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/* |
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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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#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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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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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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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
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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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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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#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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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(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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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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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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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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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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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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#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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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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DumpWriter::~DumpWriter() { |
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DumpWriter::~DumpWriter() { |
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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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dumpFile_.close(); |
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delete dumpFile_; |
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#ifdef IS_MPI |
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#endif // is_mpi |
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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::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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eta = s->getEta(); |
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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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<< 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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//write out additional parameters, such as chi and eta |
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os << chi << "\t" << integralOfChiDt << "\t;"; |
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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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<< 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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os << "\n"; |
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} |
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} |
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void DumpWriter::writeFrame(std::ostream& os) { |
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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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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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pos = integrableObject->getPos(); |
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vel = integrableObject->getVel(); |
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pos = integrableObject->getPos(); |
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vel = integrableObject->getVel(); |
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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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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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strcpy(writeLine, tempBuffer); |
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strcpy(writeLine, tempBuffer); |
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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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if (integrableObject->isDirectional()) { |
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q = integrableObject->getQ(); |
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ji = integrableObject->getJ(); |
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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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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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os << writeLine; |
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os << writeLine; |
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} |
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} |
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} |
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os.flush(); |
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int which_node; |
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double atomData[13]; |
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int isDirectional; |
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const char * atomTypeString; |
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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_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
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if (flag) { |
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MAXTAG = *tagub; |
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MAXTAG = *tagub; |
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} else { |
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MAXTAG = 32767; |
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MAXTAG = 32767; |
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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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// Node 0 needs a list of the magic potatoes for each processor; |
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// Node 0 needs a list of the magic potatoes for each processor; |
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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potatoes = new int[nProc]; |
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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potatoes = new int[nProc]; |
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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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//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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os << nTotObjects << "\n"; |
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writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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os << nTotObjects << "\n"; |
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writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
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for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
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// Get the Node number which has this atom; |
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// Get the Node number which has this atom; |
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which_node = info_->getMolToProc(i); |
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which_node = info_->getMolToProc(i); |
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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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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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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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myPotato = potatoes[which_node]; |
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> |
myPotato = potatoes[which_node]; |
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//recieve the number of integrableObject in current molecule |
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MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
338 |
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MPI_COMM_WORLD, &istatus); |
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myPotato++; |
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//recieve the number of integrableObject in current molecule |
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MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
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MPI_COMM_WORLD, &istatus); |
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myPotato++; |
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|
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< |
for(int l = 0; l < nCurObj; l++) { |
342 |
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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: |
323 |
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|
324 |
< |
potatoes[which_node] = 0; |
325 |
< |
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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for(int l = 0; l < nCurObj; l++) { |
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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: |
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|
|
346 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
347 |
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which_node, myPotato, MPI_COMM_WORLD, |
348 |
< |
&istatus); |
346 |
> |
potatoes[which_node] = 0; |
347 |
> |
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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< |
atomTypeString = MPIatomTypeString; |
351 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
352 |
> |
which_node, myPotato, MPI_COMM_WORLD, |
353 |
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&istatus); |
354 |
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|
355 |
< |
myPotato++; |
355 |
> |
myPotato++; |
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|
357 |
< |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
