454
|
||||
2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
|
||||
1635 3517 1719 3475
|
||||
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 7
|
||||
732 3559 732 3601 816 3601 963 3559 963 3538 816 3559
|
||||
732 3559
|
||||
2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
|
||||
1490 3596 1490 3641 1594 3643 1594 3601 1490 3596
|
||||
2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
|
||||
1594 3643 1635 3601 1635 3580 1594 3601 1594 3643
|
||||
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 5
|
||||
1846 3475 1846 3496 1803 3517 1803 3496 1846 3475
|
||||
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 4
|
||||
1803 3517 1740 3517 1803 3496 1803 3517
|
||||
2 3 0 1 -1 7 4 0 15 0.000 1 0 -1 0 0 6
|
||||
879 3307 732 3349 1594 3371 1846 3279 1762 3265 879 3307
|
||||
2 3 0 1 -1 7 0 0 10 0.000 1 0 -1 0 0 5
|
||||
1719 2509 1719 3307 1762 3265 1762 2552 1719 2509
|
||||
3 1 0 1 -1 7 1 0 20 0.000 0 0 0 11
|
||||
774 2656 816 2614 1488 2572 1510 2593 1530 2636 1530 3139
|
||||
1510 3181 1467 3203 837 3203 795 3181 774 3160
|
||||
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
|
||||
1.000 1.000 1.000
|
||||
-6
|
||||
6 375 3675 1650 4050
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
|
||||
1207 3935 1205 3897 1229 3888 1265 3890 1264 3922 1244 3937
|
||||
1212 3937 1207 3935
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
|
||||
1264 3939 1261 3900 1285 3892 1320 3893 1319 3925 1300 3940
|
||||
1268 3940 1264 3939
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
|
||||
1318 3950 1315 3912 1339 3904 1374 3905 1374 3937 1355 3953
|
||||
1322 3953 1318 3950
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
|
||||
1151 3935 1150 3897 1173 3888 1209 3890 1207 3922 1188 3937
|
||||
1157 3937 1151 3935
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
1169 3900 1166 3861 1190 3853 1226 3854 1224 3886 1205 3901
|
||||
1173 3901 1169 3900
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
1225 3904 1223 3865 1247 3857 1282 3858 1281 3891 1262 3906
|
||||
1230 3906 1225 3904
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
1281 3908 1279 3869 1303 3860 1338 3862 1337 3893 1318 3909
|
||||
1286 3909 1281 3908
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
1344 3909 1342 3870 1366 3862 1401 3863 1399 3895 1381 3911
|
||||
1349 3911 1344 3909
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1214 3854 1214 3835 1233 3822 1272 3825 1272 3831 1260 3839
|
||||
1258 3856 1211 3854 1214 3854
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1258 3855 1258 3836 1277 3823 1315 3826 1315 3831 1304 3839
|
||||
1302 3857 1255 3855 1258 3855
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1300 3862 1300 3843 1319 3830 1359 3833 1359 3838 1346 3846
|
||||
1344 3863 1297 3862 1300 3862
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1344 3863 1344 3845 1363 3831 1402 3835 1402 3839 1390 3848
|
||||
1389 3865 1341 3863 1344 3863
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1387 3869 1387 3850 1406 3836 1444 3839 1444 3845 1436 3871
|
||||
1417 3882 1383 3869 1387 3869
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
708 3798 708 3779 727 3766 766 3769 766 3774 755 3783
|
||||
752 3800 705 3798 708 3798
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
747 3803 747 3784 766 3771 805 3775 805 3780 793 3788
|
||||
791 3805 744 3803 747 3803
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
794 3805 794 3787 813 3773 852 3777 852 3781 840 3790
|
||||
839 3807 791 3805 794 3805
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
832 3810 832 3792 850 3778 889 3781 889 3787 878 3795
|
||||
876 3812 828 3810 832 3810
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
876 3812 876 3793 894 3780 934 3784 934 3788 921 3797
|
||||
919 3814 872 3812 876 3812
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
919 3816 919 3797 938 3784 977 3787 977 3792 965 3800
|
||||
964 3817 916 3816 919 3816
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
962 3816 962 3797 981 3784 1019 3787 1019 3792 1008 3800
|
||||
1006 3817 959 3816 962 3816
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1001 3819 1001 3800 1019 3787 1058 3790 1058 3795 1047 3803
|
||||
1045 3820 997 3819 1001 3819
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1049 3819 1049 3800 1067 3787 1106 3790 1106 3795 1094 3803
|
||||
1092 3820 1045 3819 1049 3819
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
661 3822 661 3803 679 3790 718 3793 718 3799 706 3807
|
||||
704 3824 658 3822 661 3822
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
704 3831 704 3812 724 3799 762 3802 762 3807 750 3816
|
||||
748 3832 702 3831 704 3831
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
748 3834 748 3816 768 3802 806 3805 806 3810 794 3819
|
||||
793 3835 746 3834 748 3834
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
789 3838 789 3819 808 3805 847 3808 847 3814 835 3822
|
||||
833 3839 786 3838 789 3838
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
832 3840 832 3822 850 3808 889 3812 889 3817 878 3825
|
||||
876 3842 828 3840 832 3840
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
874 3842 874 3824 893 3810 932 3814 932 3819 919 3827
|
||||
918 3844 871 3842 874 3842
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
916 3846 916 3827 934 3814 974 3817 974 3822 962 3831
|
||||
960 3847 913 3846 916 3846
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
961 3846 961 3828 980 3814 1018 3817 1018 3823 1007 3831
|
||||
1005 3847 957 3846 961 3846
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1005 3849 1005 3831 1023 3817 1062 3821 1062 3826 1050 3834
|
||||
1049 3851 1002 3849 1005 3849
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
1049 3851 1049 3832 1067 3819 1107 3823 1107 3828 1095 3836
|
||||
1093 3853 1045 3851 1049 3851
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
656 3866 655 3827 678 3819 714 3820 713 3853 693 3868
|
||||
662 3868 656 3866
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
700 3869 698 3831 722 3822 757 3824 755 3856 737 3871
|
||||
704 3871 700 3869
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
744 3876 741 3838 766 3829 801 3831 799 3862 781 3878
|
||||
748 3878 744 3876
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
792 3882 790 3842 814 3834 849 3835 848 3868 829 3883
|
||||
797 3883 792 3882
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
832 3884 830 3846 854 3837 889 3839 887 3870 869 3886
|
||||
836 3886 832 3884
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
880 3890 879 3851 902 3842 938 3844 936 3876 918 3892
|
||||
886 3892 880 3890
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
932 3893 930 3854 954 3846 989 3847 988 3879 969 3895
|
||||
936 3895 932 3893
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
982 3895 981 3856 1004 3847 1040 3849 1038 3882 1019 3897
|
||||
988 3897 982 3895
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
1025 3898 1023 3860 1047 3851 1082 3853 1080 3885 1062 3900
|
||||
1029 3900 1025 3898
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
618 3861 616 3822 640 3814 675 3816 674 3847 655 3862
|
||||
623 3862 618 3861
|
||||
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
|
||||
572 3888 571 3849 594 3840 630 3842 629 3875 609 3890
|
||||
578 3890 572 3888
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
609 3888 609 3869 629 3856 667 3860 667 3864 655 3873
|
||||
654 3890 607 3888 609 3888
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 7
|
||||
654 3893 984 3934 988 3898 664 3866 652 3882 652 3888
|
||||
654 3893
|
||||
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
|
||||
986 3931 986 3913 1004 3900 1043 3902 1043 3908 1032 3916
|
||||
1029 3933 982 3931 986 3931
|
||||
2 3 0 1 -1 7 5 0 15 0.000 0 0 -1 0 0 9
|
||||
429 3871 683 3743 1551 3816 1576 3831 1573 3840 1426 3990
|
||||
427 3883 427 3869 429 3871
|
||||
2 1 0 1 -1 7 0 0 -1 0.000 0 0 -1 0 0 3
|
||||
423 3910 1434 4014 1575 3875
|
||||
2 3 0 0 -1 7 5 0 10 0.000 0 0 -1 0 0 8
|
||||
429 3885 429 3928 1430 4050 1580 3895 1576 3831 1423 3990
|
||||
425 3882 429 3885
|
||||
-6
|
||||
-6
|
||||
6 4050 3000 7500 3750
|
||||
2 1 0 1 0 0 0 0 -1 0.000 0 0 -1 0 0 4
|
||||
7500 3000 5430 3000 6120 3690 4050 3690
|
||||
-6
|
||||
# TB Data
|
||||
6 8025 6000 9000 7425
|
||||
5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 5700.000 8040 6300 8490 6450 8940 6300
|
||||
5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 6600.000 8040 7200 8490 7350 8940 7200
|
||||
1 2 0 1 -1 -1 0 0 -1 0.000 1 0.0000 8490 6150 450 150 8040 6000 8940 6300
|
||||
2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
|
||||
8940 6225 8940 7200
|
||||
2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
|
||||
8040 6225 8040 7200
|
||||
4 1 -1 0 0 2 12 0.0000 6 135 270 8490 6675 TB\001
|
||||
4 1 -1 0 0 2 12 0.0000 6 135 405 8490 7275 Data\001
|
||||
-6
|
||||
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 1 1 2
|
||||
0 0 1.00 60.00 120.00
|
||||
0 0 1.00 60.00 120.00
|
||||
2025 3075 2475 3075
|
||||
2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
|
||||
3750 4650 3750 2100 2550 2100 2550 4650 3750 4650
|
||||
2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
|
||||
9075 4650 9075 2100 7875 2100 7875 4650 9075 4650
|
||||
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
|
||||
0 0 3.00 60.00 120.00
|
||||
8400 4800 8400 6000
|
||||
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
|
||||
0 0 3.00 60.00 120.00
|
||||
8250 4800 8250 6000
|
||||
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
|
||||
0 0 3.00 60.00 120.00
|
||||
8100 4800 8100 6000
|
||||
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
|
||||
0 0 3.00 60.00 120.00
|
||||
8850 4800 8850 6000
|
||||
2 4 0 1 0 7 50 -1 -1 0.000 0 0 7 0 0 5
|
||||
12000 4500 12000 3975 8175 3975 8175 4500 12000 4500
|
||||
4 0 0 50 0 2 15 0.0000 4 30 360 8475 5550 ......\001
|
||||
4 0 0 50 0 0 20 0.0000 4 195 570 2625 3375 VisIt\001
|
||||
4 0 0 50 0 0 20 0.0000 4 195 570 7950 3375 VisIt\001
|
||||
4 0 0 50 -1 2 16 0.0000 4 225 1410 9375 4275 H5xxx plugin\001
|
||||
4 0 0 50 0 0 20 0.0000 4 255 1650 6450 5550 n-way parallel\001
|
||||
Binary file not shown.
Binary file not shown.
File diff suppressed because one or more lines are too long
@@ -0,0 +1,262 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
|
||||
<head>
|
||||
<title>Building H5Part</title>
|
||||
</head>
|
||||
|
||||
<body bgcolor="#F0F0F0">
|
||||
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
|
||||
<UL>
|
||||
<LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
|
||||
<LI><a href="#Details">Details of the Configuration Script</a>
|
||||
<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
|
||||
<LI><a href="#ConfigOptions">Important Configure Options</a>
|
||||
<LI><a href="#EnvVariables">Important Environment Variables</a>
|
||||
</UL>
|
||||
|
||||
<hr>
|
||||
<a name="Quickstart">
|
||||
<h2>Quickstart <i>for the impatient</i></h2>
|
||||
</a>
|
||||
|
||||
<OL>
|
||||
|
||||
<LI><b>Configure</b>:<br>
|
||||
For the serial implementation
|
||||
<pre>
|
||||
./configure
|
||||
</pre>
|
||||
For the parallel implementation configure with
|
||||
<pre>
|
||||
./configure --enable-parallel
|
||||
</pre>
|
||||
If you also want to build fortran bindings, add the
|
||||
<code>--enable-fortran</code> flag to the configure line.
|
||||
</LI><p>
|
||||
|
||||
<LI><b>Make the Library</b>:<br>
|
||||
Type <code>make</code> to build the library. The libraries are
|
||||
named accordingly.
|
||||
<UL>
|
||||
<LI>libH5Part.a: Serial C/C++ Library.</LI>
|
||||
<LI>libpH5Part.a: Parallel C/C++ library.</LI>
|
||||
<LI>libH5PartF.a: Serial F77/F90 library.</LI>
|
||||
<LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
|
||||
</UL>
|
||||
</LI><p>
|
||||
|
||||
<LI><b>Make Regression Tests and Examples</b>:<br>
|
||||
Just type <code>make tests</code> to build regression tests
|
||||
and/or example programs for H5Part. These tests are
|
||||
<UL>
|
||||
<LI>H5PartF: Fortran example (only build if --enable-fortran
|
||||
is specified).</LI>
|
||||
<LI>H5PartFpar: Parallel Fortran example (only built if both
|
||||
--enable-fortran and --enable-parallel are specified).</LI>
|
||||
<LI>H5PartTest: Serial C example. This test writes a sample
|
||||
datafile and then reopens it for reading. It demonstrates
|
||||
the most basic reading/writing capabilities.</LI>
|
||||
<LI>H5PartTestP: Parallel C example (only built if
|
||||
--enable-parallel is specified). This program only works
|
||||
as an MPI/parallel program.</LI>
|
||||
<LI>Bench: This program will only be built if
|
||||
--enable-parallel is specified. It compares the
|
||||
performance of raw binary
|
||||
I/O (one file per processor), raw binary MPI-IO based
|
||||
parallel I/O to a single file, and the parallel H5Part/HDF5 to
|
||||
a single file. Generally, H5Part should be very close to the
|
||||
MPI-IO implementation in terms of performance, but slower
|
||||
than one-file-per-processor. If HDF5 is slower the
|
||||
MPI-IO, it would indicate that some performance tuning
|
||||
will be required for your platform (contact us, and we will
|
||||
see what we can do!).</LI>
|
||||
</UL>
|
||||
</LI><p>
|
||||
<LI><b>Building Your Own Programs</b>:<br>
|
||||
There are many different subtleties to linking on various
|
||||
computer platforms, but typically one does the following.
|
||||
<UL>
|
||||
<LI>C/C++ Serial:
|
||||
<br><code>#include
|
||||
< H5Part.h > </code> into your
|
||||
source file.
|
||||
<br><code>$CC -I<i>path_to_H5Part.h</i>
|
||||
-I<i>path_to_hdf5.h</i> -o outfile
|
||||
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
|
||||
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
|
||||
</LI>
|
||||
<LI>C/C++ Parallel:
|
||||
<br><code>#include
|
||||
< H5Part.h > </code> into your
|
||||
source file.
|
||||
<br><code>$MPICC -I<i>path_to_H5Part.h</i>
|
||||
-I<i>path_to_hdf5.h</i> -DPARALLEL_IO
|
||||
-DH5_HAVE_PARALLEL -o outfile
|
||||
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
|
||||
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
|
||||
</LI>
|
||||
|
||||
<LI>Fortran Serial:
|
||||
<br><code>include
|
||||
'H5Part.inc'</code> into your
|
||||
source file.
|
||||
<br><code>$FC -I<i>path_to_H5Part.h</i>
|
||||
-I<i>path_to_hdf5.h</i> -o outfile
|
||||
MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
|
||||
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
|
||||
</LI>
|
||||
<LI>Fortran Parallel:
|
||||
<br><code>include
|
||||
'H5Part.inc'</code> into your
|
||||
source file.
