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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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/* |
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* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "io/DumpWriter.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_teebuf.hpp" |
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+ |
#include "io/gzstream.hpp" |
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+ |
#include "io/Globals.hpp" |
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+ |
|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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< |
DumpWriter::DumpWriter(SimInfo* info) |
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< |
: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
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> |
DumpWriter::DumpWriter(SimInfo* info) |
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> |
: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
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> |
|
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> |
Globals* simParams = info->getSimParams(); |
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> |
needCompression_ = simParams->getCompressDumpFile(); |
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> |
needForceVector_ = simParams->getOutputForceVector(); |
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> |
createDumpFile_ = true; |
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> |
#ifdef HAVE_LIBZ |
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> |
if (needCompression_) { |
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> |
filename_ += ".gz"; |
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> |
eorFilename_ += ".gz"; |
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> |
} |
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> |
#endif |
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> |
|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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+ |
|
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+ |
dumpFile_ = createOStream(filename_); |
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|
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< |
dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
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> |
if (!dumpFile_) { |
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> |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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> |
filename_.c_str()); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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|
| 61 |
– |
if (!dumpFile_) { |
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– |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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– |
filename_.c_str()); |
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– |
painCave.isFatal = 1; |
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– |
simError(); |
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– |
} |
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– |
|
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#ifdef IS_MPI |
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|
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} |
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|
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– |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
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– |
MPIcheckPoint(); |
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– |
|
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#endif // is_mpi |
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|
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< |
} |
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> |
} |
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|
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|
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< |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
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< |
: info_(info), filename_(filename){ |
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> |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
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> |
: info_(info), filename_(filename){ |
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> |
|
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> |