358 |
< |
MPI_COMM_WORLD, &istatus); |
359 |
< |
myPotato++; |
357 |
> |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
358 |
> |
MPI_COMM_WORLD, &istatus); |
359 |
> |
myPotato++; |
360 |
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|
361 |
< |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
361 |
> |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
362 |
|
|
363 |
< |
if (msgLen == 13) |
364 |
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isDirectional = 1; |
365 |
< |
else |
366 |
< |
isDirectional = 0; |
363 |
> |
if (msgLen == 13) |
364 |
> |
isDirectional = 1; |
365 |
> |
else |
366 |
> |
isDirectional = 0; |
367 |
|
|
368 |
< |
// If we've survived to here, format the line: |
368 |
> |
// If we've survived to here, format the line: |
369 |
|
|
370 |
< |
if (!isDirectional) { |
371 |
< |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
372 |
< |
atomTypeString, atomData[0], |
373 |
< |
atomData[1], atomData[2], |
374 |
< |
atomData[3], atomData[4], |
375 |
< |
atomData[5]); |
370 |
> |
if (!isDirectional) { |
371 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
372 |
> |
MPIatomTypeString, atomData[0], |
373 |
> |
atomData[1], atomData[2], |
374 |
> |
atomData[3], atomData[4], |
375 |
> |
atomData[5]); |
376 |
|
|
377 |
< |
strcat(writeLine, |
378 |
< |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
379 |
< |
} else { |
380 |
< |
sprintf(writeLine, |
381 |
< |
"%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", |
382 |
< |
atomTypeString, |
383 |
< |
atomData[0], |
384 |
< |
atomData[1], |
385 |
< |
atomData[2], |
386 |
< |
atomData[3], |
387 |
< |
atomData[4], |
388 |
< |
atomData[5], |
389 |
< |
atomData[6], |
390 |
< |
atomData[7], |
391 |
< |
atomData[8], |
392 |
< |
atomData[9], |
393 |
< |
atomData[10], |
394 |
< |
atomData[11], |
395 |
< |
atomData[12]); |
396 |
< |
} |
377 |
> |
strcat(writeLine, |
378 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
379 |
> |
} else { |
380 |
> |
sprintf(writeLine, |
381 |
> |
"%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", |
382 |
> |
MPIatomTypeString, |
383 |
> |
atomData[0], |
384 |
> |
atomData[1], |
385 |
> |
atomData[2], |
386 |
> |
atomData[3], |
387 |
> |
atomData[4], |
388 |
> |
atomData[5], |
389 |
> |
atomData[6], |
390 |
> |
atomData[7], |
391 |
> |
atomData[8], |
392 |
> |
atomData[9], |
393 |
> |
atomData[10], |
394 |
> |
atomData[11], |
395 |
> |
atomData[12]); |
396 |
> |
} |
397 |
|
|
398 |
< |
os << writeLine; |
398 |
> |
os << writeLine; |
399 |
|
|
400 |
< |
} // end for(int l =0) |
400 |
> |
} // end for(int l =0) |
401 |
|
|
402 |
< |
potatoes[which_node] = myPotato; |
403 |
< |
} else { //master node has current molecule |
402 |
> |
potatoes[which_node] = myPotato; |
403 |
> |
} else { //master node has current molecule |
404 |
|
|
405 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
405 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
406 |
|
|
407 |
< |
if (mol == NULL) { |
408 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
409 |
< |
painCave.isFatal = 1; |
410 |
< |
simError(); |
411 |
< |
} |
407 |
> |
if (mol == NULL) { |
408 |
> |
sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
409 |
> |
painCave.isFatal = 1; |
410 |
> |
simError(); |
411 |
> |
} |
412 |
|
|
413 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
414 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
395 |
< |
|
396 |
< |
atomTypeString = integrableObject->getType().c_str(); |
413 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
414 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
415 |
|
|
416 |
< |
pos = integrableObject->getPos(); |
417 |
< |
vel = integrableObject->getVel(); |
416 |
> |
pos = integrableObject->getPos(); |
417 |
> |
vel = integrableObject->getVel(); |
418 |
|
|
419 |
< |
atomData[0] = pos[0]; |
420 |
< |
atomData[1] = pos[1]; |
421 |
< |
atomData[2] = pos[2]; |
419 |
> |
atomData[0] = pos[0]; |
420 |
> |
atomData[1] = pos[1]; |
421 |
> |
atomData[2] = pos[2]; |
422 |
|
|
423 |
< |
atomData[3] = vel[0]; |
424 |
< |
atomData[4] = vel[1]; |
425 |
< |
atomData[5] = vel[2]; |
423 |
> |
atomData[3] = vel[0]; |
424 |
> |
atomData[4] = vel[1]; |
425 |
> |
atomData[5] = vel[2]; |
426 |
|
|
427 |
< |
isDirectional = 0; |
427 |
> |
isDirectional = 0; |
428 |
|
|
429 |
< |
if (integrableObject->isDirectional()) { |
430 |
< |
isDirectional = 1; |
429 |
> |
if (integrableObject->isDirectional()) { |
430 |
> |
isDirectional = 1; |
431 |
|
|
432 |
< |
q = integrableObject->getQ(); |
433 |
< |
ji = integrableObject->getJ(); |
432 |
> |
q = integrableObject->getQ(); |
433 |
> |
ji = integrableObject->getJ(); |
434 |
|
|
435 |
< |
for(int j = 0; j < 6; j++) { |
436 |
< |
atomData[j] = atomData[j]; |
437 |
< |
} |
435 |
> |
for(int j = 0; j < 6; j++) { |
436 |
> |
atomData[j] = atomData[j]; |
437 |
> |
} |
438 |
|
|
439 |
< |
atomData[6] = q[0]; |
440 |
< |
atomData[7] = q[1]; |
441 |
< |
atomData[8] = q[2]; |
442 |
< |
atomData[9] = q[3]; |
439 |
> |
atomData[6] = q[0]; |
440 |
> |
atomData[7] = q[1]; |
441 |
> |
atomData[8] = q[2]; |
442 |
> |
atomData[9] = q[3]; |
443 |
|
|
444 |
< |
atomData[10] = ji[0]; |
445 |
< |
atomData[11] = ji[1]; |
446 |
< |
atomData[12] = ji[2]; |
447 |
< |
} |
444 |
> |
atomData[10] = ji[0]; |
445 |
> |
atomData[11] = ji[1]; |
446 |
> |
atomData[12] = ji[2]; |
447 |
> |
} |