|
||||
<br><code>$MPIF90 -I<i>path_to_H5Part.h</i>
|
||||
-o outfile
|
||||
MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
|
||||
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
|
||||
</LI><p>
|
||||
</UL>
|
||||
|
||||
</OL>
|
||||
|
||||
<hr>
|
||||
|
||||
<a name="Details">
|
||||
<h1>Details for H5Part Configure and Build</h1>
|
||||
</a>
|
||||
|
||||
|
||||
<a name="ConfigOptions">
|
||||
<h2>Configure Options</h2>
|
||||
</a>
|
||||
H5Part uses GNU Autoconf to generate a Makefile from the makefile
|
||||
template called <code>Makefile.in</code>.
|
||||
The configure script pays attention to the following
|
||||
configure options;<p>
|
||||
|
||||
<UL>
|
||||
<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
|
||||
<LI><b>--enable-fortran</b> By default H5part will make no attempt to
|
||||
build Fortran bindings. If you add the
|
||||
<code>--enable-fortran</code> flag to the ./configure line, it
|
||||
will create a small test program to determine how to generate
|
||||
the fortran bindings and then create a library that includes
|
||||
those bindings. You may need to set the fortran compiler by
|
||||
setting the <code>FC</code> environment variable in your shell.</LI>
|
||||
<LI><b>--enable-parallel</b> The version of HDF5 that you build for
|
||||
Parallel I/O differs from the library you would build for
|
||||
serial I/O. Consequently, the H5Part libraries must be built
|
||||
specifically for the kind of I/O you have in mind (parallel or
|
||||
serial). The configure script will attempt to find an
|
||||
<code>mpicc</code> if it is available. If no
|
||||
<code>mpicc</code> is available it will use the regular
|
||||
C-compiler and will try to locate the location of the MPI
|
||||
include files and libraries. You can assist the configure
|
||||
program in its search by setting the <code>MPIROOT</code>
|
||||
environment variable.</LI>
|
||||
<LI><b>--enable-tools</b> Builds the currently available tools
|
||||
<br>
|
||||
<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
|
||||
the file attributes, the step attributes, the dataset names and their values.
|
||||
<br>
|
||||
<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
|
||||
</LI>
|
||||
<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
|
||||
</LI>
|
||||
<LI><b>--help</b> Prints configure options.
|
||||
</LI>
|
||||
</UL>
|
||||
<p>
|
||||
|
||||
<a name="MakeOptions">
|
||||
<h2>Make Options</h2>
|
||||
</a>
|
||||
|
||||
<UL>
|
||||
<LI>make</LI>builds the libraries and test programs
|
||||
<LI>make install</LI>builds and installs
|
||||
<LI>make clean</LI>removes extraneous object files
|
||||
<LI>make distclean</LI>returns configuration to unconfigured state
|
||||
</UL>
|
||||
|
||||
<a name="EnvVariables">
|
||||
<h2>Environment Variables for Configure</h2>
|
||||
</a>
|
||||
The
|
||||
configuration script is of limited intelligence. Sometimes, you
|
||||
have to define the following environment variables in order to
|
||||
help it on its way. You will often only need to tell it where to
|
||||
find the HDF5 libraries (<code>H5ROOT</code> for serial or
|
||||
<code>PHDF5ROOT</code> for parallel builds). All of these
|
||||
environment variables can also be overidden in the Makefile that
|
||||
is generated by the autoconfigure script.
|
||||
The configure script pays attention to the following
|
||||
environment variables;
|
||||
<p>
|
||||
|
||||
<UL>
|
||||
<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
|
||||
configure script where to find the C compiler. You can
|
||||
also directly modify this variable in the
|
||||
<code>Makefile</code> that is generated by the autoconfigure</LI>
|
||||
<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
|
||||
configure script where to find the C++ compiler. You can
|
||||
also directly modify this variable in the
|
||||
<code>Makefile</code> that is generated by the autoconfigure</LI>
|
||||
<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
|
||||
configure script where to find the fortran compiler. You can
|
||||
also directly modify this variable in the
|
||||
<code>Makefile</code> that is generated by the autoconfigure</LI>
|
||||
<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
|
||||
useful to tell the configure script where to find the
|
||||
<code>mpicc</code> script. Normally, <code>mpicc</code> is
|
||||
merely a wrapper script for a build using a regular C-compiler.
|
||||
If no <code>mpicc</code> is available, then the
|
||||
<code>configure</code> script will attempt to locate the mpi
|
||||
header files and libraries. In that case, it may be useful to
|
||||
define the <code>MPI_HOME</code> environment variable.</LI>
|
||||
<LI><b>MPICXX</b>If you are building for parallel C++</LI>
|
||||
<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
|
||||
useful to tell the configure script where to find the parallel fortran compiler.
|
||||
<LI><b>MPIROOT</b>: Set this environment variable to help the
|
||||
configure script to locate the MPI libraries that should be
|
||||
used to build the parallel version of the libraries. This
|
||||
variable will be ignored if configured only to build the
|
||||
serial implementation of the library.</LI>
|
||||
<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation. If you
|
||||
are building the serial version of H5part, then you should set
|
||||
the <code>PHDF5ROOT</code> environment variable.</LI>
|
||||
</UL><p>
|
||||
|
||||
<h3>Common compiler environemt variables for NERSC platforms</h3>
|
||||
<UL>
|
||||
<LI><b>DaVinci</b>: Linux ia64 </LI>
|
||||
CC=icc CXX=icc F90=ifort MPICC=icc MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
|
||||
<LI><b>Bassi</b>: AIX</LI>
|
||||
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
|
||||
<LI><b>Jacquard</b>: Linux x86_64</LI>
|
||||
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
|
||||
<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
|
||||
CC=gcc CXX=g++ FC=g95
|
||||
</UL>
|
||||
<br>
|
||||
NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
|
||||
MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r MPIINC=-I/usr/lpp/ppe.poe/include/thread
|
||||
<h3>How to set the variables for configure:</h3>
|
||||
It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
|
||||
<pre>
|
||||
% env CC=icc CXX=icc F90=ifort MPICC=icc MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
|
||||
</pre>
|
||||
In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
|
||||
needed to perform the proper build.
|
||||
</div>
|
||||
|
||||
Executable
+68
@@ -0,0 +1,68 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
<!--#include virtual="/include/topIncludes.html"-->
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
|
||||
<head>
|
||||
<title>Building HDF5</title>
|
||||
</head>
|
||||
|
||||
<body bgcolor="#F0F0F0">
|
||||
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
|
||||
<UL>
|
||||
<LI><a href="#ConfigOptions">Configure Options</a>
|
||||
<LI><a href="#EnvVariables">Important Environment Variables</a>
|
||||
</UL>
|
||||
|
||||
<hr>
|
||||
<a name="ConfigOptions">
|
||||
<h2>Configure options</h2></a>
|
||||
</a>
|
||||
To set the installation path configure with
|
||||
<pre>
|
||||
./configure --prefix=your hdf5 installation full path, e.g.--prefix=/usr/local/hdf5
|
||||
</pre>
|
||||
For the serial implementation configure with
|
||||
<pre>
|
||||
./configure
|
||||
</pre>
|
||||
For the parallel implementation configure with
|
||||
<pre>
|
||||
./configure --enable-parallel
|
||||
</pre>
|
||||
To enable shared objects configure with
|
||||
<pre>
|
||||
./configure --enable-shared
|
||||
</pre>
|
||||
<a name="EnvVariables">
|
||||
<h2>Environment Variables</h2></a>
|
||||
</a>
|
||||
To add HDF5 to your PATH and LD_LIBRARY_PATH edit your
|
||||
.tcshr, or .cshrc depending on the shell you are using and add
|
||||
<pre>
|
||||
setenv HDF5 "your hdf5 installation full path"
|
||||
setenv PATH ${PATH}:${HDF5}/bin
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5}/lib
|
||||
</pre>
|
||||
if you are using bash, add to your .bashrc
|
||||
<pre>
|
||||
export HDF5="your hdf5 installation full path"
|
||||
export PATH=$PATH:${HDF5}/bin
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib
|
||||
</pre>
|
||||
|
||||
Open a new terminal or do a
|
||||
source .tcshr (.cshrc, .bashrc) in the one that you are using.
|
||||
|
||||
You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
|
||||
</div>
|
||||
|
||||
<!--#include virtual="/include/dateFooter.html"-->
|
||||
@@ -0,0 +1,48 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
<!--#include virtual="/include/topIncludes.html"-->
|
||||
|
||||
<div id="maincenter">
|
||||
<head>
|
||||
<title>Downloading H5Part</title>
|
||||
</head>
|
||||
|
||||
<body bgcolor="#F0F0F0">
|
||||
<font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
|
||||
<UL>
|
||||
<LI><a href="#svnano">Subversion access.</a>
|
||||
</UL>
|
||||
<hr>
|
||||
<a name="svnano">
|
||||
<h2>Subversion access</h2>
|
||||
</a>
|
||||
|
||||
<LI><b>Anonymous via. Savannah</b>:<br>
|
||||
Use svn from <a href="http://subversion.tigris.org"> tigris </a>
|
||||
<pre>
|
||||
svn checkout svn+ssh://svn@savannah.psi.ch/afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
|
||||
</pre>
|
||||
Password is svn.
|
||||
<LI><b>Using AFS</b>:<br>
|
||||
You need AFS (openAFS) and must have an AFS-Account at PSI which in consequence gives you
|
||||
the needed access right.
|
||||
</LI><p>
|
||||
<pre>
|
||||
svn checkout file:///afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
|
||||
</pre>
|
||||
In case of trouble please contact the person mentioned at the bottom of this page.
|
||||
<hr>
|
||||
<address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>
|
||||
<!-- Created: March 7 12:52:52 PST 2005 -->
|
||||
<!-- hhmts start -->
|
||||
Last modified: Mon Jan 9 22:18:55 CET 2006
|
||||
<!-- hhmts end -->
|
||||
</div>
|
||||
|
||||
<!--#include virtual="/include/dateFooter.html"-->
|
||||
+109
-2255
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1,77 +0,0 @@
|
||||
NumLevels: 2
|
||||
|
||||
NumVerticesOnLevel: 11 20 29
|
||||
|
||||
Vertices:
|
||||
1 0.0 0.0
|
||||
2 60.0 -70.0
|
||||
3 90.0 -10.0
|
||||
4 140.0 -70.0
|
||||
5 180.0 -10.0
|
||||
6 240.0 -60.0
|
||||
7 220.0 60.0
|
||||
8 140.0 90.0
|
||||
9 200.0 120.0
|
||||
10 130.0 150.0
|
||||
11 50.0 80.0
|
||||
12 115.0 40.0
|
||||
13 95.0 85.0
|
||||
14 70.0 35.0
|
||||
15 160.0 -40.0
|
||||
16 135.0 -10.0
|
||||
17 115.0 -40.0
|
||||
18 200.0 25.0
|
||||
19 180.0 75.0
|
||||
20 160.0 40.0
|
||||
|
||||
21 125.0 15.0
|
||||
22 112.5 -10.0
|
||||
23 102.5 15.0
|
||||
24 147.5 15.0
|
||||
25 137.5 40.0
|
||||
26 150.0 65.0
|
||||
27 127.5 65.0
|
||||
28 117.5 87.5
|
||||
29 105.0 62.5
|
||||
|
||||
NumElemsOnLevel: 12 24 36
|
||||
NumElems: 12 28 44
|
||||
|
||||
Elements:
|
||||
ID PID CID VertexIDs Adj Translation Tbl (dim num lvls - 1)
|
||||
1 -1 -1 1 2 3 2 11 -1 1
|
||||
2 -1 -1 2 3 4 3 -1 1 2
|
||||
3 -1 12 3 4 5 4 12 2 -1
|
||||
4 -1 -1 4 5 6 5 -1 3 3
|
||||
5 -1 -1 5 7 6 -1 4 6 4
|
||||
6 -1 17 8 5 7 5 7 12 -1
|
||||
7 -1 -1 8 9 7 -1 6 8 5
|
||||
8 -1 -1 10 8 9 7 -1 9 6
|
||||
9 -1 -1 11 10 8 8 10 -1 7
|
||||
10 -1 25 11 3 8 12 9 11 -1
|
||||
11 -1 -1 1 11 3 10 1 -1 8
|
||||
12 -1 21 3 8 5 6 3 10 -1
|
||||
13 3 -1 3 14 13 16 21 2 9
|
||||
14 3 -1 14 4 12 4 16 2 10
|
||||
15 3 -1 13 12 5 4 23 16 11
|
||||
16 3 -1 14 13 12 15 14 13 12
|
||||
17 6 -1 8 17 16 20 5 22 13
|
||||
18 6 -1 17 5 15 5 20 23 14
|
||||
19 6 -1 16 15 7 5 7 20 15
|
||||
20 6 -1 17 16 15 19 18 17 16
|
||||
21 12 -1 3 18 13 24 13 26 17
|
||||
22 12 -1 18 8 17 17 24 27 18
|
||||
23 12 -1 13 17 5 18 15 24 19
|
||||
24 12 -1 18 13 17 23 22 21 20
|
||||
25 10 -1 11 20 19 28 9 11 21
|
||||
26 10 -1 20 3 18 21 28 11 22
|
||||
27 10 -1 19 18 8 22 9 28 23
|
||||
28 10 -1 20 3 18 27 26 25 24
|
||||
|
||||
3,0 3,1 4,2 2,3 16,4
|
||||
|
||||
1 2 -1 3 4
|
||||
|
||||
1 2 3
|
||||
1 3 6
|
||||
2 11 1 13 14
|
||||
@@ -1,107 +0,0 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 17 DOUBLE
|
||||
-1 0 0
|
||||
1 0 0
|
||||
0 1 0
|
||||
0 0 1
|
||||
0 -1 0
|
||||
-0.5 0 0.5
|
||||
-0.5 0.5 0
|
||||
0 0 0
|
||||
0 0.5 0.5
|
||||
0.5 0 0.5
|
||||
0.5 0.5 0
|
||||
-0.75 0 0.25
|
||||
-0.75 0.25 0
|
||||
-0.5 0 0
|
||||
-0.5 0.25 0.25
|
||||
-0.25 0 0.25
|
||||
-0.25 0.25 0
|
||||
|
||||
CELLS 18 90
|
||||
4 0 3 2 1
|
||||
4 0 4 3 1
|
||||
4 0 5 6 7
|
||||
4 5 3 8 9
|
||||
4 6 8 2 10
|
||||
4 7 9 10 1
|
||||
4 5 6 7 9
|
||||
4 5 6 8 9
|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
||||
4 0 11 12 13
|
||||
4 11 5 14 15
|
||||
4 12 14 6 16
|
||||
4 13 15 16 7
|
||||
4 11 12 13 15
|
||||
4 11 12 14 15
|
||||
4 12 13 15 16
|