Globals* simParams = info->getSimParams(); |
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> |
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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> |
|
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> |
needCompression_ = simParams->getCompressDumpFile(); |
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> |
needForceVector_ = simParams->getOutputForceVector(); |
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> |
createDumpFile_ = true; |
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> |
#ifdef HAVE_LIBZ |
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> |
if (needCompression_) { |
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> |
filename_ += ".gz"; |
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> |
eorFilename_ += ".gz"; |
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> |
} |
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> |
#endif |
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> |
|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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< |
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
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> |
|
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> |
dumpFile_ = createOStream(filename_); |
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|
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< |
if (!dumpFile_) { |
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< |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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< |
filename_.c_str()); |
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< |
painCave.isFatal = 1; |
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simError(); |
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} |
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> |
if (!dumpFile_) { |
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> |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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> |
filename_.c_str()); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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< |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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> |
#endif // is_mpi |
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|
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+ |
} |
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|
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+ |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) |
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: info_(info), filename_(filename){ |
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|
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Globals* simParams = info->getSimParams(); |
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+ |
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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|
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+ |
needCompression_ = simParams->getCompressDumpFile(); |
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+ |
needForceVector_ = simParams->getOutputForceVector(); |
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+ |
|
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+ |
#ifdef HAVE_LIBZ |
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+ |
if (needCompression_) { |
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+ |
filename_ += ".gz"; |
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+ |
eorFilename_ += ".gz"; |
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+ |
} |
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+ |
#endif |
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|
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+ |
#ifdef IS_MPI |
| 148 |
+ |
|
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+ |
if (worldRank == 0) { |
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#endif // is_mpi |
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|
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createDumpFile_ = writeDumpFile; |
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if (createDumpFile_) { |
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dumpFile_ = createOStream(filename_); |
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+ |
|
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+ |
if (!dumpFile_) { |
