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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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* 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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* 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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|
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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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|
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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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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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#endif // is_mpi |
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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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|
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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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|
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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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#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 |
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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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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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#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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|
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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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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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void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { |
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|
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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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hmat = s->getHmat(); |
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sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
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hmat(0, 0), hmat(1, 0), hmat(2, 0), |
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hmat(0, 1), hmat(1, 1), hmat(2, 1), |
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hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
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os << buffer; |
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|
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RealType chi = s->getChi(); |
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RealType integralOfChiDt = s->getIntegralOfChiDt(); |
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sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
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os << buffer; |
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|
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Mat3x3d eta; |
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eta = s->getEta(); |
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sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
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eta(0, 0), eta(1, 0), eta(2, 0), |
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eta(0, 1), eta(1, 1), eta(2, 1), |
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eta(0, 2), eta(1, 2), eta(2, 2)); |
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os << buffer; |
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|
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os << " </FrameData>\n"; |
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} |
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|
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void DumpWriter::writeFrame(std::ostream& os) { |
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|
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#ifdef IS_MPI |
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MPI_Status istatus; |
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#endif |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ii; |
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|
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#ifndef IS_MPI |
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os << " <Snapshot>\n"; |
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|
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writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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os << " <StuntDoubles>\n"; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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os << prepareDumpLine(integrableObject); |
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|
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} |
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} |
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os << " </StuntDoubles>\n"; |
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|
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os << " </Snapshot>\n"; |
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|
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os.flush(); |
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#else |
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//every node prepares the dump lines for integrable objects belong to itself |
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std::string buffer; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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buffer += prepareDumpLine(integrableObject); |
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} |
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} |
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|
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const int masterNode = 0; |
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|
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if (worldRank == masterNode) { |
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os << " <Snapshot>\n"; |
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writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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os << " <StuntDoubles>\n"; |
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|
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os << buffer; |
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|
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int nProc; |
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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for (int i = 1; i < nProc; ++i) { |
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|
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// receive the length of the string buffer that was |
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// prepared by processor i |
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|
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int recvLength; |
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MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
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char* recvBuffer = new char[recvLength]; |
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if (recvBuffer == NULL) { |
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} else { |
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MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
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os << recvBuffer; |
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delete recvBuffer; |
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} |
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} |
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os << " </StuntDoubles>\n"; |
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|
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os << " </Snapshot>\n"; |
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os.flush(); |
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} else { |
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int sendBufferLength = buffer.size() + 1; |
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MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
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MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
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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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std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
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|
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int index = integrableObject->getGlobalIntegrableObjectIndex(); |
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std::string type("pv"); |
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std::string line; |
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char tempBuffer[4096]; |
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|
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Vector3d pos; |
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Vector3d vel; |
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pos = integrableObject->getPos(); |
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vel = integrableObject->getVel(); |
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sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
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pos[0], pos[1], pos[2], |
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vel[0], vel[1], vel[2]); |
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line += tempBuffer; |
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|
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if (integrableObject->isDirectional()) { |
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type += "qj"; |
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Quat4d q; |
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Vector3d ji; |
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q = integrableObject->getQ(); |
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ji = integrableObject->getJ(); |
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sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
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q[0], q[1], q[2], q[3], |
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ji[0], ji[1], ji[2]); |
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line += tempBuffer; |
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} |
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|
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if (needForceVector_) { |
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type += "ft"; |
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Vector3d frc; |
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Vector3d trq; |
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frc = integrableObject->getFrc(); |
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trq = integrableObject->getTrq(); |
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|
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sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", |
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frc[0], frc[1], frc[2], |
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trq[0], trq[1], trq[2]); |
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line += tempBuffer; |
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} |
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|
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sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
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return std::string(tempBuffer); |
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} |
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|
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void DumpWriter::writeDump() { |
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writeFrame(*dumpFile_); |
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} |
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|
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void DumpWriter::writeEor() { |
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std::ostream* eorStream; |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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eorStream = createOStream(eorFilename_); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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|
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writeFrame(*eorStream); |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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writeClosing(*eorStream); |
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delete eorStream; |
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#ifdef IS_MPI |
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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::writeDumpAndEor() { |
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std::vector<std::streambuf*> buffers; |
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std::ostream* eorStream; |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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buffers.push_back(dumpFile_->rdbuf()); |
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|
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eorStream = createOStream(eorFilename_); |
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|
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buffers.push_back(eorStream->rdbuf()); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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|
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TeeBuf tbuf(buffers.begin(), buffers.end()); |
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std::ostream os(&tbuf); |
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|
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writeFrame(os); |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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writeClosing(*eorStream); |
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delete eorStream; |
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#ifdef IS_MPI |
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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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std::ostream* DumpWriter::createOStream(const std::string& filename) { |
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|
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std::ostream* newOStream; |
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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newOStream = new ogzstream(filename.c_str()); |
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} else { |
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newOStream = new std::ofstream(filename.c_str()); |
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} |
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#else |
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newOStream = new std::ofstream(filename.c_str()); |
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#endif |
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//write out MetaData first |
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(*newOStream) << "<OOPSE version=4>" << std::endl; |
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(*newOStream) << " <MetaData>" << std::endl; |
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(*newOStream) << info_->getRawMetaData(); |
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(*newOStream) << " </MetaData>" << std::endl; |
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return newOStream; |
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} |
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|
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void DumpWriter::writeClosing(std::ostream& os) { |
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|
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os << "</OOPSE>\n"; |
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os.flush(); |
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} |
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|
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}//end namespace oopse |