||||
4 12 14 15 16
|
||||
|
||||
CELL_TYPES 18
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 18
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
17
|
||||
|
||||
@@ -1,59 +0,0 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 17 DOUBLE
|
||||
-1 0 0
|
||||
1 0 0
|
||||
0 1 0
|
||||
0 0 1
|
||||
0 -1 0
|
||||
-0.5 0 0.5
|
||||
-0.5 0.5 0
|
||||
0 0 0
|
||||
0 0.5 0.5
|
||||
0.5 0 0.5
|
||||
0.5 0.5 0
|
||||
-0.75 0 0.25
|
||||
-0.75 0.25 0
|
||||
-0.5 0 0
|
||||
-0.5 0.25 0.25
|
||||
-0.25 0 0.25
|
||||
-0.25 0.25 0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 3 2 1
|
||||
4 0 4 3 1
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
|
||||
@@ -1,80 +0,0 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 17 DOUBLE
|
||||
-1 0 0
|
||||
1 0 0
|
||||
0 1 0
|
||||
0 0 1
|
||||
0 -1 0
|
||||
-0.5 0 0.5
|
||||
-0.5 0.5 0
|
||||
0 0 0
|
||||
0 0.5 0.5
|
||||
0.5 0 0.5
|
||||
0.5 0.5 0
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||||
-0.75 0 0.25
|
||||
-0.75 0.25 0
|
||||
-0.5 0 0
|
||||
-0.5 0.25 0.25
|
||||
-0.25 0 0.25
|
||||
-0.25 0.25 0
|
||||
|
||||
CELLS 9 45
|
||||
4 0 4 3 1
|
||||
4 0 5 6 7
|
||||
4 5 3 8 9
|
||||
4 6 8 2 10
|
||||
4 7 9 10 1
|
||||
4 5 6 7 9
|
||||
4 5 6 8 9
|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
||||
|
||||
CELL_TYPES 9
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 9
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
|
||||
@@ -1,101 +0,0 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 17 DOUBLE
|
||||
-1 0 0
|
||||
1 0 0
|
||||
0 1 0
|
||||
0 0 1
|
||||
0 -1 0
|
||||
-0.5 0 0.5
|
||||
-0.5 0.5 0
|
||||
0 0 0
|
||||
0 0.5 0.5
|
||||
0.5 0 0.5
|
||||
0.5 0.5 0
|
||||
-0.75 0 0.25
|
||||
-0.75 0.25 0
|
||||
-0.5 0 0
|
||||
-0.5 0.25 0.25
|
||||
-0.25 0 0.25
|
||||
-0.25 0.25 0
|
||||
|
||||
CELLS 16 80
|
||||
4 0 4 3 1
|
||||
4 5 3 8 9
|
||||
4 6 8 2 10
|
||||
4 7 9 10 1
|
||||
4 5 6 7 9
|
||||
4 5 6 8 9
|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
||||
4 0 11 12 13
|
||||
4 11 5 14 15
|
||||
4 12 14 6 16
|
||||
4 13 15 16 7
|
||||
4 11 12 13 15
|
||||
4 11 12 14 15
|
||||
4 12 13 15 16
|
||||
4 12 14 15 16
|
||||
|
||||
CELL_TYPES 16
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
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|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 16
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
1
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
17
|
||||
|
||||
@@ -1,13 +0,0 @@
|
||||
12 14
|
||||
2 11
|
||||
1 3
|
||||
2 4 12
|
||||
3 5
|
||||
4 6
|
||||
5 7 12
|
||||
6 8
|
||||
7 9
|
||||
8 10
|
||||
9 11 12
|
||||
1 10
|
||||
3 6 10
|
||||
@@ -1,12 +0,0 @@
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
@@ -1,12 +0,0 @@
|
||||
1
|
||||
1
|
||||
2
|
||||
2
|
||||
2
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
2
|
||||
@@ -1,49 +0,0 @@
|
||||
24 35
|
||||
%1
|
||||
2 8
|
||||
%2
|
||||
1 9 10
|
||||
%3
|
||||
4 10 11
|
||||
%4
|
||||
3 14 15
|
||||
%5
|
||||
6 13 15
|
||||
%6
|
||||
5 7
|
||||
%7
|
||||
6 21 23
|
||||
%8
|
||||
1 21 22
|
||||
%9
|
||||
2 12 17
|
||||
%10
|
||||
2 3 12
|
||||
%11
|
||||
3 12 19
|
||||
%12
|
||||
9 10 11
|
||||
%13
|
||||
5 16 18
|
||||
%14
|
||||
4 16 19
|
||||
%15
|
||||
4 5 16
|
||||
%16
|
||||
13 14 15
|
||||
%17
|
||||
9 20 22
|
||||
%18
|
||||
13 20 23
|
||||
%19
|
||||
11 14 20
|
||||
%20
|
||||
17 18 19
|
||||
%21
|
||||
7 8 24
|
||||
%22
|
||||
8 17 24
|
||||
%23
|
||||
7 18 24
|
||||
%24
|
||||
21 22 23
|
||||
@@ -1,24 +0,0 @@
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
@@ -1,13 +0,0 @@
|
||||
12 1
|
||||
1 2 3
|
||||
2 3 4
|
||||
3 4 6
|
||||
4 5 6
|
||||
5 6 7
|
||||
6 7 8
|
||||
7 8 11
|
||||
8 10 11
|
||||
8 9 10
|
||||
3 8 9
|
||||
1 3 9
|
||||
3 6 8
|
||||
@@ -1,12 +0,0 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
@@ -1,12 +0,0 @@
|
||||
11 22
|
||||
2 3 9
|
||||
1 3 4
|
||||
1 2 4 6 8 9
|
||||
2 3 6 5
|
||||
4 6 7
|
||||
3 4 5 7 8
|
||||
5 6 8 11
|
||||
6 7 11 10 9 3
|
||||
8 10 3 1
|
||||
8 11 9
|
||||
7 8 10
|
||||
@@ -1,11 +0,0 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
@@ -1,41 +0,0 @@
|
||||
20 43
|
||||
%1
|
||||
2 3 11
|
||||
%2
|
||||
1 3 4
|
||||
%3
|
||||
1 2 14 13 18 20
|
||||
%4
|
||||
2 14 12 6
|
||||
%5
|
||||
12 6 15 17 13
|
||||
%6
|
||||
4 5 7
|
||||
%7
|
||||
6 15 16 9
|
||||
%8
|
||||
9 10 19 18 17 16
|
||||
%9
|
||||
7 8 10
|
||||
%10
|
||||
8 9 11
|
||||
%11
|
||||
1 20 19 10
|
||||
%12
|
||||
4 14 13 5
|
||||
%13
|
||||
3 14 12 5 17 18
|
||||
%14
|
||||
3 13 12 4
|
||||
%15
|
||||
5 17 17 7
|
||||
%16
|
||||
7 8 17 15
|
||||
%17
|
||||
5 15 16 8 18 13
|
||||
%18
|
||||
3 13 17 8 19 20
|
||||
%19
|
||||
8 11 20 18
|
||||
%20
|
||||
3 18 19 11
|
||||
@@ -1,20 +0,0 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
-171
@@ -1,171 +0,0 @@
|
||||
/*!
|
||||
\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
|
||||
|
||||
Particle-based simulations running on large high-performance computing systems
|
||||
over many time steps can generate an enormous amount of particle- and
|
||||
field-based data for post-processing and analysis. Achieving high-performance
|
||||
I/O for this data, effectively managing it on disk, and interfacing it with
|
||||
analysis and visualization tools can be challenging, especially for domain
|
||||
scientists who do not have I/O and data management expertise. We present the
|
||||
H5hut library, an implementation of several data models for particle-based
|
||||
simulations that encapsulates the complexity of HDF5 and is simple to use, yet
|
||||
does not compromise performance.
|
||||
|
||||
Developers:
|
||||
|
||||
<UL>
|
||||
<LI> Andreas Adelmann (PSI) </LI>
|
||||
<LI> Achim Gsell (PSI) </LI>
|
||||
<LI> Mark Howison (NERSC/LBNL) </LI>
|
||||
<LI> Prabhat (NERSC/LBNL) </LI>
|
||||
<LI> Wes Bethel (NERSC/LBNL) </LI>
|
||||
</UL>
|
||||
|
||||
Previous developers:
|
||||
|
||||
<UL>
|
||||
<LI> Benedikt Oswald (PSI) </LI>
|
||||
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
|
||||
<LI> John Shalf (NERSC/LBNL)</LI>
|
||||
</UL>
|
||||
|
||||
For more information, please contact the
|
||||
<a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
|
||||
|
||||
\defgroup c_api C API
|
||||
@{
|
||||
\note The C API is implemented with '\c static \c inline' functions to minimize overhead.
|
||||
\defgroup h5_c_api H5
|
||||
@{
|
||||
\defgroup h5_file File interface
|
||||
|
||||
In this section we document the interface for accessing H5hut files.
|
||||
|
||||
\defgroup h5_model Setting up the data model
|
||||
|
||||
The fundamental data model of H5hut is pretty simple. There
|
||||
are (time-)steps to group data, that's it. In this section we
|
||||
document the interface to these (time-)steps.
|
||||
|
||||
\defgroup h5_file_attribs File attributes interface
|
||||
|
||||
File attributes are small datasets that can be used to
|
||||
describe specific properties of a file. The H5hut API provides
|
||||
functions to attach (write), read and inquire file attributes.
|
||||
|
||||
\defgroup h5_step_attribs Step attributes interface
|
||||
|
||||
Step attributes are similar to file attributes but are
|
||||
attached to (time-)steps. They can be used to describe
|
||||
specific properties of a specific step. The H5hut API provides
|
||||
functions to attach (write), read and inquire step attributes.
|
||||
|
||||
\defgroup h5_attach Attaching files
|
||||
|
||||
Sometimes it is required (or at least useful) to attach
|
||||
additional information to H5hut files. H5hut provides
|
||||
functions to attach other files to H5hut files. The attached
|
||||
files can be of any type.
|
||||
|
||||
\defgroup h5_log Controlling verbosity level
|
||||
|
||||
Controlling the verbosity level of H5hut. By default only
|
||||
error messages are printed. For debugging it might be helpful
|
||||
to increase the verbosity level.
|
||||
|
||||
\defgroup h5_debug Controlling debug output
|
||||
|
||||
Debug output mainly intended for developers.
|
||||
|
||||
\defgroup h5_error Error handling interface
|
||||
|
||||
H5hut comes with two error handler. The default error handler
|
||||
prints an error message (which can be suppressed by setting
|
||||
the verbosity level to \c 0), sets an internal error number
|
||||
and returns to the calling program with the value \c
|
||||
H5_FAILURE. It is up to the programmer to handle the error
|
||||
properly. In certain use-cases it make sense just to abort the
|
||||
program, so no additional error handling is needed. H5hut
|
||||
provides an abort error-handler for this use-cases-
|
||||
|
||||
@}
|
||||
\defgroup h5part_c_api H5Part
|
||||
@{
|
||||
\defgroup h5part_model Setting up the data model
|
||||
|
||||
The H5Part data model interface provides functions to set and
|
||||
inquire (per core) views on datasets.
|
||||
|
||||
\defgroup h5part_io Dataset interface
|
||||
|
||||
The dataset interface provides functions to read and write
|
||||
datasets. The following data types are supported:
|
||||
|
||||
- 64-bit floating point numbers (\c h5_float64_t)
|
||||
- 32-bit floating point numbers (\c h5_float32_t)
|
||||
- 64-bit integers (\c h5_int64_t)
|
||||
- 32-bit integers (\c h5_int32_t)
|
||||
|
||||
\note Before you can write or read a dataset, you have to
|
||||
define a "view" on the dataset for each core.
|
||||
|
||||
@}
|
||||
\defgroup h5block_c_api H5Block
|
||||
@{
|
||||
\defgroup h5block_model Setting up the data model
|
||||
|
||||
The H5Block data model interface provides functions to set and
|
||||
inquire (per core) views on fields.
|
||||
|
||||
\defgroup h5block_io Interface to block structured data
|
||||
|
||||
H5Block provides functions to store and retrieve
|
||||
|
||||
- 3-dimensional fields with scalar values
|
||||
- 3-dimensional fields with 3-dimensional vectors as values
|
||||
|
||||
The following datatypes are supported:
|
||||
|
||||
- 64-bit floating point numbers (\c h5_float64_t)
|
||||
- 32-bit floating point numbers (\c h5_float32_t)
|
||||
- 64-bit integers (\c h5_int64_t)
|
||||
- 32-bit integers (\c h5_int32_t)
|
||||
|
||||
\defgroup h5block_attrib Attaching attributes to field data
|
||||
|
||||
Field attributes are small datasets that can be used to
|
||||
describe specific properties of a field like origin, spacing
|
||||
or coordinates. The H5hut API provides functions to attach
|
||||
(write), read and inquire file attributes.
|
||||
|
||||
@}
|
||||
@}
|
||||
*/
|
||||
|
||||
/*!
|
||||
\defgroup f90_api Fortran90 API
|
||||
@{
|
||||
\defgroup h5_f90_api H5
|
||||
@{
|
||||
\defgroup h5_file_f file interface
|
||||
\defgroup h5_model_f setting up the data model
|
||||
\defgroup h5_file_attribs_f reading and writing file attributes
|
||||
\defgroup h5_step_attribs_f reading and writing step attributes
|
||||
\defgroup h5_log_f control verbosity level
|
||||
\defgroup h5_debug_f control debug output
|
||||
\defgroup h5_error_f error handling interface
|
||||
@}
|
||||
\defgroup h5part_f90_api H5Part
|
||||
@{
|
||||
\defgroup h5part_model_f setting up the data model
|
||||
\defgroup h5part_io_f reading and writing datasets
|
||||
@}
|
||||
\defgroup h5block_f90_api H5Block
|
||||
@{
|
||||
\defgroup h5block_model_f setting up the data model
|
||||
\defgroup h5block_io_f reading and writing datasets
|
||||
\defgroup h5block_attrib_f reading and writing attributes
|
||||
@}
|
||||
@}
|
||||
*/
|
||||
|
||||
Executable
+14
@@ -0,0 +1,14 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
Under construction, will be here soon.
|
||||
</div>
|
||||
|
||||
Executable
+15
@@ -0,0 +1,15 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
Under construction, will be here soon.
|
||||
|
||||
</div>
|
||||
|
||||
Executable
+15
@@ -0,0 +1,15 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
Under construction, will be here soon.
|
||||
|
||||
</div>
|
||||
|
||||
@@ -0,0 +1,99 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>Put your title here!!</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
<!--#include virtual="/include/topIncludes.html"-->
|
||||
|
||||
<div id="maincenter">
|
||||
|
||||
|
||||
<head>
|
||||
<title>H5Part Utility Tools</title>
|
||||
</head>
|
||||
|
||||
<body bgcolor="#F0F0F0">
|
||||
<font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
|
||||
<UL>
|
||||
<LI><a href="h5pAttrib">h5pAttrib</a>
|
||||
<LI><a href="h5pToGNUplot">h5pToGNUplot</a>
|
||||
</UL>
|
||||
|
||||
<hr>
|
||||
|
||||
<a name="h5pAttrib">
|
||||
<h2>h5pAttrib</h2>
|
||||
</a>
|
||||
|
||||
<b>h5pAttrib</b> is an inspection tool that prints to stdout the number of timesteps in a file
|
||||
the file attributes, the step attributes, the dataset names and their values. It's simpler to use than h5dump.