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+ |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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+ |
filename_.c_str()); |
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+ |
painCave.isFatal = 1; |
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+ |
simError(); |
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+ |
} |
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+ |
} |
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+ |
#ifdef IS_MPI |
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|
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+ |
} |
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|
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< |
} |
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> |
|
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> |
#endif // is_mpi |
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> |
|
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> |
} |
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|
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< |
DumpWriter::~DumpWriter() { |
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> |
DumpWriter::~DumpWriter() { |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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< |
|
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< |
dumpFile_.close(); |
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< |
|
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> |
if (createDumpFile_){ |
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> |
writeClosing(*dumpFile_); |
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> |
delete dumpFile_; |
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> |
} |
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#ifdef IS_MPI |
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|
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} |
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|
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#endif // is_mpi |
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|
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< |
} |
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> |
} |
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|
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< |
void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
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> |
void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { |
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|
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< |
double currentTime; |
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> |
char buffer[1024]; |
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> |
|
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> |
os << " <FrameData>\n"; |
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> |
|
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> |
RealType currentTime = s->getTime(); |
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> |
sprintf(buffer, " Time: %.10g\n", currentTime); |
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> |
os << buffer; |
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> |
|
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|
Mat3x3d hmat; |
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– |
double chi; |
| 130 |
– |
double integralOfChiDt; |
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– |
Mat3x3d eta; |
| 132 |
– |
|
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– |
currentTime = s->getTime(); |
| 201 |
|
hmat = s->getHmat(); |
| 202 |
< |
chi = s->getChi(); |
| 203 |
< |
integralOfChiDt = s->getIntegralOfChiDt(); |
| 204 |
< |
eta = s->getEta(); |
| 205 |
< |
|
| 206 |
< |
os << currentTime << ";\t" |
| 140 |
< |
<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
| 141 |
< |
<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
| 142 |
< |
<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
| 202 |
> |
sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
| 203 |
> |
hmat(0, 0), hmat(1, 0), hmat(2, 0), |
| 204 |
> |
hmat(0, 1), hmat(1, 1), hmat(2, 1), |
| 205 |
> |
hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
| 206 |
> |
os << buffer; |
| 207 |
|
|
| 208 |
< |
//write out additional parameters, such as chi and eta |
| 208 |
> |
RealType chi = s->getChi(); |
| 209 |
> |
RealType integralOfChiDt = s->getIntegralOfChiDt(); |
| 210 |
> |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
| 211 |
> |
os << buffer; |
| 212 |
|
|
| 213 |
< |
