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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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|
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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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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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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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|
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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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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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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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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::writeCommentLine(std::ostream& os, Snapshot* s) { |
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|
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double currentTime; |
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Mat3x3d hmat; |
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double chi; |
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double integralOfChiDt; |
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Mat3x3d eta; |
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|
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currentTime = s->getTime(); |
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hmat = s->getHmat(); |
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chi = s->getChi(); |
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integralOfChiDt = s->getIntegralOfChiDt(); |
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eta = s->getEta(); |
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|
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os << currentTime << ";\t" |
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<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
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<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
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<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
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|
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//write out additional parameters, such as chi and eta |
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|
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os << chi << "\t" << integralOfChiDt << "\t;"; |
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|
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os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
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<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
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<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
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|
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os << "\n"; |
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} |
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|
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void DumpWriter::writeFrame(std::ostream& os) { |
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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Quat4d q; |
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Vector3d ji; |
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Vector3d pos; |
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Vector3d vel; |
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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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int nTotObjects; |
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nTotObjects = info_->getNGlobalIntegrableObjects(); |
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|
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#ifndef IS_MPI |
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|
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|
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os << nTotObjects << "\n"; |
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|
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writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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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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|
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|
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pos = integrableObject->getPos(); |
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vel = integrableObject->getVel(); |
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|
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sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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integrableObject->getType().c_str(), |
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pos[0], pos[1], pos[2], |
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vel[0], vel[1], vel[2]); |
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|
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strcpy(writeLine, tempBuffer); |
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|
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if (integrableObject->isDirectional()) { |
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q = integrableObject->getQ(); |
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ji = integrableObject->getJ(); |
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|
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sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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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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strcat(writeLine, tempBuffer); |
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} else { |
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strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
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} |
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|
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os << writeLine; |
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|
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} |
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} |
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|
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os.flush(); |
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#else // is_mpi |
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/********************************************************************* |
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* Documentation? You want DOCUMENTATION? |
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* |
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* Why all the potatoes below? |
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* |
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* To make a long story short, the original version of DumpWriter |
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* worked in the most inefficient way possible. Node 0 would |
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* poke each of the node for an individual atom's formatted data |
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* as node 0 worked its way down the global index. This was particularly |
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* inefficient since the method blocked all processors at every atom |
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* (and did it twice!). |