|
||||
Usage options are given by typing:
|
||||
<br><br>
|
||||
<PRE>
|
||||
% ./h5pAttrib -h
|
||||
usage: h5pAttrib [OPTIONS] file
|
||||
|
||||
OPTIONS
|
||||
-h, --help Print help page
|
||||
-n, --nstep Print number of steps
|
||||
-A, --fileA Print file attributes
|
||||
-a, --stepA Print step attributes & values for time step n
|
||||
-d, --dataset Print data sets names & values for time step n
|
||||
-H, --header Print shorter version without the values
|
||||
</PRE>
|
||||
|
||||
<h3>Examples</h3>
|
||||
<OL>
|
||||
<LI>
|
||||
Show file attribute names & values of sample.h5part
|
||||
</LI>
|
||||
h5pAttrib -A sample.h5part
|
||||
<LI>
|
||||
Show step attribute names for time step 5 of sample.h5part
|
||||
</LI>
|
||||
h5pAttrib -a 5 -H sample.h5part
|
||||
</OL>
|
||||
|
||||
<a name="h5pToGNUplot">
|
||||
<h2>h5pToGNUplot</h2>
|
||||
</a>
|
||||
|
||||
<b>h5pToGNUplot</b> is a converter from H5Part to two column ASCII text format for loading into GNUplot. Usage options are given by typing:
|
||||
<br><br>
|
||||
<PRE>
|
||||
% ./h5pToGNUplot -h
|
||||
|
||||
usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]
|
||||
|
||||
FLAGS
|
||||
-h, --help Print help page
|
||||
-1, --1var (REQUIRED) Takes first variable parameter
|
||||
-2, --2var (REQUIRED) Takes second variable parameter
|
||||
-i, --input (REQUIRED) Takes input file name
|
||||
-t, --timestep (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
|
||||
-o, --output (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
|
||||
-n, --number (OPTIONAL) Sets number of output points
|
||||
-s, --start (OPTIONAL) Sets the starting particle index
|
||||
</PRE>
|
||||
|
||||
<h3>Examples</h3>
|
||||
<OL>
|
||||
<LI>
|
||||
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
|
||||
</LI>
|
||||
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt
|
||||
<LI>
|
||||
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
|
||||
using 1200 points from particle index 76
|
||||
</LI>
|
||||
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200
|
||||
</OL>
|
||||
|
||||
</div>
|
||||
|
||||
<!--#include virtual="/include/dateFooter.html"-->
|
||||
|
||||
|
||||
Executable
+75
@@ -0,0 +1,75 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>H5Part: VisIt Plugins</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
<font face="arial,helvetica"><h1>H5Part: VisIt Plugins</h1></font>
|
||||
<font face="arial,helvetica" color="#555588"><h2>Introduction</h2></font>
|
||||
<P>
|
||||
<a href="http://www.llnl.gov/visit">VisIt</a> is an open source point-and-click 3D scientific visualization application that supports most of the common visualization techniques on structured and unstructured grids. One of its advantages is that it employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines. See this link for <a href="http://vis.lbl.gov/NERSC/Software/visit/">details</a> on how to run VisIt in NERSC.
|
||||
</P>
|
||||
<P>
|
||||
VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins. The user describes the properties of the plugin and then the tool generates most of the code necessary to implement the plugin. For example, in the case of an operator, the plugin creation tool creates the code necessary for the graphical user interface attribute window; the C++, Python, and Java interfaces; and the code necessary to interface to VisIt. The only code you need to write is the C++ code that actually performs the operation.
|
||||
</P>
|
||||
<font face="arial,helvetica" color="#555588"><h2>H5Part in VisIt</h2></font>
|
||||
<font face="arial,helvetica" color="#555588"><h3>Database Reader Plugin</h3></font>
|
||||
<P>
|
||||
We wrote a Multiple Time Step Multiple Domain database reader to read H5Part data into VisIt. H5Part datasets should be named with the extension <font color=red>".h5part"</font> to be recognized by the reader since VisIt does not have a format selection mechanism at the time of reading. Figure 1 shows a Pseudocolor plot of a data set and Figure 2 shows a Scatter plot x-y (any combination of x, px, y, py, z, pz, id are possible).
|
||||
</P>
|
||||
<P>
|
||||
<TABLE>
|
||||
<TR>
|
||||
<TD>
|
||||
<a href="H5PartVisIt/cloud_visit.png"><img src="H5PartVisIt/cloud_visit.s.png" width=400 height=300></a>
|
||||
</TD
|
||||
></TR>
|
||||
<TR>
|
||||
<TD width=300>
|
||||
Figure 1. VisIt User interface showing an H5Part particle file rendered as spheres using the Pseudocolor plot.
|
||||
</TD>
|
||||
</TR>
|
||||
<TR>
|
||||
<TD>
|
||||
<a href="H5PartVisIt/cloud_visit_2D.png"><img src="H5PartVisIt/cloud_visit_2D.s.png" width=300 height=300></a>
|
||||
</TD>
|
||||
</TR>
|
||||
<TR>
|
||||
<TD>
|
||||
Figure 2. A Scatter plot of the x-y projection of the particles.
|
||||
</TD>
|
||||
</TR>
|
||||
</TABLE>
|
||||
</P>
|
||||
|
||||
<P>
|
||||
VisIt provides a Query interface, for single time steps and for time series. Figure 3 shows the query interace over time for the sum of the x position and the z position of the particoes.
|
||||
</P>
|
||||
<P>
|
||||
<TABLE>
|
||||
<TR>
|
||||
<TD>
|
||||
<a href="H5PartVisIt/visit_query1.png"><img src="H5PartVisIt/visit_query1.s.png" width=400 height=300></a>
|
||||
</TD
|
||||
></TR>
|
||||
<TR>
|
||||
<TD width=300>
|
||||
Figure 3. VisIt's Time Query Output.
|
||||
</TD>
|
||||
</TR>
|
||||
</TABLE>
|
||||
</p>
|
||||
<font face="arial,helvetica" color="#555588"><h2>Operator Plugins</h2></font>
|
||||
<P>
|
||||
<font face="arial,helvetica" color="#555588"><h3>Particle Random Sampler</h3></font>
|
||||
|
||||
|
||||
</P>
|
||||
<P>
|
||||
<font face="arial,helvetica" color="#555588"><h3>Particle Binner</h3></font>
|
||||
</P>
|
||||
</div>
|
||||
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|
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|
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|
After Width: | Height: | Size: 79 KiB |
@@ -1,170 +0,0 @@
|
||||
Proposal for a more general file format used by H5Part/H5Block
|
||||
|
||||
Authors: Achim Gsell
|
||||
Status: Draft
|
||||
|
||||
1. Introduction
|
||||
|
||||
H5X is the file format used by H5Part and H5Block. H5X is designed on
|
||||
top of HDF5: A H5X file is a very special HDF5 file.
|
||||
|
||||
+--------------------+
|
||||
| Application |
|
||||
+--------------------+
|
||||
| H5Part/H5Block API |
|
||||
+--------------------+
|
||||
| H5X API |
|
||||
+--------------------+
|
||||
| HDF5 API |
|
||||
+--------------------+
|
||||
| Filesystem of OS |
|
||||
+--------------------+
|
||||
|
||||
|
||||
2. H5X file format specification
|
||||
|
||||
2.1 The root group
|
||||
|
||||
2.1.1 File attributes
|
||||
|
||||
Attributes of the HDF5 root group are called "file attributes". There
|
||||
are no restrictions on file attribute names. Names with "__" as prefix and
|
||||
postfix are intended for internal use. Supported values for file attributes
|
||||
are scalars and arrays of 64bit integer and 64bit floating point number as
|
||||
well as string values. Arrays of strings are not supported.
|
||||
|
||||
2.1.1.1 Predefined file attributes
|
||||
|
||||
__stepname__ (optional)
|
||||
See below.
|
||||
|
||||
__stepnumwidth__ (optional)
|
||||
See below.
|
||||
|
||||
2.1.2 Members of the root group
|
||||
|
||||
Members of the root group are special formated HDF5 groups called
|
||||
"step groups". The name of a step group is "<name>#<number>".
|
||||
Whereby <name> is either defined by the optional file attribute
|
||||
__stepname__ or set to "Step" by default. <number> is an
|
||||
unsigned integer less than 2^63.
|
||||
|
||||
/
|
||||
+- Step#0
|
||||
+- Step#1
|
||||
...
|
||||
+- Step#n
|
||||
+- StepProperties [NEW]
|
||||
+- Mesh [NEW]
|
||||
|
||||
The optional file attribute __stepnumwidth__ defines the minimum width
|
||||
of <number> in the name of the step group. The number is padded with
|
||||
'0'. The minimum width defaults to zero, so that no paddings occurs.
|
||||
Example: With __stepnumwidth__ := 5 the name of the step group with
|
||||
number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
|
||||
"Step#42".
|
||||
|
||||
Step groups may be unsorted in the HDF5 file und needn't be number
|
||||
consecutively.
|
||||
|
||||
2.1.3 Other members of the root group
|
||||
|
||||
Other sub-groups of the root group are allowed, but the group names are restricted
|
||||
to names not matching "Step#.*".
|
||||
|
||||
2.2 Format of a step group
|
||||
|
||||
2.2.1 Step attributes
|
||||
|
||||
Step attributes are HDF5 attributes asigned to a step group. There
|
||||
are no restrictions on step attribute names. As with file attributes names
|
||||
enclosed in "__" are intended for internal use. Supported values are the same
|
||||
as for file attributes:
|
||||
* 64bit integer value
|
||||
* arrays of 64bit integer values
|
||||
* 64bit floating point number
|
||||
* array of 64bit floating point number
|
||||
* strings
|
||||
Note that array of strings are not supported!
|
||||
|
||||
2.2.2 Predefined step attributes
|
||||
|
||||
No predefined step attributes exists.
|
||||
|
||||
|
||||
2.2.3 Members of a step group
|
||||
|
||||
Members of a step group are HDF5 datasets and optional one HDF5 group
|
||||
with the name "Block". HDF5 datasets in a step group are called "step
|
||||
datasets". The optional block group is called "block data".
|
||||
|
||||
Mesh?!
|
||||
|
||||
2.2.4 Step datasets
|
||||
|
||||
Step datasets are arrays of rank 1. The dataset size must be the same
|
||||
for all datasets inside a step. The size of the dataset may vary
|
||||
from step to step. Array values are 64bit integer or 64bit floating
|
||||
point numbers. No limitations (other than given by HDF5) are given on
|
||||
step dataset names.
|
||||
|
||||
|
||||
2.2.5 Block Data
|
||||
|
||||
The block data group is a container for an arbitrary number of field
|
||||
data. A field is a data structure to store arrays of rank m with
|
||||
n-dimensional vector values. Fields are represented within HDF5
|
||||
groups. The HDF5 group name is the unique identifier for a field in
|
||||
the current step.
|
||||
|
||||
2.2.5.1 m-rank fields with n-dimensional-vector values
|
||||
|
||||
Values are stored per dimension in separate datasets. Thus we have n
|
||||
datasets for a field with n-dimensional vector values. Each dataset
|
||||
corresponse to one dimension. The datasets are numbered from '0' to
|
||||
'n-1'. Arrays are stored in column major order (Fortran indexing
|
||||
scheme).
|
||||
|
||||
/ # HDF5 root group
|
||||
...
|
||||
+- Step#<i> # HDF5 group
|
||||
|
|
||||
+- Block # HDF5 group
|
||||
|
|
||||
+- <field name> # HDF5 group
|
||||
|
|
||||
+- 0 # HDF5 dataset, first dim of vector
|
||||
+- 1 # HDF5 dataset, second dim of vector
|
||||
...
|
||||
+- n-1 # HDF5 dataset, last dim of vector
|
||||
...
|
||||
|
||||
2.2.5.2 m-rank fields with scalar values
|
||||
|
||||
Fields with scalar values are stored as special case of fields with
|
||||
n-dimensional vector values with n := 1.
|
||||
|
||||
/ # HDF5 root group
|
||||
...
|
||||
+- Step#<i> # HDF5 group
|
||||
|
|
||||
+- Block # HDF5 group
|
||||
|
|
||||
+- <field name> # HDF5 group
|
||||
|
|
||||
+- 0 # HDF5 dataset, scalar value
|
||||
...
|
||||
|
||||
|
||||
2.3 Step properties [NEW]
|
||||
|
||||
Why? Much faster than step attributes if you need to access consecutive values
|
||||
|
||||
Group of root group with name "StepProperties"
|
||||
|
||||
Members are datasets
|
||||
|
||||
Supported values are the same as for step attributes
|
||||
|
||||
Mapping of value to step via object index of step group
|
||||
|
||||
@@ -0,0 +1,417 @@
|
||||
<html><head><title>H5Part Tools How-to</title>
|
||||
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=euc-kr"></head>
|
||||
<body bgcolor="#ffffff" text="#000000">
|
||||
|
||||
<table border="0" cellpadding="0" cellspacing="0" width="987">
|
||||
<tbody><tr>
|
||||
<td height="6050" width="27"></td>
|
||||
<td colspan="3" valign="top">
|
||||
<div id="body">
|
||||
<div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a>
|
||||
</font></div>
|
||||
<div id="maincenter"> <font face="arial,helvetica">
|
||||
<h1 align="center"><font face="Arial, Helvetica, sans-serif"><b><font color="#666699">H5Part
|
||||
Tools How-to</font></b></font></h1>
|
||||
</font><font color="#555588" face="arial,helvetica">
|
||||
<h2><font color="#666699" face="Arial, Helvetica, sans-serif">Table
|
||||
of Contents</font></h2>
|
||||
</font>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b><a href="#Quick%20Guide">
|
||||
[1] Quick Guide</a></b> </font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
|
||||
For h5pAttrib</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
|
||||
<b><br>
|
||||
<a href="#timesteps">[2] To see number of timesteps in a h5part file</a><br>
|
||||
<br>
|
||||
<a href="#file%20attributes">[3] To see file attributes in a h5part
|
||||
file</a><br>
|
||||
<br>
|
||||
<a href="#step%20attributes"> [4] To see step attributes in a h5part
|
||||
file</a><br>
|
||||
<br>
|
||||
<a href="#dataset">[5] To see dataset in a h5part file</a><br>
|
||||
<br>
|
||||
<a href="#flags">[6] Providing more than one flag at once for h5pAttrib</a></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
|
||||
For h5pToGNUplot</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
|
||||
<br>
|
||||
<b><a href="#parameters">[7] What parameters to provide</a><br>
|
||||
<br>
|
||||
<a href="#input%20file">[8] How to create an input file to GNUplot</a></b></font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<p> </p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="Quick Guide">[1]
|
||||
Quick Guide</a></font></h2>
|
||||
<p><font face="Arial, Helvetica, sans-serif">Executing the program with
|
||||
-h option will display a concise help page.</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$></font></b><font face="Courier New, Courier, mono">./h5pAttrib
|
||||
-h</font></font></p>
|
||||
<p><font face="Courier New, Courier, mono">usage: h5pAttrib [OPTIONS]
|
||||
file</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> OPTIONS<br>
|
||||
-h, --help Print help page<br>
|
||||
-n, --nstep Print number of steps<br>
|
||||
-A, --fileA Print file attributes<br>
|
||||
-a n, --stepA n Print step attributes & values for time step n<br>
|
||||
-d n, --dataset n Print data sets names & values for time step
|
||||
n<br>
|
||||
-H, --header Print shorter version without the values</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> Examples:</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> 1) Show file attribute names
|
||||
& values of sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> h5pAttrib -A sample.h5part<br>
|
||||
OR<br>
|
||||
h5pAttrib --fileA sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> 2) Show step attribute names
|
||||
for time step 5 of sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> h5pAttrib -a 5 -H sample.h5part<br>
|
||||
OR<br>
|
||||
h5pAttrib --stepA 5 -H sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono"><br>
|
||||
<b><font size="+1">$></font></b> ./h5pToGNUplot -h</font></p>
|
||||
<p><font face="Courier New, Courier, mono">usage: h5pToGNUplot -t TIMESTEP
|
||||
-1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> FLAGS<br>
|
||||
-h, --help Print help page</font><br>
|
||||
<font face="Courier New, Courier, mono">-1 par, --1var par (REQUIRED)
|
||||
Takes first variable parameter to "par"<br>
|
||||
-2 par, --2var par (REQUIRED) Takes second variable parameter to "par"<br>
|
||||
-i file, --input file (REQUIRED) Takes input file name to "file"<br>
|
||||
</font><font face="Courier New, Courier, mono">-t step, --timestep
|
||||
step (REQUIRED) Sets the timestep to "step" (Value -1 will
|
||||
result in dumping values of all timesteps.)<br>
|
||||
-o file, --output file (OPTIONAL) Takes output file name to "file"
|
||||
(without this flag, the program will print to stdout)<br>
|
||||
-n num, --number num (OPTIONAL) Sets number of output points to "num"<br>
|
||||
-s idx, --start idx (OPTIONAL) Sets the starting particle index to
|
||||
"idx"</font></p>
|
||||
<p><font face="Courier New, Courier, mono"><br>
|
||||
Examples:</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> 1) Create GNU plot file
|
||||
output.txt from sample.h5part by ploting x vs px for timestep 54</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
|
||||
-2 px -i sample.h5part -o output.txt</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> 2) Create GNU plot file
|
||||
output.txt from sample.h5part by ploting x vs px for timestep 54<br>
|
||||
using 1200 points from particle index 76</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
|
||||
-2 px -i sample.h5part -o output.txt -s 76 -n 1200</font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<p> </p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
|
||||
For h5pAttrib</font></b></font></p>
|
||||
<p> </p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="timesteps">[2]
|
||||
To see number of timesteps in a h5part file</a></font></h2>
|
||||
<p>Executing the program h5pAttrib with -n flag will display the number
|
||||
of timesteps in the file.</p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$></font></b></font><font face="Courier New, Courier, mono">
|
||||
./h5pAttrib -n sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing number of timesteps
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">There are total 252 number
|
||||
of timesteps.<br>
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">done</font><font face="Arial, Helvetica, sans-serif"><br>
|
||||
</font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<h2><font color="#666699" face="Arial, Helvetica, sans-serif"><br>
|
||||
<font color="#555588"><a name="file attributes">[3] To see file attributes
|
||||
in a h5part file</a></font></font></h2>
|
||||
<p>File attribute contains information about the file. (file description
|
||||
etc...) Executing the program h5pAttrib with -A flag will display
|
||||
the file attributes in the file.</p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$></font></b></font><font face="Courier New, Courier, mono">
|
||||
./h5pAttrib -A sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing file attributes
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">The number of file attributes
|
||||
for file sample.h5part is 0 ...<br>
|
||||
There are no file attributes.<br>
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">done</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><br>
|
||||
<i>NOTE: -H option will omit the list of values of file attributes.</i></font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<p align="center"> </p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="step attributes">[4]
|
||||
To see step attributes in a h5part file</a></font></h2>
|
||||
<p>Step attribute contains information that belongs to a specific step.