os << chi << "\t" << integralOfChiDt << "\t;"; |
| 213 |
> |
Mat3x3d eta; |
| 214 |
> |
eta = s->getEta(); |
| 215 |
> |
sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
| 216 |
> |
eta(0, 0), eta(1, 0), eta(2, 0), |
| 217 |
> |
eta(0, 1), eta(1, 1), eta(2, 1), |
| 218 |
> |
eta(0, 2), eta(1, 2), eta(2, 2)); |
| 219 |
> |
os << buffer; |
| 220 |
|
|
| 221 |
< |
os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
| 222 |
< |
<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
| 150 |
< |
<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
| 151 |
< |
|
| 152 |
< |
os << "\n"; |
| 153 |
< |
} |
| 221 |
> |
os << " </FrameData>\n"; |
| 222 |
> |
} |
| 223 |
|
|
| 224 |
< |
void DumpWriter::writeFrame(std::ostream& os) { |
| 156 |
< |
const int BUFFERSIZE = 2000; |
| 157 |
< |
const int MINIBUFFERSIZE = 100; |
| 224 |
> |
void DumpWriter::writeFrame(std::ostream& os) { |
| 225 |
|
|
| 226 |
< |
char tempBuffer[BUFFERSIZE]; |
| 227 |
< |
char writeLine[BUFFERSIZE]; |
| 226 |
> |
#ifdef IS_MPI |
| 227 |
> |
MPI_Status istatus; |
| 228 |
> |
#endif |
| 229 |
|
|
| 162 |
– |
Quat4d q; |
| 163 |
– |
Vector3d ji; |
| 164 |
– |
Vector3d pos; |
| 165 |
– |
Vector3d vel; |
| 166 |
– |
|
| 230 |
|
Molecule* mol; |
| 231 |
|
StuntDouble* integrableObject; |
| 232 |
|
SimInfo::MoleculeIterator mi; |
| 233 |
|
Molecule::IntegrableObjectIterator ii; |
| 171 |
– |
|
| 172 |
– |
int nTotObjects; |
| 173 |
– |
nTotObjects = info_->getNGlobalIntegrableObjects(); |
| 234 |
|
|
| 235 |
|
#ifndef IS_MPI |
| 236 |
+ |
os << " <Snapshot>\n"; |
| 237 |
+ |
|
| 238 |
+ |
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 239 |
|
|
| 240 |
+ |
os << " <StuntDoubles>\n"; |
| 241 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 242 |
|
|
| 243 |
< |
os << nTotObjects << "\n"; |
| 244 |
< |
|
| 245 |
< |
writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 243 |
> |
|
| 244 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 245 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 246 |
> |
os << prepareDumpLine(integrableObject); |
| 247 |
> |
|
| 248 |
> |
} |
| 249 |
> |
} |
| 250 |
> |
os << " </StuntDoubles>\n"; |
| 251 |
> |
|
| 252 |
> |
os << " </Snapshot>\n"; |
| 253 |
|
|
| 254 |
+ |
os.flush(); |
| 255 |
+ |
#else |
| 256 |
+ |
//every node prepares the dump lines for integrable objects belong to itself |
| 257 |
+ |
std::string buffer; |
| 258 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 259 |
|
|
| 184 |
– |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 185 |
– |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 186 |
– |
|
| 260 |
|
|
| 261 |
< |
pos = integrableObject->getPos(); |
| 262 |
< |
vel = integrableObject->getVel(); |
| 261 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 262 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 263 |
> |
buffer += prepareDumpLine(integrableObject); |
| 264 |
> |
} |
| 265 |
> |
} |
| 266 |
> |
|
| 267 |
> |
const int masterNode = 0; |
| 268 |
|
|
| 269 |
< |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 270 |
< |
integrableObject->getType().c_str(), |
| 271 |
< |
pos[0], pos[1], pos[2], |
| 272 |
< |
vel[0], vel[1], vel[2]); |
| 269 |
> |
if (worldRank == masterNode) { |
| 270 |
> |
os << " <Snapshot>\n"; |
| 271 |
> |
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 272 |
> |
os << " <StuntDoubles>\n"; |
| 273 |
> |
|
| 274 |
> |
os << buffer; |
| 275 |
|
|
| 276 |
< |
strcpy(writeLine, tempBuffer); |
| 276 |
> |
int nProc; |
| 277 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 278 |
> |
for (int i = 1; i < nProc; ++i) { |
| 279 |
|
|
| 280 |
< |
if (integrableObject->isDirectional()) { |
| 281 |
< |
q = integrableObject->getQ(); |
| 200 |
< |
ji = integrableObject->getJ(); |
| 280 |
> |
// receive the length of the string buffer that was |
| 281 |
> |
// prepared by processor i |
| 282 |
|
|
| 283 |
< |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 284 |
< |
q[0], q[1], q[2], q[3], |
| 285 |
< |
ji[0], ji[1], ji[2]); |
| 286 |
< |
strcat(writeLine, tempBuffer); |
| 287 |
< |
} else { |
| 288 |
< |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 289 |
< |
} |
| 290 |
< |
|
| 210 |
< |
os << writeLine; |
| 211 |
< |
|
| 283 |
> |
int recvLength; |
| 284 |
> |
MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
| 285 |
> |
char* recvBuffer = new char[recvLength]; |
| 286 |
> |
if (recvBuffer == NULL) { |
| 287 |
> |
} else { |
| 288 |
> |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
| 289 |
> |
os << recvBuffer; |
| 290 |
> |
delete [] recvBuffer; |
| 291 |
|
} |
| 292 |
+ |
} |
| 293 |
+ |
os << " </StuntDoubles>\n"; |