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* |
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* An intermediate version of DumpWriter could be described from Node |
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* zero's perspective as follows: |
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* |
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* 1) Have 100 of your friends stand in a circle. |
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* 2) When you say go, have all of them start tossing potatoes at |
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* you (one at a time). |
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* 3) Catch the potatoes. |
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* |
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* It was an improvement, but MPI has buffers and caches that could |
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* best be described in this analogy as "potato nets", so there's no |
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* need to block the processors atom-by-atom. |
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* |
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* This new and improved DumpWriter works in an even more efficient |
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* way: |
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* |
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* 1) Have 100 of your friend stand in a circle. |
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* 2) When you say go, have them start tossing 5-pound bags of |
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* potatoes at you. |
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* 3) Once you've caught a friend's bag of potatoes, |
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* toss them a spud to let them know they can toss another bag. |
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* |
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* How's THAT for documentation? |
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* |
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*********************************************************************/ |
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const int masterNode = 0; |
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|
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int * potatoes; |
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int myPotato; |
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int nProc; |
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int which_node; |
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double atomData[13]; |
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int isDirectional; |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
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int msgLen; // the length of message actually recieved at master nodes |
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int haveError; |
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MPI_Status istatus; |
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int nCurObj; |
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|
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// code to find maximum tag value |
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int * tagub; |
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int flag; |
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int MAXTAG; |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
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|
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if (flag) { |
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MAXTAG = *tagub; |
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} else { |
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MAXTAG = 32767; |
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} |
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|
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if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
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|
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// Node 0 needs a list of the magic potatoes for each processor; |
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|
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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potatoes = new int[nProc]; |
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|
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//write out the comment lines |
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for(int i = 0; i < nProc; i++) { |
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potatoes[i] = 0; |
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} |
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|
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|
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os << nTotObjects << "\n"; |
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writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
324 |
|
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// Get the Node number which has this atom; |
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|
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which_node = info_->getMolToProc(i); |
328 |
|
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if (which_node != masterNode) { //current molecule is in slave node |
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if (potatoes[which_node] + 1 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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|
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potatoes[which_node] = 0; |
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MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
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MPI_COMM_WORLD); |
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} |
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|
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myPotato = potatoes[which_node]; |
340 |
|
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//recieve the number of integrableObject in current molecule |
342 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
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MPI_COMM_WORLD, &istatus); |
344 |
myPotato++; |
345 |
|
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for(int l = 0; l < nCurObj; l++) { |
347 |
if (potatoes[which_node] + 2 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
350 |
|
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potatoes[which_node] = 0; |
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MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
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0, MPI_COMM_WORLD); |
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} |
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|
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MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
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which_node, myPotato, MPI_COMM_WORLD, |
358 |
&istatus); |
359 |
|
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myPotato++; |
361 |
|
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MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
363 |
MPI_COMM_WORLD, &istatus); |
364 |
myPotato++; |
365 |
|
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MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
367 |
|
368 |
if (msgLen == 13) |
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isDirectional = 1; |
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else |
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isDirectional = 0; |
372 |
|
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// If we've survived to here, format the line: |