|
||||
(step name, timestep number, etc...) Executing the program h5pAttrib
|
||||
with -a flag will display the step attributes in the file.<br>
|
||||
Note that the timestep index should follow -a flag.</p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$></font></b><font face="Courier New, Courier, mono">
|
||||
./h5pAttrib -a 2 sample.h5part</font></font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing step attributes
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">The number of step attributes
|
||||
for timestep #2 is 10 ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
|
||||
There are 1 elements in the attribute<br>
|
||||
Attribute Type is H5T_NATIVE_INT64<br>
|
||||
Printing 1 element value(s):<br>
|
||||
COUNT[0]: 2</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Attribute #1 = Spos<br>
|
||||
There are 1 elements in the attribute<br>
|
||||
Attribute Type is H5T_NATIVE_DOUBLE<br>
|
||||
Printing 1 element value(s):<br>
|
||||
COUNT[0]: 0.143580</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Attribute #2 = structLen<br>
|
||||
There are 1 elements in the attribute<br>
|
||||
Attribute Type is H5T_NATIVE_DOUBLE<br>
|
||||
Printing 1 element value(s):<br>
|
||||
COUNT[0]: 2.393000</font></p>
|
||||
<p><font face="Courier New, Courier, mono">.<br>
|
||||
.<br>
|
||||
.</font></p>
|
||||
<p><font face="Courier New, Courier, mono"><br>
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">done</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><br>
|
||||
<i>NOTE: -H option will omit the list of values of step attributes.</i></font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
|
||||
<a name="dataset">[5] To see dataset in a h5part file</a></font></h2>
|
||||
<p>Executing the program h5pAttrib with -d flag will display the datasets
|
||||
information in the file. (dataset name, type, number of elements,
|
||||
etc...) Executing the program h5pAttrib with -d flag will display
|
||||
the datasets information in the file.<br>
|
||||
Note that the timestep index should follow -d flag.</p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$></font></b></font><font face="Courier New, Courier, mono">
|
||||
./h5pAttrib -d 2 -H sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing names of datasets
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">The number of datasets for
|
||||
timestep #2 is 7 ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
|
||||
Dataset Type is H5T_NATIVE_INT64<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 67587</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">done</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><br>
|
||||
<i>NOTE: -H option will omit the list of values of datasets.</i></font></p>
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<p> </p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="flags">[6]
|
||||
Providing more than one flag at once</a></font></h2>
|
||||
<p><font face="Arial, Helvetica, sans-serif">When more than one flags
|
||||
are provided, one result after another will be displayed.</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$></font></b></font><font face="Courier New, Courier, mono">
|
||||
./h5pAttrib -H -a 1 -d 1 sample.h5part</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing step attributes
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">The number of step attributes
|
||||
for timestep #1 is 10 ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
|
||||
Attribute #1 = Spos<br>
|
||||
Attribute #2 = structLen<br>
|
||||
Attribute #3 = org<br>
|
||||
Attribute #4 = maxX<br>
|
||||
Attribute #5 = minX<br>
|
||||
Attribute #6 = maxP<br>
|
||||
Attribute #7 = minP<br>
|
||||
Attribute #8 = centroid<br>
|
||||
Attribute #9 = nloc<br>
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono"><br>
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Printing names of datasets
|
||||
for: sample.h5part ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">The number of datasets for
|
||||
timestep #1 is 7 ...</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
|
||||
Dataset Type is H5T_NATIVE_INT64<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
|
||||
Dataset Type is H5T_NATIVE_DOUBLE<br>
|
||||
Number of elements: 60214</font></p>
|
||||
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
|
||||
<p><font face="Courier New, Courier, mono">done</font></p>
|
||||
<p> </p>
|
||||
<div align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></div>
|
||||
</div>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td height="80"></td>
|
||||
<td colspan="3" valign="top">
|
||||
<h2><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
|
||||
For h5pToGNUplot</font></b></font></h2>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="parameters">[7]
|
||||
What parameters to provide</a></font></h2>
|
||||
<p><font face="Arial, Helvetica, sans-serif">When you execute the program
|
||||
with -h option, it displays what flags are necessary and what flags are
|
||||
optional.</font></p>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td height="200"></td>
|
||||
<td valign="top" width="137">
|
||||
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Short Version</font></b></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif">-h<br>
|
||||
-1<br>
|
||||
-2<br>
|
||||
-i<br>
|
||||
-t<br>
|
||||
-o<br>
|
||||
-n<br>
|
||||
-s </font></p>
|
||||
</td>
|
||||
<td valign="top" width="144">
|
||||
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Long Version</font></b></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif">--help<br>
|
||||
--1var<br>
|
||||
--2var<br>
|
||||
--input<br>
|
||||
--timestep<br>
|
||||
--output<br>
|
||||
--number<br>
|
||||
--start </font></p>
|
||||
</td>
|
||||
<td valign="top" width="679">
|
||||
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Meanings</font></b></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif">Print help page<br>
|
||||
(REQUIRED) Takes first variable parameter<br>
|
||||
(REQUIRED) Takes second variable parameter<br>
|
||||
(REQUIRED) Takes input file name<br>
|
||||
(REQUIRED) Sets the timestep (Value -1 will result in dumping values of
|
||||
all timesteps.)<br>
|
||||
(OPTIONAL) Takes output file name (without this flag, the program will
|
||||
print to stdout)<br>
|
||||
(OPTIONAL) Sets number of output points<br>
|
||||
(OPTIONAL) Sets the starting particle index</font> </p>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td height="1786"></td>
|
||||
<td colspan="3" valign="top">
|
||||
<p> </p>
|
||||
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP"><back
|
||||
to top></a></font></p>
|
||||
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
|
||||
<a name="input file">[8] How to create an input file to GNUplot</a></font></h2>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE>></b><br>
|
||||
<i>Create input file to GNUplot that plots x vs. y.</i></font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$></font></b><font face="Courier New, Courier, mono">
|
||||
./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt<br>
|
||||
<b><font size="+1">$></font></b> cat output.txt<br>
|
||||
-0.390779 -0.254793<br>
|
||||
-0.396527 -0.252781<br>
|
||||
-0.375362 -0.285137<br>
|
||||
-0.396527 -0.252781<br>
|
||||
-0.379917 -0.283147<br>
|
||||
-0.390779 -0.254793<br>
|
||||
-0.387536 -0.287346<br>
|
||||
-0.371787 -0.319797<br>
|
||||
-0.379917 -0.283147<br>
|
||||
-0.378967 -0.326058<br>
|
||||
-0.378976 -0.326078<br>
|
||||
-0.387536 -0.287346<br>
|
||||
-0.378957 -0.326069<br>
|
||||
-0.379917 -0.283147<br>
|
||||
-0.388762 -0.265390<br>
|
||||
-0.371787 -0.319797<br>
|
||||
-0.390779 -0.254793<br>
|
||||
-0.376825 -0.266804<br>
|
||||
-0.379917 -0.283147<br>
|
||||
-0.375362 -0.285137<br>
|
||||
...</font></font></p>
|
||||
<p><font face="Courier New, Courier, mono"><i>Then run GNUplot...</i></font></p>
|
||||
<p><font face="Courier New, Courier, mono"><b><font size="+1">$></font></b>
|
||||
gnuplot</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> G N U P L O T<br>
|
||||
Version 4.0 patchlevel 0<br>
|
||||
last modified Thu Apr 15 14:44:22 CEST 2004<br>
|
||||
System: Linux 2.6.11.4-21.11-smp</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> Copyright (C) 1986 - 1993, 1998,
|
||||
2004<br>
|
||||
Thomas Williams, Colin Kelley and many others</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> This is gnuplot version 4.0.
|
||||
Please refer to the documentation<br>
|
||||
for command syntax changes. The old syntax will be accepted<br>
|
||||
throughout the 4.0 series, but all save files use the new syntax.</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> Type `help` to access the on-line
|
||||
reference manual.<br>
|
||||
The gnuplot FAQ is available from<br>
|
||||
http://www.gnuplot.info/faq/</font></p>
|
||||
<p><font face="Courier New, Courier, mono"> Send comments and requests for
|
||||
help to<br>
|
||||
<gnuplot-info@lists.sourceforge.net><br>
|
||||
Send bugs, suggestions and mods to<br>
|
||||
<gnuplot-bugs@lists.sourceforge.net></font></p>
|
||||
<p><font face="Courier New, Courier, mono"><br>
|
||||
Terminal type set to 'x11'<br>
|
||||
<font size="+1"><b>gnuplot></b></font> plot "output.txt"</font></p>
|
||||
<p><font face="Arial, Helvetica, sans-serif"><i>This will open a GNUplot
|
||||
window that plots output.txt.</i></font></p>
|
||||
<p align="center"><img src="H5tools_files/snapshot1.jpg" height="541" width="672"><br>
|
||||
<font face="Arial, Helvetica, sans-serif"><Sample screen shot of GNUplot
|
||||
with input datafile generated by h5pToGNUplot></font></p>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td height="44"></td>
|
||||
<td></td>
|
||||
<td></td>
|
||||
<td></td>
|
||||
</tr>
|
||||
</tbody></table>
|
||||
</body></html>
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 239 KiB |
Executable
+345
@@ -0,0 +1,345 @@
|
||||
\documentclass[acus]{JAC2003}
|
||||
|
||||
%%
|
||||
%% Use \documentclass[boxit]{JAC2003}
|
||||
%% to draw a frame with the correct margins on the output.
|
||||
%%
|
||||
%% Use \documentclass[acus]{JAC2003}
|
||||
%% for US letter paper layout
|
||||
%%
|
||||
|
||||
\usepackage{graphicx}
|
||||
|
||||
%%
|
||||
%% VARIABLE HEIGHT FOR THE TITLE BOX (default 35mm)
|
||||
%%
|
||||
|
||||
\setlength{\titleblockheight}{40mm}
|
||||
|
||||
\begin{document}
|
||||
\title{H5Pie: A Portable High Performance Parallel Data Interface for Electromagnetics Simulations Including Particles\thanks{
|
||||
This work (LBNL-57607) was supported by the Director, Office of Science, Office of Advanced Scientific Computing Research, of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098 and the DOE SciDAC project on ``Advanced Computing for 21st Century Accelerator Science and Technology.''.
|
||||
}}
|
||||
|
||||
\author{A. Adelmann, A. Gsell, B. Oswald, PSI, Villigen, Switzerland \\
|
||||
R.D. Ryne, LBNL/AFR, Berkeley, California, USA\\
|
||||
W. Bethel, J.M. Shalf, C. Siegerist, LBNL/NERSC, Berkeley, California, USA}
|
||||
|
||||
\maketitle
|
||||
\begin{abstract}
|
||||
The very largest parallel particle simulations, for problems
|
||||
involving six dimensional phase space,
|
||||
generate vast quantities of data. It is desirable to
|
||||
store such enormous datasets efficiently and also to share data
|
||||
effortlessly between data analysis tools
|
||||
such as VisIt or ParaView
|
||||
among other groups who are working on particle-based accelerator
|
||||
simulations. We define a very simple file schema built on top of HDF5~\cite{hdf5hp}
|
||||
(Hierarchical Data Format version 5) as well as an API that simplifies
|
||||
the reading/writing of the data to the HDF5 file format. HDF5 offers a
|
||||
self-describing machine-independent binary file format that supports
|
||||
scalable parallel I/O performance for MPI codes on computer systems
|
||||
ranging from laptops to supercomputers.
|
||||
|
||||
H5Pie is actually a composition of three parts. On a very abstract view we have,
|
||||
H5Part which handles the macro particles of a simulation. H5Mesh defines the (spatial) geometry of the
|
||||
computational domain and H5Fields represents scalar and vector filds. (H5Pie = H5{\bf P} art + H5F{\bf i}eld+ H5M{\bf e}sh)
|
||||
|
||||
|
||||
The sample H5Pie
|
||||
API will be available for C, C++, and Fortran codes.
|
||||
The common file format will enable groups that
|
||||
use completely different simulation implementations to transparently share
|
||||
datasets.