| 294 |
+ |
|
| 295 |
+ |
os << " </Snapshot>\n"; |
| 296 |
+ |
os.flush(); |
| 297 |
+ |
} else { |
| 298 |
+ |
int sendBufferLength = buffer.size() + 1; |
| 299 |
+ |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 300 |
+ |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 301 |
|
} |
| 302 |
|
|
| 303 |
< |
os.flush(); |
| 216 |
< |
#else // is_mpi |
| 217 |
< |
/********************************************************************* |
| 218 |
< |
* Documentation? You want DOCUMENTATION? |
| 219 |
< |
* |
| 220 |
< |
* Why all the potatoes below? |
| 221 |
< |
* |
| 222 |
< |
* To make a long story short, the original version of DumpWriter |
| 223 |
< |
* worked in the most inefficient way possible. Node 0 would |
| 224 |
< |
* poke each of the node for an individual atom's formatted data |
| 225 |
< |
* as node 0 worked its way down the global index. This was particularly |
| 226 |
< |
* inefficient since the method blocked all processors at every atom |
| 227 |
< |
* (and did it twice!). |
| 228 |
< |
* |
| 229 |
< |
* An intermediate version of DumpWriter could be described from Node |
| 230 |
< |
* zero's perspective as follows: |
| 231 |
< |
* |
| 232 |
< |
* 1) Have 100 of your friends stand in a circle. |
| 233 |
< |
* 2) When you say go, have all of them start tossing potatoes at |
| 234 |
< |
* you (one at a time). |
| 235 |
< |
* 3) Catch the potatoes. |
| 236 |
< |
* |
| 237 |
< |
* It was an improvement, but MPI has buffers and caches that could |
| 238 |
< |
* best be described in this analogy as "potato nets", so there's no |
| 239 |
< |
* need to block the processors atom-by-atom. |
| 240 |
< |
* |
| 241 |
< |
* This new and improved DumpWriter works in an even more efficient |
| 242 |
< |
* way: |
| 243 |
< |
* |
| 244 |
< |
* 1) Have 100 of your friend stand in a circle. |
| 245 |
< |
* 2) When you say go, have them start tossing 5-pound bags of |
| 246 |
< |
* potatoes at you. |
| 247 |
< |
* 3) Once you've caught a friend's bag of potatoes, |
| 248 |
< |
* toss them a spud to let them know they can toss another bag. |
| 249 |
< |
* |
| 250 |
< |
* How's THAT for documentation? |
| 251 |
< |
* |
| 252 |
< |
*********************************************************************/ |
| 253 |
< |
const int masterNode = 0; |
| 303 |
> |
#endif // is_mpi |
| 304 |
|
|
| 305 |
< |
int * potatoes; |
| 256 |
< |
int myPotato; |
| 257 |
< |
int nProc; |
| 258 |
< |
int which_node; |
| 259 |
< |
double atomData[13]; |
| 260 |
< |
int isDirectional; |
| 261 |
< |
const char * atomTypeString; |
| 262 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 263 |
< |
int msgLen; // the length of message actually recieved at master nodes |
| 264 |
< |
int haveError; |
| 265 |
< |
MPI_Status istatus; |
| 266 |
< |
int nCurObj; |
| 267 |
< |
|
| 268 |
< |
// code to find maximum tag value |
| 269 |
< |
int * tagub; |
| 270 |
< |
int flag; |
| 271 |
< |
int MAXTAG; |
| 272 |
< |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 305 |
> |
} |
| 306 |
|
|
| 307 |
< |
if (flag) { |
| 308 |
< |
MAXTAG = *tagub; |
| 309 |
< |
} else { |
| 310 |
< |
MAXTAG = 32767; |
| 311 |
< |
} |
| 307 |
> |
std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
| 308 |
> |
|
| 309 |
> |
int index = integrableObject->getGlobalIntegrableObjectIndex(); |
| 310 |
> |
std::string type("pv"); |
| 311 |
> |
std::string line; |
| 312 |
> |
char tempBuffer[4096]; |
| 313 |
|
|
| 314 |
< |
if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
| 314 |
> |
Vector3d pos; |
| 315 |
> |
Vector3d vel; |
| 316 |
> |
pos = integrableObject->getPos(); |
| 317 |
> |
vel = integrableObject->getVel(); |
| 318 |
> |
sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
| 319 |
> |
pos[0], pos[1], pos[2], |
| 320 |
> |
vel[0], vel[1], vel[2]); |
| 321 |
> |
line += tempBuffer; |
| 322 |
|
|
| 323 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
| 323 |
> |
if (integrableObject->isDirectional()) { |
| 324 |
> |
type += "qj"; |
| 325 |
> |
Quat4d q; |
| 326 |
> |
Vector3d ji; |
| 327 |
> |
q = integrableObject->getQ(); |
| 328 |
> |
ji = integrableObject->getJ(); |
| 329 |
> |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
| 330 |
> |
q[0], q[1], q[2], q[3], |
| 331 |
> |
ji[0], ji[1], ji[2]); |
| 332 |
> |
line += tempBuffer; |
| 333 |
> |
} |
| 334 |
|
|
| 335 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 336 |
< |
potatoes = new int[nProc]; |
| 337 |
< |
|
| 338 |
< |
//write out the comment lines |
| 339 |
< |
for(int i = 0; i < nProc; i++) { |
| 340 |
< |
potatoes[i] = 0; |
| 341 |
< |
} |
| 342 |
< |
|
| 343 |
< |
|
| 344 |