374 |
|
375 |
if (!isDirectional) { |
376 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
377 |
MPIatomTypeString, atomData[0], |
378 |
atomData[1], atomData[2], |
379 |
atomData[3], atomData[4], |
380 |
atomData[5]); |
381 |
|
382 |
strcat(writeLine, |
383 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
384 |
} else { |
385 |
sprintf(writeLine, |
386 |
"%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", |
387 |
MPIatomTypeString, |
388 |
atomData[0], |
389 |
atomData[1], |
390 |
atomData[2], |
391 |
atomData[3], |
392 |
atomData[4], |
393 |
atomData[5], |
394 |
atomData[6], |
395 |
atomData[7], |
396 |
atomData[8], |
397 |
atomData[9], |
398 |
atomData[10], |
399 |
atomData[11], |
400 |
atomData[12]); |
401 |
} |
402 |
|
403 |
os << writeLine; |
404 |
|
405 |
} // end for(int l =0) |
406 |
|
407 |
potatoes[which_node] = myPotato; |
408 |
} else { //master node has current molecule |
409 |
|
410 |
mol = info_->getMoleculeByGlobalIndex(i); |
411 |
|
412 |
if (mol == NULL) { |
413 |
sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
414 |
painCave.isFatal = 1; |
415 |
simError(); |
416 |
} |
417 |
|
418 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
419 |
integrableObject = mol->nextIntegrableObject(ii)) { |
420 |
|
421 |
pos = integrableObject->getPos(); |
422 |
vel = integrableObject->getVel(); |
423 |
|
424 |
atomData[0] = pos[0]; |
425 |
atomData[1] = pos[1]; |
426 |
atomData[2] = pos[2]; |
427 |
|
428 |
atomData[3] = vel[0]; |
429 |
atomData[4] = vel[1]; |
430 |
atomData[5] = vel[2]; |
431 |
|
432 |
isDirectional = 0; |
433 |
|
434 |
if (integrableObject->isDirectional()) { |
435 |
isDirectional = 1; |
436 |
|
437 |
q = integrableObject->getQ(); |
438 |
ji = integrableObject->getJ(); |
439 |
|
440 |
for(int j = 0; j < 6; j++) { |
441 |
atomData[j] = atomData[j]; |
442 |
} |
443 |
|
444 |
atomData[6] = q[0]; |
445 |
atomData[7] = q[1]; |
446 |
atomData[8] = q[2]; |
447 |
atomData[9] = q[3]; |
448 |
|
449 |
atomData[10] = ji[0]; |
450 |
atomData[11] = ji[1]; |
451 |
atomData[12] = ji[2]; |
452 |
} |
453 |
|
454 |
// If we've survived to here, format the line: |
455 |
|
456 |
if (!isDirectional) { |
457 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
458 |
integrableObject->getType().c_str(), atomData[0], |
459 |
atomData[1], atomData[2], |
460 |
atomData[3], atomData[4], |
461 |
atomData[5]); |
462 |
|
463 |
strcat(writeLine, |
464 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
465 |
} else { |
466 |
sprintf(writeLine, |
467 |
"%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", |
468 |
integrableObject->getType().c_str(), |
469 |
atomData[0], |
470 |
atomData[1], |
471 |
atomData[2], |
472 |
atomData[3], |
473 |
atomData[4], |
474 |
atomData[5], |
475 |
atomData[6], |
476 |
atomData[7], |
477 |
atomData[8], |
478 |
atomData[9], |
479 |
atomData[10], |
480 |
atomData[11], |
481 |
atomData[12]); |
482 |
} |
483 |
|
484 |
|
485 |
os << writeLine; |
486 |
|
487 |
} //end for(iter = integrableObject.begin()) |
488 |
} |
489 |
} //end for(i = 0; i < mpiSim->getNmol()) |
490 |
|
491 |
os.flush(); |
492 |
|
493 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
494 |
MPIcheckPoint(); |
495 |
|
496 |
delete [] potatoes; |
497 |
} else { |
498 |
|
499 |
// worldRank != 0, so I'm a remote node. |
500 |
|
501 |
// Set my magic potato to 0: |
502 |
|
503 |
myPotato = 0; |
504 |
|
505 |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
506 |
|
507 |
// Am I the node which has this integrableObject? |
508 |
int whichNode = info_->getMolToProc(i); |
509 |
if (whichNode == worldRank) { |
510 |
if (myPotato + 1 >= MAXTAG) { |
511 |
|
512 |
// The potato was going to exceed the maximum value, |
513 |
// so wrap this processor potato back to 0 (and block until |
514 |
// node 0 says we can go: |
515 |
|
516 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
517 |
&istatus); |
518 |
} |
519 |
|
520 |
mol = info_->getMoleculeByGlobalIndex(i); |
521 |
|
522 |
|
523 |
nCurObj = mol->getNIntegrableObjects(); |
524 |
|
525 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
526 |
myPotato++; |
527 |
|
528 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
529 |
integrableObject = mol->nextIntegrableObject(ii)) { |
530 |
|
531 |
if (myPotato + 2 >= MAXTAG) { |
532 |
|
533 |
// The potato was going to exceed the maximum value, |
534 |
// so wrap this processor potato back to 0 (and block until |
535 |
// node 0 says we can go: |
536 |
|
537 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
538 |
&istatus); |
539 |
} |
540 |
|
541 |
pos = integrableObject->getPos(); |
542 |
vel = integrableObject->getVel(); |
543 |
|
544 |
atomData[0] = pos[0]; |
545 |
atomData[1] = pos[1]; |
546 |
atomData[2] = pos[2]; |
547 |
|
548 |
atomData[3] = vel[0]; |
549 |
atomData[4] = vel[1]; |
550 |
atomData[5] = vel[2]; |
551 |
|
552 |
isDirectional = 0; |
553 |
|
554 |
if (integrableObject->isDirectional()) { |
555 |
isDirectional = 1; |
556 |
|
557 |
q = integrableObject->getQ(); |
558 |
ji = integrableObject->getJ(); |
559 |
|
560 |
atomData[6] = q[0]; |
561 |
atomData[7] = q[1]; |
562 |
atomData[8] = q[2]; |
563 |
atomData[9] = q[3]; |
564 |
|
565 |
atomData[10] = ji[0]; |
566 |
atomData[11] = ji[1]; |
567 |
atomData[12] = ji[2]; |
568 |
} |
569 |
|
570 |
strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE); |
571 |
|
572 |
// null terminate the std::string before sending (just in case): |
573 |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
574 |
|
575 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
576 |
myPotato, MPI_COMM_WORLD); |
577 |
|
578 |
myPotato++; |
579 |
|
580 |
if (isDirectional) { |
581 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
582 |
MPI_COMM_WORLD); |
583 |
} else { |
584 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
585 |
MPI_COMM_WORLD); |
586 |
} |
587 |
|
588 |
myPotato++; |
589 |
} |
590 |
|
591 |
} |
592 |
|
593 |
} |
594 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
595 |
MPIcheckPoint(); |
596 |
} |
597 |
|
598 |
#endif // is_mpi |
599 |
|
600 |
} |
601 |
|
602 |
void DumpWriter::writeDump() { |
603 |
writeFrame(*dumpFile_); |
604 |
} |
605 |
|
606 |
void DumpWriter::writeEor() { |
607 |
std::ostream* eorStream; |
608 |
|
609 |
#ifdef IS_MPI |
610 |
if (worldRank == 0) { |
611 |
#endif // is_mpi |
612 |
|
613 |
eorStream = createOStream(eorFilename_); |
614 |
|
615 |
#ifdef IS_MPI |
616 |
} |
617 |
#endif // is_mpi |
618 |
|
619 |
writeFrame(*eorStream); |
620 |
|
621 |
#ifdef IS_MPI |
622 |
if (worldRank == 0) { |
623 |
#endif // is_mpi |
624 |
delete eorStream; |
625 |
|
626 |
#ifdef IS_MPI |
627 |
} |
628 |
#endif // is_mpi |
629 |
|
630 |
} |
631 |
|
632 |
|
633 |
void DumpWriter::writeDumpAndEor() { |
634 |
std::vector<std::streambuf*> buffers; |
635 |
std::ostream* eorStream; |
636 |
#ifdef IS_MPI |
637 |
if (worldRank == 0) { |
638 |
#endif // is_mpi |
639 |
|
640 |
buffers.push_back(dumpFile_->rdbuf()); |
641 |
|
642 |
eorStream = createOStream(eorFilename_); |
643 |
|
644 |
buffers.push_back(eorStream->rdbuf()); |
645 |
|
646 |
#ifdef IS_MPI |
647 |
} |
648 |
#endif // is_mpi |
649 |
|
650 |
TeeBuf tbuf(buffers.begin(), buffers.end()); |
651 |
std::ostream os(&tbuf); |
652 |
|
653 |
writeFrame(os); |
654 |
|
655 |
#ifdef IS_MPI |
656 |
if (worldRank == 0) { |
657 |
#endif // is_mpi |
658 |
delete eorStream; |
659 |
|
660 |
#ifdef IS_MPI |
661 |
} |
662 |
#endif // is_mpi |
663 |
|
664 |
} |
665 |
|
666 |
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
667 |
|
668 |
std::ostream* newOStream; |
669 |
#ifdef HAVE_LIBZ |
670 |
if (needCompression_) { |
671 |
newOStream = new ogzstream(filename.c_str()); |
672 |
} else { |
673 |
newOStream = new std::ofstream(filename.c_str()); |
674 |
} |
675 |
#else |
676 |
newOStream = new std::ofstream(filename.c_str()); |
677 |
#endif |
678 |
return newOStream; |
679 |
} |
680 |
|
681 |
}//end namespace oopse |