|
||||
\end{abstract}
|
||||
|
||||
\section{Motivation}
|
||||
The motivation for this undertaking is to create a file format that is
|
||||
suitable for large-scale parallel simulation codes.
|
||||
A suitable data format must have the following properties:
|
||||
it must be a machine-independent binary representation that is
|
||||
self-describing, easily extensible, language independent, efficient
|
||||
(both for serial and parallel), and produces files that are seamlessly sharable
|
||||
between different programs. In the following sections we describe
|
||||
the motivation for these features and how they can be accomplished
|
||||
using the proposed implementation.
|
||||
|
||||
\subsection{Machine Independence}
|
||||
Processor architectures use different binary representations
|
||||
for data. While the IEEE 754 standard has decreased the number of
|
||||
differing floating point number represenations, byte-order still remains
|
||||
a source of incompatibility. While it is trivial to byte-swap a file from
|
||||
a programming standpoint, it creates a number of long-term file management
|
||||
difficulties for groups that are sharing or maintaining a repository of simulation
|
||||
data. Given files that store data structures with differently sized elements,
|
||||
one must know the storage format precisely in order to apply byte-swapping
|
||||
properly.
|
||||
HDF5 does not suffer from these problems because the file format is completely
|
||||
self-describing and the internal binary structures are all machine independent.
|
||||
The HDF5 library is able to convert data that is stored in any native machine
|
||||
represenation in the data file into a native binary representation in memory
|
||||
as part of the reading process with little performance penalty.
|
||||
|
||||
\subsection{Language Independence}
|
||||
The three most common languages used for implementing applications
|
||||
in the arena of computational sciences are
|
||||
Fortran, C and C++. The file format and associated API must hide
|
||||
differences in the binary file-storage conventions of these languages
|
||||
as well as offering native API bindings for each of these
|
||||
programming languages.
|
||||
|
||||
For instance, Fortran unformatted binary files contain integer fields
|
||||
at the beginning and the end of each record that describe the length
|
||||
of the record. The size of these integer tags is usually 32-bits, but some
|
||||
fortran compiler implementations will use larger tags in order to represent
|
||||
larger record sizes. C and C++ binary files have no such convention for
|
||||
record-oriented storage. The language-dependent differences in
|
||||
binary storage layout conventions
|
||||
can cause difficulties for scientists who wish to share data files between
|
||||
Fortran and C/C++ implementations of a code, or with visualization tools
|
||||
that are primarily written in C/C++. The API bindings and underlying file format
|
||||
provided by the H5Part API and the underlying HDF5 file format are able to
|
||||
hide these differences in order to provide symmetric access via all languages.
|
||||
|
||||
\subsection{Self-Describing}
|
||||
The data is accessed by names, for example, one might ask for `the
|
||||
column of data called $p_x$' -- affording a layer of file-layout independence.
|
||||
In other words, self-describing data is
|
||||
not accessed by a position in a file but by name of the datasets. Various attributes
|
||||
of the data that may be necessary to using it are available. For
|
||||
example, one can ask ``what are the units of column $p_x$?'.
|
||||
|
||||
There are a number of examples of self-describing file formats. Examples include HDF earlier HDF implementations leading up to HDF version 5 and the Unidata NetCDF format. Another
|
||||
very popular approach is the Self Describing Data Sets (SDDS) \cite{SDDS} although it
|
||||
is only serial in nature. HDF5 is a complete rewrite of the HDF file format that supports
|
||||
parallel I/O and offers a much leaner, more flexible interface.
|
||||
Because it is self-describing, the entire contents of an HDF5 file can be
|
||||
browsed and even converted to ASCII text, including XML syntax text files,
|
||||
using the built-in 'h5ls' and 'h5dump'
|
||||
tools without specific knowledge of the internal file format.
|
||||
|
||||
\begin{figure}[htb]
|
||||
\begin{minipage}[b]{0.5\textwidth}
|
||||
%\includegraphics[scale=0.095]{./partview1.eps}
|
||||
%\includegraphics[scale=0.097]{./density70.eps}
|
||||
\end{minipage}
|
||||
\caption{color: A common self-describing file format allows different codes to share a common set of visualization and data analysis tools. PartView and AVS/Express, pictured above, are able to read and display contents of an H5Part/HDF5 file written on any machine in any language, regardless of how many processors are used.}
|
||||
\label{fig:vis}
|
||||
\end{figure}
|
||||
|
||||
The primary advantage of accessing data and its attributes is that one
|
||||
can then construct more flexible data manipulation tools that are capable
|
||||
of surviving the natural evolution of file formats. Data formats can be extended
|
||||
to include additional information without breaking older file readers.
|
||||
Self-describing data contains all the information
|
||||
that analysis tools need to manipulate various types of data
|
||||
correctly. Two examples of such tools using the proposed file format
|
||||
are shown in Figure ~\ref{fig:vis} As a result, data exchange between different simulations tools is
|
||||
much simpler, robust and better defined by using self-describing data sets.
|
||||
|
||||
\subsection{High Performance}
|
||||
The HDF5 file format allows data elements to be written to disk in the
|
||||
native binary representation. The file format stores a description of
|
||||
the native data representation of the machine that wrote the data so
|
||||
that it can be automatically translated to the native binary
|
||||
representation of the machine that reading the data (eg. if the byte
|
||||
order differs). In contrast to XDR, where the data always gets
|
||||
translated to/from an intermediate machine-neutral format, the HDF5
|
||||
data conversion only occurs if the stored data represenation is
|
||||
different from the native binary representation of the machine that is
|
||||
reading the file, so there is no performance penalty if the machines
|
||||
have the compatible binary data formats. [ada: need work] In general, HDF5 offers
|
||||
performance that is very close to what can be achieved by writing an
|
||||
ad-hoc machine-dependent binary for F77 unformatted data file.
|
||||
|
||||
\subsection{Parallel I/O}
|
||||
HDF5 also supports parallel I/O capabilities for MPI programs.
|
||||
The naive approach to writing data from a parallel program is to
|
||||
write one file per processor. While this is simple to implement and
|
||||
very efficient on most cluster filesystems, it leads to file management
|
||||
headaches when it comes the time to analyze the data. One must either
|
||||
recombine these separate files into a single file or create ponderous
|
||||
user-interfaces that allow a data analysis application to read from a
|
||||
directory full of files instead of just one file.
|
||||
|
||||
Parallel I/O methods, allow you to write data into a single file from all
|
||||
of the tasks of a parallel program. The performance is typically lower
|
||||
than that of writing one-file-per-processor, but it makes data management
|
||||
much simpler after the program has finished. No additional recombining
|
||||
steps are required to make the file accessible by vis-tools or for
|
||||
restarting a simulation using a different number of processors.
|
||||
|
||||
Parallel HDF5 uses MPI-I/O for its low-level implementation. The
|
||||
mechanics of using MPI-I/O are all hidden from the user by our
|
||||
H5Part file API (the code looks nearly identical to reading/writing the data
|
||||
from a serial program). While the performance is not as good as
|
||||
writing one-file-per-processor, we demonstrate that writing files
|
||||
with Parallel HDF5 is consistently faster than writing the data
|
||||
in raw/native binary using the MPI-I/O library. This efficiency is
|
||||
made possible through sophisticated HDF5 tuning directives that
|
||||
control data alignment and caching within the HDF5 layer.
|
||||
Therefore, we argue that it would be difficult to match
|
||||
HDF5 performance even using a home-grown binary file format.
|
||||
|
||||
\section{H5Mesh File Organization and API}
|
||||
|
||||
\section{H5Field File Organization and API}
|
||||
|
||||
\section{H5Part File Organization and API}
|
||||
The proposed file storage format uses HDF5 for the low-level file
|
||||
storage and a simple API to provide a high-level interface to that
|
||||
file format. A programmer can either use the H5Part API to access
|
||||
the data files or write directly to the file format using some simple
|
||||
conventions for organizing and naming the objects stored in the
|
||||
file.
|
||||
|
||||
The HDF5 format, its benefits, and its file organization is decribed
|
||||
at \cite{hdf5hp}. The file format was also adopted by the DOE
|
||||
ASCI-VIEWS effort, so the library has been tuned and adapted to read
|
||||
and write data efficiently on large-scale parallel computing
|
||||
systems. We adopted HDF5 for our file storage needs because it offers
|
||||
all that is needed as stipulated in the motivation section.
|
||||
|
||||
We describe now the H5Part conventions for storing
|
||||
objects in the HDF5 file as well as some examples of the API.
|
||||
\subsection{H5Part File Organization}
|
||||
In order to store Particle Data in the HDF5 file format, we have
|
||||
formalized the hierarchical arrangement of the datasets and naming
|
||||
conventions for the groups and associated datasets. The sample H5Part API formally
|
||||
encodes these conventions in order to provide a simple and uniform
|
||||
way to access these files from C, C++, and Fortran codes. The API makes
|
||||
it easier to write very portable data adaptors for visualization tools in order to
|
||||
expand the number of tools available to access the data. Even so,
|
||||
anyone can use the HDF5 $h5ls$ utility to examine the organization
|
||||
of the H5Part files and even write their own HDF5-based interface for reading and writing the
|
||||
file format. The standards offered by the sample API are completely independent of the
|
||||
standard for organizing data within the file.
|
||||
|
||||
The file format supports the storage of multiple timesteps of
|
||||
datasets that contain multiple fields. The fields correspond to different properties of
|
||||
the particles at that particular time step -- for instance,
|
||||
the 3-dimensional cartesian position of the particles
|
||||
$(X,Y,Z)$ as well as the 3-dimensional phase of each
|
||||
particle $(PX,PY,PZ)$. These two degrees of freedom
|
||||
are organized such that the timesteps are groups (time groups) that are added sequentially
|
||||
to the root group (``/''). The fields are datasets that are nested within the
|
||||
time groups. The convention for naming the time group is $Particles<integer>$ where $<integer>$ is a monotonically increasing counter for the number of timesteps stored in the file.
|
||||
|
||||
The fields contained within a given time group are simply named for the property of the particle they represent. For instance, the phase of the particle stored in a simulation variable called 'px' is simply named $``px''$. The field names are user-defined and
|
||||
can be understood automatically by the visualization
|
||||
tools that read the file. The only other convention is that each time group must contain the same set of fields -- the contents of the fields will change, but the set of names for these fields must remain the same for all timesteps.
|
||||
|
||||
The fields can be either integer or real data types. Initially, the file format supports double precision float and 64-bit integers in order to simplify the requirements for file readers, but HDF5 is capable of automatically down-converting to 32-bit data types upon request. The API will be extended accordingly to support these conversions.
|
||||
|
||||
Finally, the file, the individual timesteps, and the individual data arrays can contain {\em attributes} that provide additional information about the data. For instance, the datasets can be annotated with attributes containing {\em units} for a given data field, simulation parameters, or code revision information. The {\em attributes} are key-value pairs where the $key$ is a string that is associated with the file, group, or dataset, and the $value$ is either a string, a real value, or an integer associated with that key.
|
||||
|
||||
%Visualization and data analysis tools can take advantage of this additional information if they are programmed to recognize it, but less-sophisticated tools can safely ignore it without compromising their ability to read the file format.
|
||||
|
||||
% ada: to philosophic for a 3 page paper, although it is very important and of course right!
|
||||
%The ability to ignore such information is arguably one of the most powerful capabilities of the HDF5 file format. Whereas changes to headers or data layout in conventional, non-self-describing file formats can render an older reader interface useless, one can continuously add new descriptive information to the HDF5 file without having any detrimental effect on readers that were designed to work with older versions of the file format. This provides enormous benefits for the long term maintenance and evolution of the file format.
|
||||
|
||||
\section{GENERAL FORM IN PSEUDOCODE}
|
||||
In Figure \ref{fig:usage} we show the very simple API for writing
|
||||
data. The API for reading is almost symmetric. It is also worth to
|
||||
note that there are minimal differences whether one read/write serial
|
||||
or in parallel. The API consists of a small number of C, C++ and
|
||||
Fortran functions and will be described elsewhere.
|
||||
In the parallel case the original domain decomposition can be used or
|
||||
the data can be decomposed according to the new number of processor
|
||||
nodes available.
|
||||
The resulting HDF5 file will contains a simple directory structure that can be navigated using the generic 'h5ls' utility;
|
||||
\begin{figure}[h!] \label{fig:sbendVect}
|
||||
\newsavebox{\gogo}
|
||||
\setbox\gogo=\hbox{%
|
||||
\begin{minipage}{0.4\textwidth}
|
||||
\small
|
||||
\begin{tabbing}
|
||||
111111\=aaaa\=aaaa\=aaaa\=\kill
|
||||
\texttt{if(not parallel);}\\
|
||||
\quad\texttt{filehandle=OpenFile(filename,mode)} \\
|
||||
\texttt{else}\\
|
||||
\quad\texttt{filehandle=OpenFile(filename,mode,mpicomm)} \\
|
||||
\texttt{SetNumberOfParticles(filehandle);}\\
|
||||
\texttt{loop(step=1,NSteps);}\\
|
||||
\quad\texttt{SetStep(filehandle,step);}\\
|
||||
\quad\texttt{WriteData(filehandle,fieldname1,data1);}\\
|
||||
\centerline{\texttt{{\bf write more data}}}\\
|
||||
\quad\texttt{WriteData(filehandle,fieldname<n>,data<n>);}\\
|
||||
\texttt{CloseFile(filehandle);}
|
||||
\end{tabbing}
|
||||
\end{minipage}
|
||||
}
|
||||
\fbox{\usebox{\gogo}}
|
||||
\caption{Usage of H5Part in pseudo-code}
|
||||
\label{fig:usage}
|
||||
\end{figure}
|
||||
|
||||
% \begin{figure}[h!] \label{fig:sbendVect}
|
||||
% \newsavebox{\gugu}
|
||||
% \setbox\gugu=\hbox{%
|
||||
% \begin{minipage}{0.4\textwidth}
|
||||
% \small
|
||||
% \begin{tabbing}
|
||||
% 111111\=aaaa\=aaaa\=aaaa\=\kill
|
||||
%\texttt{/Particles1/fieldname1 } \\
|
||||
%\texttt{/Particles1/fieldname2} \\
|
||||
%\texttt{ . . . } \\
|
||||
%\texttt{/Particles1/fieldname<n> } \\
|
||||
%\texttt{/Particles2/fieldname1} \\
|
||||
%\texttt{ . . .}\\
|
||||
%\texttt{ /Particles<nsteps>/fieldname<n>}
|
||||
%\end{tabbing}
|
||||
%\end{minipage}
|
||||
%}
|
||||
%\fbox{\usebox{\gugu}}
|
||||
%\end{figure}
|
||||
\vspace{-5mm}
|
||||
\section{PERFORMANCE}
|
||||
% [ada] We also have data for 4 procs
|
||||
% [ada] name for one file per proc
|
||||
Preliminary performance estimations, looking at global (GD) and local data (LD)
|
||||
rates, suggests that our HDF5 writing has a very good performance even
|
||||
with respect to raw mpi, as shown in Table \ref{tab:perf}.
|
||||
\begin{table}[h!]