< |
os << nTotObjects << "\n"; |
| 345 |
< |
writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 295 |
< |
|
| 296 |
< |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 297 |
< |
|
| 298 |
< |
// Get the Node number which has this atom; |
| 299 |
< |
|
| 300 |
< |
which_node = info_->getMolToProc(i); |
| 301 |
< |
|
| 302 |
< |
if (which_node != masterNode) { //current molecule is in slave node |
| 303 |
< |
if (potatoes[which_node] + 1 >= MAXTAG) { |
| 304 |
< |
// The potato was going to exceed the maximum value, |
| 305 |
< |
// so wrap this processor potato back to 0: |
| 306 |
< |
|
| 307 |
< |
potatoes[which_node] = 0; |
| 308 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
| 309 |
< |
MPI_COMM_WORLD); |
| 310 |
< |
} |
| 311 |
< |
|
| 312 |
< |
myPotato = potatoes[which_node]; |
| 313 |
< |
|
| 314 |
< |
//recieve the number of integrableObject in current molecule |
| 315 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
| 316 |
< |
MPI_COMM_WORLD, &istatus); |
| 317 |
< |
myPotato++; |
| 318 |
< |
|
| 319 |
< |
for(int l = 0; l < nCurObj; l++) { |
| 320 |
< |
if (potatoes[which_node] + 2 >= MAXTAG) { |
| 321 |
< |
// The potato was going to exceed the maximum value, |
| 322 |
< |
// so wrap this processor potato back to 0: |
| 323 |
< |
|
| 324 |
< |
potatoes[which_node] = 0; |
| 325 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
| 326 |
< |
0, MPI_COMM_WORLD); |
| 327 |
< |
} |
| 328 |
< |
|
| 329 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
| 330 |
< |
which_node, myPotato, MPI_COMM_WORLD, |
| 331 |
< |
&istatus); |
| 332 |
< |
|
| 333 |
< |
atomTypeString = MPIatomTypeString; |
| 334 |
< |
|
| 335 |
< |
myPotato++; |
| 336 |
< |
|
| 337 |
< |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
| 338 |
< |
MPI_COMM_WORLD, &istatus); |
| 339 |
< |
myPotato++; |
| 340 |
< |
|
| 341 |
< |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
| 342 |
< |
|
| 343 |
< |
if (msgLen == 13) |
| 344 |
< |
isDirectional = 1; |
| 345 |
< |
else |
| 346 |
< |
isDirectional = 0; |
| 347 |
< |
|
| 348 |
< |
// If we've survived to here, format the line: |
| 349 |
< |
|
| 350 |
< |
if (!isDirectional) { |
| 351 |
< |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 352 |
< |
atomTypeString, atomData[0], |
| 353 |
< |
atomData[1], atomData[2], |
| 354 |
< |
atomData[3], atomData[4], |
| 355 |
< |
atomData[5]); |
| 356 |
< |
|
| 357 |
< |
strcat(writeLine, |
| 358 |
< |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 359 |
< |
} else { |
| 360 |
< |
sprintf(writeLine, |
| 361 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 362 |
< |
atomTypeString, |
| 363 |
< |
atomData[0], |
| 364 |
< |
atomData[1], |
| 365 |
< |
atomData[2], |
| 366 |
< |
atomData[3], |
| 367 |
< |
atomData[4], |
| 368 |
< |
atomData[5], |
| 369 |
< |
atomData[6], |
| 370 |
< |
atomData[7], |
| 371 |
< |
atomData[8], |
| 372 |
< |
atomData[9], |
| 373 |
< |
atomData[10], |
| 374 |
< |
atomData[11], |
| 375 |
< |
atomData[12]); |
| 376 |
< |
} |
| 377 |
< |
|
| 378 |
< |
os << writeLine; |
| 379 |
< |
|
| 380 |
< |
} // end for(int l =0) |
| 381 |
< |
|
| 382 |
< |
potatoes[which_node] = myPotato; |
| 383 |
< |
} else { //master node has current molecule |
| 384 |
< |
|
| 385 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
| 386 |
< |
|
| 387 |
< |
if (mol == NULL) { |
| 388 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
| 389 |
< |
painCave.isFatal = 1; |
| 390 |
< |
simError(); |
| 391 |
< |
} |
| 392 |
< |
|
| 393 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 394 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 395 |
< |
|
| 396 |
< |
atomTypeString = integrableObject->getType().c_str(); |
| 397 |
< |
|
| 398 |
< |
pos = integrableObject->getPos(); |
| 399 |
< |
vel = integrableObject->getVel(); |
| 400 |
< |
|
| 401 |
< |
atomData[0] = pos[0]; |
| 402 |
< |
atomData[1] = pos[1]; |
| 403 |
< |
atomData[2] = pos[2]; |
| 404 |
< |
|
| 405 |
< |
atomData[3] = vel[0]; |
| 406 |
< |
atomData[4] = vel[1]; |
| 407 |
< |
atomData[5] = vel[2]; |
| 408 |
< |
|
| 409 |
< |
isDirectional = 0; |
| 410 |
< |
|
| 411 |
< |
if (integrableObject->isDirectional()) { |
| 412 |
< |
isDirectional = 1; |
| 413 |
< |
|
| 414 |
< |
q = integrableObject->getQ(); |
| 415 |
< |
ji = integrableObject->getJ(); |
| 416 |
< |
|
| 417 |
< |
for(int j = 0; j < 6; j++) { |
| 418 |
< |
atomData[j] = atomData[j]; |
| 419 |
< |
} |
| 420 |
< |
|
| 421 |
< |
atomData[6] = q[0]; |
| 422 |
< |
atomData[7] = q[1]; |
| 423 |
< |
atomData[8] = q[2]; |
| 424 |
< |
atomData[9] = q[3]; |
| 425 |
< |
|
| 426 |
< |
atomData[10] = ji[0]; |