448 |
|
|
449 |
< |
// If we've survived to here, format the line: |
449 |
> |
// If we've survived to here, format the line: |
450 |
|
|
451 |
< |
if (!isDirectional) { |
452 |
< |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
453 |
< |
atomTypeString, atomData[0], |
454 |
< |
atomData[1], atomData[2], |
455 |
< |
atomData[3], atomData[4], |
456 |
< |
atomData[5]); |
451 |
> |
if (!isDirectional) { |
452 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
453 |
> |
integrableObject->getType().c_str(), atomData[0], |
454 |
> |
atomData[1], atomData[2], |
455 |
> |
atomData[3], atomData[4], |
456 |
> |
atomData[5]); |
457 |
|
|
458 |
< |
strcat(writeLine, |
459 |
< |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
460 |
< |
} else { |
461 |
< |
sprintf(writeLine, |
462 |
< |
"%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", |
463 |
< |
atomTypeString, |
464 |
< |
atomData[0], |
465 |
< |
atomData[1], |
466 |
< |
atomData[2], |
467 |
< |
atomData[3], |
468 |
< |
atomData[4], |
469 |
< |
atomData[5], |
470 |
< |
atomData[6], |
471 |
< |
atomData[7], |
472 |
< |
atomData[8], |
473 |
< |
atomData[9], |
474 |
< |
atomData[10], |
475 |
< |
atomData[11], |
476 |
< |
atomData[12]); |
477 |
< |
} |
458 |
> |
strcat(writeLine, |
459 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
460 |
> |
} else { |
461 |
> |
sprintf(writeLine, |
462 |
> |
"%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", |
463 |
> |
integrableObject->getType().c_str(), |
464 |
> |
atomData[0], |
465 |
> |
atomData[1], |
466 |
> |
atomData[2], |
467 |
> |
atomData[3], |
468 |
> |
atomData[4], |
469 |
> |
atomData[5], |
470 |
> |
atomData[6], |
471 |
> |
atomData[7], |
472 |
> |
atomData[8], |
473 |
> |
atomData[9], |
474 |
> |
atomData[10], |
475 |
> |
atomData[11], |
476 |
> |
atomData[12]); |
477 |
> |
} |
478 |
|
|
479 |
|
|
480 |
< |
os << writeLine; |
480 |
> |
os << writeLine; |
481 |
|
|
482 |
< |
} //end for(iter = integrableObject.begin()) |
483 |
< |
} |
484 |
< |
} //end for(i = 0; i < mpiSim->getNmol()) |
482 |
> |
} //end for(iter = integrableObject.begin()) |
483 |
> |
} |
484 |
> |
} //end for(i = 0; i < mpiSim->getNmol()) |
485 |
|
|
486 |
< |
os.flush(); |
486 |
> |
os.flush(); |
487 |
|
|
488 |
< |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
489 |
< |
MPIcheckPoint(); |
488 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
489 |
> |
MPIcheckPoint(); |
490 |
|
|
491 |
< |
delete [] potatoes; |
491 |
> |
delete [] potatoes; |
492 |
|
} else { |
493 |
|
|
494 |
< |
// worldRank != 0, so I'm a remote node. |
494 |
> |
// worldRank != 0, so I'm a remote node. |
495 |
|
|
496 |
< |
// Set my magic potato to 0: |
496 |
> |
// Set my magic potato to 0: |
497 |
|
|
498 |
< |
myPotato = 0; |
498 |
> |
myPotato = 0; |
499 |
|
|
500 |
< |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
500 |
> |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
501 |
|
|
502 |
< |
// Am I the node which has this integrableObject? |
503 |
< |
int whichNode = info_->getMolToProc(i); |
504 |
< |
if (whichNode == worldRank) { |
505 |
< |
if (myPotato + 1 >= MAXTAG) { |
502 |
> |
// Am I the node which has this integrableObject? |
503 |
> |
int whichNode = info_->getMolToProc(i); |
504 |
> |
if (whichNode == worldRank) { |
505 |
> |
if (myPotato + 1 >= MAXTAG) { |
506 |
|
|
507 |
< |
// The potato was going to exceed the maximum value, |
508 |
< |
// so wrap this processor potato back to 0 (and block until |
509 |
< |
// node 0 says we can go: |
507 |
> |
// The potato was going to exceed the maximum value, |
508 |
> |
// so wrap this processor potato back to 0 (and block until |
509 |
> |
// node 0 says we can go: |
510 |
|
|
511 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
512 |
< |
&istatus); |
513 |
< |
} |
511 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
512 |
> |
&istatus); |
513 |
> |
} |
514 |
|
|
515 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
515 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
516 |
|
|
517 |
|
|
518 |
< |
nCurObj = mol->getNIntegrableObjects(); |
518 |
> |
nCurObj = mol->getNIntegrableObjects(); |
519 |
|
|
520 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
521 |
< |
myPotato++; |
520 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
521 |
> |
myPotato++; |
522 |
|
|
523 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
524 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
523 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
524 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
525 |
|
|
526 |
< |
if (myPotato + 2 >= MAXTAG) { |
526 |
> |
if (myPotato + 2 >= MAXTAG) { |
527 |
|
|
528 |
< |
// The potato was going to exceed the maximum value, |
529 |
< |
// so wrap this processor potato back to 0 (and block until |
530 |
< |
// node 0 says we can go: |
528 |
> |
// The potato was going to exceed the maximum value, |
529 |
> |
// so wrap this processor potato back to 0 (and block until |
530 |
> |
// node 0 says we can go: |
531 |
|
|
532 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
533 |
< |
&istatus); |
534 |
< |
} |
532 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
533 |
> |
&istatus); |
534 |
> |
} |
535 |
|
|
536 |
< |
atomTypeString = integrableObject->getType().c_str(); |
536 |
> |
pos = integrableObject->getPos(); |
537 |
> |
vel = integrableObject->getVel(); |