|
||||
\begin{flushleft} \footnotesize
|
||||
\begin{tabular}{|l|l|l|}
|
||||
\hline
|
||||
\bf Mode & \bf GD [MB/s] & \bf LD [MB/s]\\
|
||||
\hline
|
||||
mpi-io (one file) & 241 & 3.7 \\
|
||||
\hline
|
||||
one file per proc & 1288 & 20 \\
|
||||
\hline
|
||||
H5Part/pHDFf5 (one file) & 773 & 12 \\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\end{flushleft}
|
||||
\caption{\label{tab:perf}{64 IBM SP-3 nodes writing $51e6$ particles (6D). }}
|
||||
%, each having 6 double-precision floating point fields for 64 timesteps over 3 trials.}}
|
||||
\end{table}
|
||||
\vspace{-4mm}
|
||||
\section{Conclusions and Future Work}
|
||||
The file format will be extended in the near future to integrate fast bitmap indexing
|
||||
technology~\cite{DEX} in order to provide accelerated queries of data
|
||||
stored in the file. With fastbit technolgy, a user can efficiently extract subsets of data
|
||||
using compound query expressions such
|
||||
as {\it $(velocity > 1e6)$ AND $(0.4 < phase < 1.0)$}.
|
||||
%Such a query-driven approach offers advantages over scalable technologies aimed at visualizing ever-larger datasets.
|
||||
|
||||
We are also constantly tuning the performance of the parallel data
|
||||
file format implementation. We will also be porting the H5Part reader
|
||||
to a wider variety of visualization tools.
|
||||
%in order to expand the arena
|
||||
%of tools available for analyzing the stored particle data.
|
||||
\begin{thebibliography}{9} % Use for 1-9 references
|
||||
\bibitem{FPAT082}
|
||||
A. Adelmann, R.D Ryne, C. Siegerist, J. Shalf, "From Visualization to Data Mining With Large Datasets," PAC, 2005.
|
||||
\bibitem{hdf5hp}
|
||||
HDF5 Home Page, http://hdf.ncsa.uiuc.edu/HDF5.
|
||||
\bibitem{SDDS}
|
||||
Definitions and libraries for SDDS implementation may be found at the link http://www.aps.anl.gov/asd/oag/oagPackages.shtml.
|
||||
\bibitem{DEX}
|
||||
K. Stockinger, J. Shalf, W. Bethel, K. Wu. "DEX: Increasing the Capability of Scientific Data Analysis Pipelines by Using Efficient Bitmap Indices to Accelerate Scientific Visualization." Scientific and Statistical Database Management Conference (SDDBM), 2005.
|
||||
\end{thebibliography}
|
||||
|
||||
\end{document}
|
||||
@@ -0,0 +1,217 @@
|
||||
%%
|
||||
%% This file has been developed as a common template for papers
|
||||
%% destined for electronic production using Adobe Acrobat
|
||||
%% software for Accelerator Conferences
|
||||
%%
|
||||
%% See the JACo Website for more information
|
||||
%%
|
||||
%% http://www.cern.ch/accelconf/
|
||||
%%
|
||||
|
||||
% Special thanks to John Jowett and Michel Goossens from CERN and
|
||||
% Martin Comyn at TRIUMF for their significant contributions to
|
||||
% this class file over the period 1996 to 2000.
|
||||
% John Poole
|
||||
% March 2000
|
||||
|
||||
|
||||
% JAC2001.cls is a modified version of JAC2000.cls to produce indented
|
||||
% first paragraphs after section, subsection and subsubsection headings.
|
||||
%
|
||||
% Martin Comyn April 2001
|
||||
|
||||
\def\fileversion{1.2}
|
||||
\def\filedate{2003/03/10}
|
||||
\def\docdate {2003/03/10}
|
||||
|
||||
\newlength{\dsep}
|
||||
\newlength{\dwid}
|
||||
\newlength{\dht}
|
||||
\NeedsTeXFormat{LaTeX2e}
|
||||
\ProvidesClass{JAC2003}[\filedate\space Version \fileversion]
|
||||
\DeclareOption{acus}
|
||||
{\setlength{\dwid}{6mm}%
|
||||
\setlength{\dht}{-18mm}
|
||||
\setlength{\paperheight}{11in}
|
||||
\setlength{\paperwidth}{8.5in}
|
||||
\typeout{Setup for US LETTER PAPER}}
|
||||
\DeclareOption{aca4}
|
||||
{\setlength{\dwid}{0mm}%
|
||||
\setlength{\dht}{0mm}}
|
||||
\DeclareOption{boxit}
|
||||
%%
|
||||
%% This option draws a box on the output text with the correct margins
|
||||
%%
|
||||
{\special{!userdict begin /bop-hook{
|
||||
gsave
|
||||
newpath
|
||||
58 55 moveto
|
||||
58 737 lineto
|
||||
539 737 lineto
|
||||
539 55 lineto
|
||||
closepath
|
||||
stroke
|
||||
grestore
|
||||
}def end}}
|
||||
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
|
||||
|
||||
\ExecuteOptions{aca4}
|
||||
\ProcessOptions
|
||||
|
||||
\LoadClass[10pt]{article}
|
||||
%%
|
||||
%% Using Times fonts produces a Uniform, compact document
|
||||
%% suitable for the Acrobat Software and printable anywhere.
|
||||
%%
|
||||
%% In a 'modern' TeX installation
|
||||
%% e.g TeXLive Version 3 or later (more information on the JACo Website)
|
||||
%% one can use the following command
|
||||
%%
|
||||
|
||||
\renewcommand{\rmdefault}{ptm}
|
||||
|
||||
%%
|
||||
%% Older installations may require
|
||||
%% \RequirePackage{times}
|
||||
%%
|
||||
\typeout{------------------------------------------------------------------------}
|
||||
\typeout{LaTeX2e Class file for Accelerator Conference publication for LaTeX2e users}
|
||||
\typeout{ }
|
||||
\typeout{Use the boxit option to draw a box on page showing the correct margins}
|
||||
\typeout{ }
|
||||
\typeout{Itemize, Enumerate and Description environments are compact versions}
|
||||
\typeout{------------------------------------------------------------------------}
|
||||
\typeout{ }
|
||||
|
||||
%
|
||||
% DIMENSION OF TEXT:
|
||||
|
||||
\setlength{\textheight}{241mm}
|
||||
\setlength{\textwidth}{170mm}
|
||||
\setlength{\topmargin}{23mm}
|
||||
\addtolength{\topmargin}{\dht}
|
||||
\setlength{\oddsidemargin}{20mm}
|
||||
\setlength{\evensidemargin}{20mm}
|
||||
\setlength{\columnsep}{5mm}
|
||||
|
||||
|
||||
\hoffset -25.4mm
|
||||
\voffset -25.4mm
|
||||
|
||||
\columnseprule 0pt % Width of rule between columns.
|
||||
|
||||
% Use Michel Goossens' dense lists
|
||||
% Prevent infinite loops
|
||||
|
||||
\let\Otemize =\itemize
|
||||
\let\Onumerate =\enumerate
|
||||
\let\Oescription =\description
|
||||
% Zero the vertical spacing parameters
|
||||
\def\Nospacing{\itemsep=0pt\topsep=0pt\partopsep=0pt\parskip=0pt\parsep=0pt}
|
||||
% Redefine the environments in terms of the original values
|
||||
\newenvironment{Itemize}{\Otemize\Nospacing}{\endlist}
|
||||
\newenvironment{Enumerate}{\Onumerate\Nospacing}{\endlist}
|
||||
\newenvironment{Description}{\Oescription\Nospacing}{\endlist}
|
||||
|
||||
\renewcommand{\topfraction}{.95}
|
||||
\renewcommand{\bottomfraction}{.95}
|
||||
\renewcommand{\textfraction}{0.1}
|
||||
\renewcommand{\floatpagefraction}{0.8}
|
||||
|
||||
\def\@oddhead{}\def\@evenhead{}
|
||||
\def\@oddfoot{}
|
||||
\def\@evenfoot{\@oddfoot}
|
||||
|
||||
%-----------------------------------------------------------------------
|
||||
% We acknowledge the borrowing of the clever part of
|
||||
% Steven Gildea's definition of \section
|
||||
% from geophysi.sty.
|
||||
%
|
||||
% \section is tricky because we want to both support \section* and have
|
||||
% the section title uppercased.
|
||||
|
||||
\def\section{\secdef\@sectionb\@sections}
|
||||
\def\@sectionb[#1]#2{\@sections{#2}}
|
||||
\def\@sections#1{\@startsection {section}{1}{\z@}
|
||||
{2.8ex plus 0.8ex minus .1ex}{1.5ex plus .2ex}
|
||||
{\large\bf\boldmath\centering}{\uppercase{#1}}}
|
||||
% Should there be any problem with this, we can revert to the following
|
||||
% but then the onus is on the user to type the argument of \section in
|
||||
% uppercase in the input file.
|
||||
%
|
||||
%\def\section{\@startsection {section}{1}{\z@}{2.8ex plus 0.8ex minus.1ex}
|
||||
% {1.5ex plus .2ex}{\large\bf\boldmath\centering}}
|
||||
|
||||
\def\subsection{\@startsection{subsection}{2}{\z@}{2.6ex plus .8ex minus
|
||||
.17ex}{1.2ex plus .17ex}{\large\it}}
|
||||
\def\subsubsection{\@startsection{subsubsection}{3}{\parindent}
|
||||
{2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\bf}}
|
||||
\def\paragraph{\@startsection
|
||||
{paragraph}{4}{\z@}{2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\it}}
|
||||
\def\subparagraph{\@startsection
|
||||
{subparagraph}{4}{\parindent}{2.25ex plus .7ex minus
|
||||
.17ex}{-1em}{\normalsize\bf}}
|
||||
|
||||
\setcounter{secnumdepth}{0}
|
||||
|
||||
% This definition of \maketitle taken from article.sty, and has been
|
||||
% somewhat modified.
|
||||
|
||||
\def\maketitle{\par
|
||||
\begingroup
|
||||
\def\thefootnote{\fnsymbol{footnote}}
|
||||
\def\@makefnmark{\hbox
|
||||
to 5pt{$^{\@thefnmark}$\hss}}
|
||||
\twocolumn[\@maketitle]
|
||||
\@thanks
|
||||
\endgroup
|
||||
\setcounter{footnote}{0}
|
||||
\let\maketitle\relax
|
||||
\let\@maketitle\relax
|
||||
\gdef\@thanks{}\gdef\@author{}\gdef\@title{}\let\thanks\relax}
|
||||
|
||||
\newlength{\titleblockheight} % so user can change it if need be
|
||||
\setlength{\titleblockheight}{3.5cm}
|
||||
|
||||
|
||||
\def\@maketitle{\vbox to \titleblockheight {\hsize\textwidth
|
||||
\linewidth\hsize \vskip 3pt \centering
|
||||
{\Large\bf \@title \par}
|
||||
\vskip 2em % Vertical space after title.
|
||||
{\large\begin{tabular}[t]{@{}c@{}}\@author \end{tabular}\par}
|
||||
\vfil}}
|
||||
|
||||
|
||||
% The \copyrightspace command is used to produce a blank space in the first
|
||||
% column where a copyright notice may go. It works by producing a
|
||||
% blank footnote of the appropriate size. Note that it should appear
|
||||
% after any \footnote commands that produce footnotes for the first
|
||||
% column. Adjusted to leave just 1cm.
|
||||
|
||||
\def\copyrightspace{\footnotetext[0]{\mbox{}\vrule height 1cm width 0pt}}
|
||||
|
||||
\def\abstract{\subsection*{Abstract}}
|
||||
\def\endabstract{\par}
|
||||
|
||||
% Redefine to use smaller fonts
|
||||
\def\thebibliography#1{\setlength{\itemsep}{0pt}\setlength{\parsep}{0pt}
|
||||
\section*{REFERENCES\@mkboth
|
||||
{REFERENCES}{REFERENCES}}\small\list
|
||||
{[\arabic{enumi}]}{\settowidth\labelwidth{[#1]}\leftmargin\labelwidth
|
||||
\advance\leftmargin\labelsep
|
||||
\usecounter{enumi}}
|
||||
\def\newblock{\hskip .11em plus .33em minus .07em}
|
||||
\sloppy\clubpenalty4000\widowpenalty4000
|
||||
\sfcode`\.=1000\relax}
|
||||
|
||||
\let\endthebibliography=\endlist
|
||||
|
||||
\twocolumn
|
||||
\sloppy
|
||||
\parindent 1em
|
||||
\leftmargini 2em
|
||||
\leftmargin\leftmargini
|
||||
\leftmarginv .5em
|
||||
\leftmarginvi .5em
|
||||
\flushbottom
|
||||
%-----------------------------------------------------------------------
|
||||
Executable
+14
@@ -0,0 +1,14 @@
|
||||
#################################################
|
||||
##BEGIN OF makefile "makefile" - using the gnu-compiler g++
|
||||
##This file is used by the Make command.
|
||||
###################################################
|
||||
|
||||
FILE=H5xxx
|
||||
|
||||
all: $(FILE).tex
|
||||
latex $(FILE).tex
|
||||
#bibtex $(FILE)
|
||||
dvips -j0 $(FILE).dvi -o $(FILE).ps
|
||||
# dvips $(FILE).dvi -o $(FILE).ps -x 1200 -O 10mm,15mm
|
||||
clean:
|
||||
rm *~ *.bbl *.aux *.blg *.log *.dvi *.ps
|
||||
Executable
+54
@@ -0,0 +1,54 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html>
|
||||
<head>
|
||||
<title>H5Part, Logical Internal HDF5 File Layout</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
|
||||
<meta name="keywords" content="scientific visualization">
|
||||
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
|
||||
|
||||
|
||||
<div id="maincenter">
|
||||
<font face="arial,helvetica"><h1>H5Part: Logical Internal HDF5 File Layout</h1></font>
|
||||
<P>
|
||||
HDF5 is extremely flexible in the sense that it allows the user to define a higher level data model to describe domain-specific data relationships. This flexibility however makes it necessary to develop an agreement on the logical layout of the data. The H5Part data model consists of Particle groups corresponding to the simulation time steps, each with seven datasets corresponding to x, px, y, py, z, pz, id for each particle. Attributes can be added to the file and to the datasets.
|
||||
</P>
|
||||
<center><img src="layout.png"></center>
|
||||
<PRE>
|
||||
HDF5 "parttest.h5" {
|
||||
GROUP "/" {
|
||||
GROUP "Particles#0" {
|
||||
DATASET "id" {
|
||||
DATATYPE H5T_STD_I64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "px" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "py" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "pz" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "x" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "y" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
DATASET "z" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
|
||||
}
|
||||
}
|
||||
</PRE>
|
||||
<P>
|
||||
See <a href="http://www-vis.lbl.gov/Publications/2002/hdf5.pdf">hdf5.pdf</a> for an introduction on the use of HDF5.