| 427 |
< |
atomData[11] = ji[1]; |
| 428 |
< |
atomData[12] = ji[2]; |
| 429 |
< |
} |
| 430 |
< |
|
| 431 |
< |
// If we've survived to here, format the line: |
| 432 |
< |
|
| 433 |
< |
if (!isDirectional) { |
| 434 |
< |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 435 |
< |
atomTypeString, atomData[0], |
| 436 |
< |
atomData[1], atomData[2], |
| 437 |
< |
atomData[3], atomData[4], |
| 438 |
< |
atomData[5]); |
| 439 |
< |
|
| 440 |
< |
strcat(writeLine, |
| 441 |
< |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 442 |
< |
} else { |
| 443 |
< |
sprintf(writeLine, |
| 444 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 445 |
< |
atomTypeString, |
| 446 |
< |
atomData[0], |
| 447 |
< |
atomData[1], |
| 448 |
< |
atomData[2], |
| 449 |
< |
atomData[3], |
| 450 |
< |
atomData[4], |
| 451 |
< |
atomData[5], |
| 452 |
< |
atomData[6], |
| 453 |
< |
atomData[7], |
| 454 |
< |
atomData[8], |
| 455 |
< |
atomData[9], |
| 456 |
< |
atomData[10], |
| 457 |
< |
atomData[11], |
| 458 |
< |
atomData[12]); |
| 459 |
< |
} |
| 460 |
< |
|
| 461 |
< |
|
| 462 |
< |
os << writeLine; |
| 463 |
< |
|
| 464 |
< |
} //end for(iter = integrableObject.begin()) |
| 465 |
< |
} |
| 466 |
< |
} //end for(i = 0; i < mpiSim->getNmol()) |
| 467 |
< |
|
| 468 |
< |
os.flush(); |
| 469 |
< |
|
| 470 |
< |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 471 |
< |
MPIcheckPoint(); |
| 472 |
< |
|
| 473 |
< |
delete [] potatoes; |
| 474 |
< |
} else { |
| 475 |
< |
|
| 476 |
< |
// worldRank != 0, so I'm a remote node. |
| 477 |
< |
|
| 478 |
< |
// Set my magic potato to 0: |
| 479 |
< |
|
| 480 |
< |
myPotato = 0; |
| 481 |
< |
|
| 482 |
< |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 483 |
< |
|
| 484 |
< |
// Am I the node which has this integrableObject? |
| 485 |
< |
int whichNode = info_->getMolToProc(i); |
| 486 |
< |
if (whichNode == worldRank) { |
| 487 |
< |
if (myPotato + 1 >= MAXTAG) { |
| 488 |
< |
|
| 489 |
< |
// The potato was going to exceed the maximum value, |
| 490 |
< |
// so wrap this processor potato back to 0 (and block until |
| 491 |
< |
// node 0 says we can go: |
| 492 |
< |
|
| 493 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 494 |
< |
&istatus); |
| 495 |
< |
} |
| 496 |
< |
|
| 497 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
| 498 |
< |
|
| 499 |
< |
|
| 500 |
< |
nCurObj = mol->getNIntegrableObjects(); |
| 501 |
< |
|
| 502 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
| 503 |
< |
myPotato++; |
| 504 |
< |
|
| 505 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 506 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 507 |
< |
|
| 508 |
< |
if (myPotato + 2 >= MAXTAG) { |
| 509 |
< |
|
| 510 |
< |
// The potato was going to exceed the maximum value, |
| 511 |
< |
// so wrap this processor potato back to 0 (and block until |
| 512 |
< |
// node 0 says we can go: |
| 513 |
< |
|
| 514 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 515 |
< |
&istatus); |
| 516 |
< |
} |
| 517 |
< |
|
| 518 |
< |
atomTypeString = integrableObject->getType().c_str(); |
| 519 |
< |
|
| 520 |
< |
pos = integrableObject->getPos(); |
| 521 |
< |
vel = integrableObject->getVel(); |
| 522 |
< |
|
| 523 |
< |
atomData[0] = pos[0]; |
| 524 |
< |
atomData[1] = pos[1]; |
| 525 |
< |
atomData[2] = pos[2]; |
| 526 |
< |
|
| 527 |
< |
atomData[3] = vel[0]; |
| 528 |
< |
atomData[4] = vel[1]; |
| 529 |
< |
atomData[5] = vel[2]; |
| 530 |
< |
|
| 531 |
< |
isDirectional = 0; |
| 532 |
< |
|
| 533 |
< |
if (integrableObject->isDirectional()) { |
| 534 |
< |
isDirectional = 1; |
| 535 |
< |
|
| 536 |
< |
q = integrableObject->getQ(); |
| 537 |
< |
ji = integrableObject->getJ(); |
| 538 |
< |
|
| 539 |
< |
atomData[6] = q[0]; |
| 540 |
< |
atomData[7] = q[1]; |
| 541 |
< |
atomData[8] = q[2]; |
| 542 |
< |
atomData[9] = q[3]; |
| 543 |
< |
|
| 544 |
< |
atomData[10] = ji[0]; |
| 545 |
< |
atomData[11] = ji[1]; |
| 546 |
< |
atomData[12] = ji[2]; |
| 547 |
< |
} |
| 548 |
< |
|
| 549 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 550 |
< |
|
| 551 |
< |
// null terminate the std::string before sending (just in case): |
| 552 |
< |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
| 553 |
< |
|
| 554 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 555 |
< |
myPotato, MPI_COMM_WORLD); |
| 556 |
< |
|
| 557 |
< |
myPotato++; |
| 558 |
< |
|
| 559 |
< |
if (isDirectional) { |
| 560 |
< |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
| 561 |
< |
MPI_COMM_WORLD); |
| 562 |
< |
} else { |
| 563 |
< |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
| 564 |
< |