538 |
|
|
539 |
< |
pos = integrableObject->getPos(); |
540 |
< |
vel = integrableObject->getVel(); |
539 |
> |
atomData[0] = pos[0]; |
540 |
> |
atomData[1] = pos[1]; |
541 |
> |
atomData[2] = pos[2]; |
542 |
|
|
543 |
< |
atomData[0] = pos[0]; |
544 |
< |
atomData[1] = pos[1]; |
545 |
< |
atomData[2] = pos[2]; |
543 |
> |
atomData[3] = vel[0]; |
544 |
> |
atomData[4] = vel[1]; |
545 |
> |
atomData[5] = vel[2]; |
546 |
|
|
547 |
< |
atomData[3] = vel[0]; |
528 |
< |
atomData[4] = vel[1]; |
529 |
< |
atomData[5] = vel[2]; |
547 |
> |
isDirectional = 0; |
548 |
|
|
549 |
< |
isDirectional = 0; |
549 |
> |
if (integrableObject->isDirectional()) { |
550 |
> |
isDirectional = 1; |
551 |
|
|
552 |
< |
if (integrableObject->isDirectional()) { |
553 |
< |
isDirectional = 1; |
552 |
> |
q = integrableObject->getQ(); |
553 |
> |
ji = integrableObject->getJ(); |
554 |
|
|
555 |
< |
q = integrableObject->getQ(); |
556 |
< |
ji = integrableObject->getJ(); |
555 |
> |
atomData[6] = q[0]; |
556 |
> |
atomData[7] = q[1]; |
557 |
> |
atomData[8] = q[2]; |
558 |
> |
atomData[9] = q[3]; |
559 |
|
|
560 |
< |
atomData[6] = q[0]; |
561 |
< |
atomData[7] = q[1]; |
562 |
< |
atomData[8] = q[2]; |
563 |
< |
atomData[9] = q[3]; |
560 |
> |
atomData[10] = ji[0]; |
561 |
> |
atomData[11] = ji[1]; |
562 |
> |
atomData[12] = ji[2]; |
563 |
> |
} |
564 |
|
|
565 |
< |
atomData[10] = ji[0]; |
545 |
< |
atomData[11] = ji[1]; |
546 |
< |
atomData[12] = ji[2]; |
547 |
< |
} |
565 |
> |
strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE); |
566 |
|
|
567 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
567 |
> |
// null terminate the std::string before sending (just in case): |
568 |
> |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
569 |
|
|
570 |
< |
// null terminate the std::string before sending (just in case): |
571 |
< |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
570 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
571 |
> |
myPotato, MPI_COMM_WORLD); |
572 |
|
|
573 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
555 |
< |
myPotato, MPI_COMM_WORLD); |
573 |
> |
myPotato++; |
574 |
|
|
575 |
< |
myPotato++; |
575 |
> |
if (isDirectional) { |
576 |
> |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
577 |
> |
MPI_COMM_WORLD); |
578 |
> |
} else { |
579 |
> |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
580 |
> |
MPI_COMM_WORLD); |
581 |
> |
} |
582 |
|
|
583 |
< |
if (isDirectional) { |
584 |
< |
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 |
< |
} |
583 |
> |
myPotato++; |
584 |
> |
} |
585 |
|
|
586 |
< |
} |
586 |
> |
} |
587 |
|
|
588 |
< |
} |
589 |
< |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
590 |
< |
MPIcheckPoint(); |
588 |
> |
} |
589 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
590 |
> |
MPIcheckPoint(); |
591 |
|
} |
592 |
|
|
593 |
|
#endif // is_mpi |
594 |
|
|
595 |
< |
} |
595 |
> |
} |
596 |
|
|
597 |
< |
void DumpWriter::writeDump() { |
598 |
< |
writeFrame(dumpFile_); |
597 |
> |
void DumpWriter::writeDump() { |
598 |
> |
writeFrame(*dumpFile_); |
599 |
> |
} |
600 |
|
|
601 |
< |
} |
602 |
< |
|
586 |
< |
void DumpWriter::writeEor() { |
587 |
< |
std::ofstream eorStream; |
601 |
> |
void DumpWriter::writeEor() { |
602 |
> |
std::ostream* eorStream; |
603 |
|
|
604 |
|
#ifdef IS_MPI |
605 |
|
if (worldRank == 0) { |
606 |
|
#endif // is_mpi |
607 |
|
|
608 |
< |
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 |
< |
} |
608 |
> |
eorStream = createOStream(eorFilename_); |
609 |
|
|
610 |
|
#ifdef IS_MPI |
611 |
|
} |
612 |
|
#endif // is_mpi |
613 |
|
|
614 |
< |
writeFrame(eorStream); |
606 |
< |
} |
614 |
> |
writeFrame(*eorStream); |
615 |
|
|
616 |
+ |
#ifdef IS_MPI |
617 |
+ |
if (worldRank == 0) { |
618 |
+ |
#endif // is_mpi |
619 |
+ |
delete eorStream; |
620 |
|
|
621 |
< |
void DumpWriter::writeDumpAndEor() { |
622 |
< |
std::ofstream eorStream; |
621 |
> |
#ifdef IS_MPI |
622 |
> |
} |
623 |
> |
#endif // is_mpi |
624 |
> |
|
625 |
> |
} |
626 |
> |
|
627 |
> |
|
628 |
> |
void DumpWriter::writeDumpAndEor() { |
629 |
|
std::vector<std::streambuf*> buffers; |
630 |
+ |
std::ostream* eorStream; |
631 |
|
#ifdef IS_MPI |
632 |
|
if (worldRank == 0) { |
633 |
|
#endif // is_mpi |
634 |
|
|
635 |
< |
buffers.push_back(dumpFile_.rdbuf()); |
635 |
> |
buffers.push_back(dumpFile_->rdbuf()); |
636 |
|
|
637 |
< |
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 |
< |
} |
637 |
> |
eorStream = createOStream(eorFilename_); |
638 |
|
|
639 |
< |
buffers.push_back(eorStream.rdbuf()); |
639 |
> |
buffers.push_back(eorStream->rdbuf()); |
640 |
|
|
641 |
|
#ifdef IS_MPI |
642 |
|
} |
646 |
|
std::ostream os(&tbuf); |
647 |
|
|
648 |
|
writeFrame(os); |
636 |
– |
|
637 |
– |
} |
649 |
|
|
650 |
+ |
#ifdef IS_MPI |
651 |
+ |
if (worldRank == 0) { |
652 |
+ |
#endif // is_mpi |
653 |
+ |
delete eorStream; |
654 |
|
|
655 |
+ |
#ifdef IS_MPI |
656 |
+ |
} |
657 |
+ |
#endif // is_mpi |
658 |
+ |
|
659 |
+ |
} |
660 |
|
|
661 |
+ |
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
662 |
+ |
std::ostream* newOStream; |
663 |
+ |
if (needCompression_) { |
664 |
+ |
newOStream = new ogzstream(filename.c_str()); |
665 |
+ |
} else { |
666 |
+ |
newOStream = new std::ofstream(filename.c_str()); |
667 |
+ |
} |
668 |
+ |
return newOStream; |
669 |
+ |
} |
670 |
+ |
|
671 |
|
}//end namespace oopse |