|
||||
</P>
|
||||
</div>
|
||||
|
||||
@@ -1,14 +0,0 @@
|
||||
EXTRA_DIST = \
|
||||
Doxyfile \
|
||||
H5.dox
|
||||
|
||||
all:
|
||||
|
||||
doc:
|
||||
|
||||
doxydoc:
|
||||
doxygen
|
||||
|
||||
clean-local:
|
||||
$(RM) -r ReferencePages TWiki
|
||||
$(RM) *~
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,146 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
|
||||
<title>H5Part: H5Part.h Source File</title>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css">
|
||||
</head><body>
|
||||
<!-- Generated by Doxygen 1.4.4 -->
|
||||
<div class="qindex"><a class="qindex" href="index.html">Main Page</a> | <a class="qindex" href="annotated.html">Class List</a> | <a class="qindex" href="files.html">File List</a> | <a class="qindex" href="functions.html">Class Members</a> | <a class="qindex" href="globals.html">File Members</a></div>
|
||||
<h1>H5Part.h</h1><a href="H5Part_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef _H5Part_H_</span>
|
||||
<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define _H5Part_H_</span>
|
||||
<a name="l00003"></a>00003 <span class="preprocessor"></span>
|
||||
<a name="l00004"></a>00004 <span class="preprocessor">#include <hdf5.h></span>
|
||||
<a name="l00005"></a>00005 <span class="preprocessor">#ifdef PARALLEL_IO</span>
|
||||
<a name="l00006"></a>00006 <span class="preprocessor"></span><span class="preprocessor">#include <mpi.h></span>
|
||||
<a name="l00007"></a>00007 <span class="preprocessor">#endif</span>
|
||||
<a name="l00008"></a>00008 <span class="preprocessor"></span>
|
||||
<a name="l00016"></a><a class="code" href="structH5PartFile.html">00016</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structH5PartFile.html">H5PartFile</a> {
|
||||
<a name="l00017"></a><a class="code" href="structH5PartFile.html#o0">00017</a> hid_t <a class="code" href="structH5PartFile.html#o0">file</a>;
|
||||
<a name="l00018"></a><a class="code" href="structH5PartFile.html#o1">00018</a> <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o1">timestep</a>;
|
||||
<a name="l00019"></a>00019
|
||||
<a name="l00020"></a><a class="code" href="structH5PartFile.html#o2">00020</a> hid_t <a class="code" href="structH5PartFile.html#o2">timegroup</a>;
|
||||
<a name="l00021"></a><a class="code" href="structH5PartFile.html#o3">00021</a> hid_t <a class="code" href="structH5PartFile.html#o3">properties</a>;
|
||||
<a name="l00022"></a><a class="code" href="structH5PartFile.html#o4">00022</a> hsize_t <a class="code" href="structH5PartFile.html#o4">nparticles</a>;
|
||||
<a name="l00023"></a><a class="code" href="structH5PartFile.html#o5">00023</a> hid_t <a class="code" href="structH5PartFile.html#o5">shape</a>;
|
||||
<a name="l00024"></a><a class="code" href="structH5PartFile.html#o6">00024</a> <span class="keywordtype">unsigned</span> <a class="code" href="structH5PartFile.html#o6">mode</a>;
|
||||
<a name="l00025"></a><a class="code" href="structH5PartFile.html#o7">00025</a> <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o7">maxstep</a>;
|
||||
<a name="l00026"></a><a class="code" href="structH5PartFile.html#o8">00026</a> hid_t <a class="code" href="structH5PartFile.html#o8">xfer_prop</a>,<a class="code" href="structH5PartFile.html#o9">create_prop</a>,<a class="code" href="structH5PartFile.html#o10">access_prop</a>;
|
||||
<a name="l00027"></a><a class="code" href="structH5PartFile.html#o12">00027</a> hid_t <a class="code" href="structH5PartFile.html#o11">diskshape</a>,<a class="code" href="structH5PartFile.html#o12">memshape</a>; <span class="comment">/* for parallel I/O (this is on-disk) H5S_ALL </span>
|
||||
<a name="l00028"></a>00028 <span class="comment"> if serial I/O */</span>
|
||||
<a name="l00029"></a><a class="code" href="structH5PartFile.html#o13">00029</a> <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="structH5PartFile.html#o13">viewstart</a>,<a class="code" href="structH5PartFile.html#o14">viewend</a>; <span class="comment">/* -1 if no view is available: A "view" looks at a subset of the data. */</span>
|
||||
<a name="l00030"></a>00030
|
||||
<a name="l00031"></a>00031 <span class="preprocessor">#ifdef PARALLEL_IO</span>
|
||||
<a name="l00032"></a>00032 <span class="preprocessor"></span> <span class="keywordtype">long</span> <span class="keywordtype">long</span> *pnparticles; <span class="comment">/* the number of particles in each processor.</span>
|
||||
<a name="l00033"></a>00033 <span class="comment"> With respect to the "VIEW", these numbers</span>
|
||||
<a name="l00034"></a>00034 <span class="comment"> can be regarded as non-overlapping subsections</span>
|
||||
<a name="l00035"></a>00035 <span class="comment"> of the particle array stored in the file.</span>
|
||||
<a name="l00036"></a>00036 <span class="comment"> So they can be used to compute the offset of</span>
|
||||
<a name="l00037"></a>00037 <span class="comment"> the view for each processor */</span>
|
||||
<a name="l00038"></a>00038 MPI_Comm comm;
|
||||
<a name="l00039"></a>00039 <span class="keywordtype">int</span> nprocs,myproc;
|
||||
<a name="l00040"></a>00040 <span class="preprocessor">#endif</span>
|
||||
<a name="l00041"></a>00041 <span class="preprocessor"></span>}<a class="code" href="structH5PartFile.html">H5PartFile</a>;
|
||||
<a name="l00042"></a>00042
|
||||
<a name="l00043"></a><a class="code" href="H5Part_8h.html#a0">00043</a> <span class="preprocessor">#define H5PART_READ 0x01</span>
|
||||
<a name="l00044"></a><a class="code" href="H5Part_8h.html#a1">00044</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PART_WRITE 0x02</span>
|
||||
<a name="l00045"></a>00045 <span class="preprocessor"></span>
|
||||
<a name="l00046"></a>00046 <span class="comment">/*========== File Opening/Closing ===============*/</span>
|
||||
<a name="l00047"></a>00047 <span class="preprocessor">#ifdef PARALLEL_IO</span>
|
||||
<a name="l00048"></a>00048 <span class="preprocessor"></span><span class="preprocessor">#include <mpi.h></span>
|
||||
<a name="l00049"></a>00049 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a3">H5PartOpenFileParallel</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename,
|
||||
<a name="l00050"></a>00050 <span class="keywordtype">unsigned</span> flags,
|
||||
<a name="l00051"></a>00051 MPI_Comm communicator);
|
||||
<a name="l00052"></a>00052 <span class="preprocessor">#endif</span>
|
||||
<a name="l00053"></a><a class="code" href="H5Part_8h.html#a2">00053</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartOpenFileSerial(x,y) H5PartOpenFile(x,y)</span>
|
||||
<a name="l00054"></a>00054 <span class="preprocessor"></span>
|
||||
<a name="l00055"></a>00055 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a4">H5PartOpenFile</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename, <span class="comment">/* name of datafile */</span>
|
||||
<a name="l00056"></a>00056 <span class="keywordtype">unsigned</span> flags); <span class="comment">/* H5PART_READ | H5PART_WRITE */</span>
|
||||
<a name="l00057"></a>00057 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a5">H5PartFileIsValid</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00058"></a>00058 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a6">H5PartCloseFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00059"></a>00059
|
||||
<a name="l00060"></a>00060
|
||||
<a name="l00061"></a>00061 <span class="comment">/*============== File Writing Functions ==================== */</span>
|
||||
<a name="l00062"></a>00062 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a7">H5PartSetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> nparticles);
|
||||
<a name="l00063"></a>00063 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a8">H5PartWriteDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">double</span> *array);
|
||||
<a name="l00064"></a>00064 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a9">H5PartWriteDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *array);
|
||||
<a name="l00065"></a>00065
|
||||
<a name="l00066"></a>00066 <span class="comment">/*================== File Reading Routines =================*/</span>
|
||||
<a name="l00067"></a>00067 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a24">H5PartSetStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* file handle */</span>
|
||||
<a name="l00068"></a>00068 <span class="keywordtype">int</span> step); <span class="comment">/* current timestep to select (0 to n-1) */</span>
|
||||
<a name="l00069"></a>00069 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a27">H5PartGetNumSteps</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00070"></a>00070 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a28">H5PartGetNumDatasets</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00071"></a>00071 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a29">H5PartGetDatasetName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> index,<span class="keywordtype">char</span> *name,<span class="keywordtype">int</span> maxlen);
|
||||
<a name="l00072"></a>00072 <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="H5Part_8c.html#a33">H5PartGetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00073"></a>00073 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a34">H5PartSetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> end);
|
||||
<a name="l00074"></a><a class="code" href="H5Part_8h.html#a3">00074</a> <span class="preprocessor">#define H5PartResetView(f) H5PartSetView(f,-1,-1)</span>
|
||||
<a name="l00075"></a><a class="code" href="H5Part_8h.html#a4">00075</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartHasView(f) ((f->viewstart<0||f->viewend<0)?0:1)</span>
|
||||
<a name="l00076"></a>00076 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a35">H5PartGetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *end);
|
||||
<a name="l00077"></a>00077 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a36">H5PartSetCanonicalView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00078"></a>00078
|
||||
<a name="l00079"></a>00079 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a37">H5PartReadDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
|
||||
<a name="l00080"></a>00080 <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
|
||||
<a name="l00081"></a>00081 <span class="comment"> "x"=position in x direction (y,z)</span>
|
||||
<a name="l00082"></a>00082 <span class="comment"> "vx"=velocity in x directio (y,z)</span>
|
||||
<a name="l00083"></a>00083 <span class="comment"> "px"=position in x dir (y,z) */</span>
|
||||
<a name="l00084"></a>00084 <span class="keywordtype">double</span> *array); <span class="comment">/* array to read data into */</span>
|
||||
<a name="l00085"></a>00085 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a38">H5PartReadDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
|
||||
<a name="l00086"></a>00086 <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
|
||||
<a name="l00087"></a>00087 <span class="comment"> "x"=position in x direction (y,z)</span>
|
||||
<a name="l00088"></a>00088 <span class="comment"> "vx"=velocity in x directio (y,z)</span>
|
||||
<a name="l00089"></a>00089 <span class="comment"> "px"=position in x dir (y,z) */</span>
|
||||
<a name="l00090"></a>00090 <span class="keywordtype">long</span> <span class="keywordtype">long</span> *array); <span class="comment">/* array to read data into */</span>
|
||||
<a name="l00091"></a>00091
|
||||
<a name="l00092"></a>00092 <span class="comment">/* the following is a back-door for extensions to the data writing */</span>
|
||||
<a name="l00093"></a>00093 <span class="preprocessor">#if 0</span>
|
||||
<a name="l00094"></a>00094 <span class="preprocessor"></span><span class="keywordtype">int</span> H5PartReadData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
|
||||
<a name="l00095"></a>00095 <span class="keywordtype">int</span> H5PartWriteData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
|
||||
<a name="l00096"></a>00096 <span class="preprocessor">#endif</span>
|
||||
<a name="l00097"></a>00097 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a39">H5PartReadParticleStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* filehandle */</span>
|
||||
<a name="l00098"></a>00098 <span class="keywordtype">int</span> step, <span class="comment">/* selects timestep to read from*/</span>
|
||||
<a name="l00099"></a>00099 <span class="keywordtype">double</span> *x,<span class="keywordtype">double</span> *y,<span class="keywordtype">double</span> *z, <span class="comment">/* particle positions */</span>
|
||||
<a name="l00100"></a>00100 <span class="keywordtype">double</span> *px,<span class="keywordtype">double</span> *py,<span class="keywordtype">double</span> *pz, <span class="comment">/* particle momenta */</span>
|
||||
<a name="l00101"></a>00101 <span class="keywordtype">long</span> <span class="keywordtype">long</span> *<span class="keywordtype">id</span>); <span class="comment">/* and phase */</span>
|
||||
<a name="l00102"></a>00102 <span class="comment">/**********==============Attributes Interface============***************/</span>
|
||||
<a name="l00103"></a>00103 <span class="comment">/* currently there is file attributes: Attributes bound to the file</span>
|
||||
<a name="l00104"></a>00104 <span class="comment"> and step attributes which are bound to the current timestep. You </span>
|
||||
<a name="l00105"></a>00105 <span class="comment"> must set the timestep explicitly before writing the attributes (just</span>
|
||||
<a name="l00106"></a>00106 <span class="comment"> as you must do when you write a new dataset. Currently there are no</span>
|
||||
<a name="l00107"></a>00107 <span class="comment"> attributes that are bound to a particular data array, but this could</span>
|
||||
<a name="l00108"></a>00108 <span class="comment"> easily be done if required.</span>
|
||||
<a name="l00109"></a>00109 <span class="comment">*/</span>
|
||||
<a name="l00110"></a>00110 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a12">H5PartWriteStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
|
||||
<a name="l00111"></a>00111 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
|
||||
<a name="l00112"></a>00112 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a14">H5PartWriteFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
|
||||
<a name="l00113"></a>00113 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
|
||||
<a name="l00114"></a>00114 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a13">H5PartWriteAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
|
||||
<a name="l00115"></a>00115 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem); <span class="comment">/* this should be deprecated */</span>
|
||||
<a name="l00116"></a>00116
|
||||
<a name="l00117"></a>00117 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a10">H5PartWriteFileAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
|
||||
<a name="l00118"></a>00118 <span class="keywordtype">char</span> *attrib);
|
||||
<a name="l00119"></a>00119 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a11">H5PartWriteStepAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
|
||||
<a name="l00120"></a>00120 <span class="keywordtype">char</span> *attrib);
|
||||
<a name="l00121"></a>00121 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a16">H5PartGetNumStepAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f); <span class="comment">/* for current filestep */</span>
|
||||
<a name="l00122"></a>00122 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a17">H5PartGetNumFileAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00123"></a>00123 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a19">H5PartGetStepAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
|
||||
<a name="l00124"></a>00124 <span class="keywordtype">char</span> *name,size_t maxnamelen,
|
||||
<a name="l00125"></a>00125 hid_t *type,<span class="keywordtype">int</span> *nelem);
|
||||
<a name="l00126"></a>00126 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a20">H5PartGetFileAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
|
||||
<a name="l00127"></a>00127 <span class="keywordtype">char</span> *name,size_t maxnamelen,
|
||||
<a name="l00128"></a>00128 hid_t *type,<span class="keywordtype">int</span> *nelem);
|
||||
<a name="l00129"></a>00129 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a21">H5PartReadStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
|
||||
<a name="l00130"></a>00130 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a22">H5PartReadAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
|
||||
<a name="l00131"></a>00131 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a23">H5PartReadFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
|
||||
<a name="l00132"></a>00132
|
||||
<a name="l00133"></a>00133
|
||||
<a name="l00134"></a>00134 <span class="comment">/**************** File Stashing Interfaces *************************/</span>
|
||||
<a name="l00135"></a>00135 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a42">H5PartStashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *filename);
|
||||
<a name="l00136"></a>00136 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a43">H5PartUnstashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="keywordtype">char</span> *filename, <span class="keywordtype">char</span> *outputpath); <span class="comment">/* outputpath can be null for cwd */</span>
|
||||
<a name="l00137"></a>00137 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a44">H5PartGetNumStashFiles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
|
||||
<a name="l00138"></a>00138 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a45">H5PartFileGetStashFileName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> nameindex,<span class="keywordtype">char</span> *filename,<span class="keywordtype">int</span> maxnamelen);
|
||||
<a name="l00139"></a>00139
|
||||
<a name="l00140"></a>00140
|
||||
<a name="l00141"></a>00141 <span class="preprocessor">#endif</span>
|
||||
</pre></div><hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by
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<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
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|
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<h1>H5Part Class List</h1>Here are the classes, structs, unions and interfaces with brief descriptions:<table>
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