MPI_COMM_WORLD); |
| 565 |
< |
} |
| 566 |
< |
|
| 567 |
< |
myPotato++; |
| 568 |
< |
} |
| 569 |
< |
|
| 570 |
< |
} |
| 571 |
< |
|
| 572 |
< |
} |
| 573 |
< |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 574 |
< |
MPIcheckPoint(); |
| 335 |
> |
if (needForceVector_) { |
| 336 |
> |
type += "ft"; |
| 337 |
> |
Vector3d frc; |
| 338 |
> |
Vector3d trq; |
| 339 |
> |
frc = integrableObject->getFrc(); |
| 340 |
> |
trq = integrableObject->getTrq(); |
| 341 |
> |
|
| 342 |
> |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", |
| 343 |
> |
frc[0], frc[1], frc[2], |
| 344 |
> |
trq[0], trq[1], trq[2]); |
| 345 |
> |
line += tempBuffer; |
| 346 |
|
} |
| 347 |
+ |
|
| 348 |
+ |
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 349 |
+ |
return std::string(tempBuffer); |
| 350 |
+ |
} |
| 351 |
|
|
| 352 |
< |
#endif // is_mpi |
| 352 |
> |
void DumpWriter::writeDump() { |
| 353 |
> |
writeFrame(*dumpFile_); |
| 354 |
> |
} |
| 355 |
|
|
| 356 |
< |
} |
| 357 |
< |
|
| 581 |
< |
void DumpWriter::writeDump() { |
| 582 |
< |
writeFrame(dumpFile_); |
| 583 |
< |
|
| 584 |
< |
} |
| 585 |
< |
|
| 586 |
< |
void DumpWriter::writeEor() { |
| 587 |
< |
std::ofstream eorStream; |
| 356 |
> |
void DumpWriter::writeEor() { |
| 357 |
> |
std::ostream* eorStream; |
| 358 |
|
|
| 359 |
|
#ifdef IS_MPI |
| 360 |
|
if (worldRank == 0) { |
| 361 |
|
#endif // is_mpi |
| 362 |
|
|
| 363 |
< |
eorStream.open(eorFilename_.c_str()); |
| 594 |
< |
if (!eorStream.is_open()) { |
| 595 |
< |
sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n", |
| 596 |
< |
eorFilename_.c_str()); |
| 597 |
< |
painCave.isFatal = 1; |
| 598 |
< |
simError(); |
| 599 |
< |
} |
| 363 |
> |
eorStream = createOStream(eorFilename_); |
| 364 |
|
|
| 365 |
|
#ifdef IS_MPI |
| 366 |
|
} |
| 367 |
|
#endif // is_mpi |
| 368 |
|
|
| 369 |
< |
writeFrame(eorStream); |
| 606 |
< |
} |
| 369 |
> |
writeFrame(*eorStream); |
| 370 |
|
|
| 371 |
+ |
#ifdef IS_MPI |
| 372 |
+ |
if (worldRank == 0) { |
| 373 |
+ |
#endif // is_mpi |
| 374 |
+ |
writeClosing(*eorStream); |
| 375 |
+ |
delete eorStream; |
| 376 |
+ |
#ifdef IS_MPI |
| 377 |
+ |
} |
| 378 |
+ |
#endif // is_mpi |
| 379 |
|
|
| 380 |
< |
void DumpWriter::writeDumpAndEor() { |
| 381 |
< |
std::ofstream eorStream; |
| 380 |
> |
} |
| 381 |
> |
|
| 382 |
> |
|
| 383 |
> |
void DumpWriter::writeDumpAndEor() { |
| 384 |
|
std::vector<std::streambuf*> buffers; |
| 385 |
+ |
std::ostream* eorStream; |
| 386 |
|
#ifdef IS_MPI |
| 387 |
|
if (worldRank == 0) { |
| 388 |
|
#endif // is_mpi |
| 389 |
|
|
| 390 |
< |
buffers.push_back(dumpFile_.rdbuf()); |
| 390 |
> |
buffers.push_back(dumpFile_->rdbuf()); |
| 391 |
|
|
| 392 |
< |
eorStream.open(eorFilename_.c_str()); |
| 619 |
< |
if (!eorStream.is_open()) { |
| 620 |
< |
sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n", |
| 621 |
< |
eorFilename_.c_str()); |
| 622 |
< |
painCave.isFatal = 1; |
| 623 |
< |
simError(); |
| 624 |
< |
} |
| 392 |
> |
eorStream = createOStream(eorFilename_); |
| 393 |
|
|
| 394 |
< |
buffers.push_back(eorStream.rdbuf()); |
| 394 |
> |
buffers.push_back(eorStream->rdbuf()); |
| 395 |
|
|
| 396 |
|
#ifdef IS_MPI |
| 397 |
|
} |
| 401 |
|
std::ostream os(&tbuf); |
| 402 |
|
|
| 403 |
|
writeFrame(os); |
| 404 |
+ |
|
| 405 |
+ |
#ifdef IS_MPI |
| 406 |
+ |
if (worldRank == 0) { |
| 407 |
+ |
#endif // is_mpi |
| 408 |
+ |
writeClosing(*eorStream); |
| 409 |
+ |
delete eorStream; |
| 410 |
+ |
#ifdef IS_MPI |
| 411 |
+ |
} |
| 412 |
+ |
#endif // is_mpi |
| 413 |
|
|
| 414 |
< |
} |
| 414 |
> |
} |
| 415 |
|
|
| 416 |
+ |
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
| 417 |
|
|
| 418 |
+ |
std::ostream* newOStream; |
| 419 |
+ |
#ifdef HAVE_LIBZ |
| 420 |
+ |
if (needCompression_) { |
| 421 |
+ |
newOStream = new ogzstream(filename.c_str()); |
| 422 |
+ |
} else { |
| 423 |
+ |
newOStream = new std::ofstream(filename.c_str()); |
| 424 |
+ |
} |
| 425 |
+ |
#else |
| 426 |
+ |
newOStream = new std::ofstream(filename.c_str()); |
| 427 |
+ |
#endif |
| 428 |
+ |
//write out MetaData first |
| 429 |
+ |
(*newOStream) << "<OpenMD version=1>" << std::endl; |
| 430 |
+ |
(*newOStream) << " <MetaData>" << std::endl; |
| 431 |
+ |
(*newOStream) << info_->getRawMetaData(); |
| 432 |
+ |
(*newOStream) << " </MetaData>" << std::endl; |
| 433 |
+ |
return newOStream; |
| 434 |
+ |
} |
| 435 |
|
|
| 436 |
< |
}//end namespace oopse |
| 436 |
> |
void DumpWriter::writeClosing(std::ostream& os) { |
| 437 |
> |
|
| 438 |
> |
os << "</OpenMD>\n"; |
| 439 |
> |
os.flush(); |
| 440 |
> |
} |
| 441 |
> |
|
| 442 |
> |
}//end namespace OpenMD |
