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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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#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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#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_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
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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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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
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|
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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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dumpFile_.close(); |
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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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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_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++) { |
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|
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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); |
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|
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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]; |
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|
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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++) { |
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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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|
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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, |
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&istatus); |
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|
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atomTypeString = MPIatomTypeString; |
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|
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myPotato++; |
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|
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MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
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MPI_COMM_WORLD, &istatus); |
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myPotato++; |
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|
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MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
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|
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if (msgLen == 13) |
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isDirectional = 1; |
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else |
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isDirectional = 0; |
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|
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// If we've survived to here, format the line: |
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|
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if (!isDirectional) { |
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sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atomTypeString, atomData[0], |
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atomData[1], atomData[2], |
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atomData[3], atomData[4], |
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atomData[5]); |
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|
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strcat(writeLine, |
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"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
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} else { |
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sprintf(writeLine, |
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"%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", |
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atomTypeString, |
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atomData[0], |
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atomData[1], |
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atomData[2], |
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atomData[3], |
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atomData[4], |
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atomData[5], |
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atomData[6], |
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atomData[7], |
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atomData[8], |
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atomData[9], |
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atomData[10], |
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atomData[11], |
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atomData[12]); |
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} |
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|
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os << writeLine; |
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|
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} // end for(int l =0) |
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|
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potatoes[which_node] = myPotato; |
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} else { //master node has current molecule |
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|
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mol = info_->getMoleculeByGlobalIndex(i); |
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|
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if (mol == NULL) { |
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sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
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painCave.isFatal = 1; |
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simError(); |
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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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|
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atomTypeString = integrableObject->getType().c_str(); |
| 397 |
|
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pos = integrableObject->getPos(); |
| 399 |
vel = integrableObject->getVel(); |
| 400 |
|
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atomData[0] = pos[0]; |
| 402 |
atomData[1] = pos[1]; |
| 403 |
atomData[2] = pos[2]; |
| 404 |
|
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atomData[3] = vel[0]; |
| 406 |
atomData[4] = vel[1]; |
| 407 |
atomData[5] = vel[2]; |
| 408 |
|
| 409 |
isDirectional = 0; |
| 410 |
|
| 411 |
if (integrableObject->isDirectional()) { |
| 412 |
isDirectional = 1; |
| 413 |
|
| 414 |
q = integrableObject->getQ(); |
| 415 |
ji = integrableObject->getJ(); |
| 416 |
|
| 417 |
for(int j = 0; j < 6; j++) { |
| 418 |
atomData[j] = atomData[j]; |
| 419 |
} |
| 420 |
|
| 421 |
atomData[6] = q[0]; |
| 422 |
atomData[7] = q[1]; |
| 423 |
atomData[8] = q[2]; |
| 424 |
atomData[9] = q[3]; |
| 425 |
|
| 426 |
atomData[10] = ji[0]; |
| 427 |
atomData[11] = ji[1]; |
| 428 |
atomData[12] = ji[2]; |
| 429 |
} |
| 430 |
|
| 431 |
// If we've survived to here, format the line: |
| 432 |
|
| 433 |
if (!isDirectional) { |
| 434 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 435 |
atomTypeString, atomData[0], |
| 436 |
atomData[1], atomData[2], |
| 437 |
atomData[3], atomData[4], |
| 438 |
atomData[5]); |
| 439 |
|
| 440 |
strcat(writeLine, |
| 441 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 442 |
} else { |
| 443 |
sprintf(writeLine, |
| 444 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 445 |
atomTypeString, |
| 446 |
atomData[0], |
| 447 |
atomData[1], |
| 448 |
atomData[2], |
| 449 |
atomData[3], |
| 450 |
atomData[4], |
| 451 |
atomData[5], |
| 452 |
atomData[6], |
| 453 |
atomData[7], |
| 454 |
atomData[8], |
| 455 |
atomData[9], |
| 456 |
atomData[10], |
| 457 |
atomData[11], |
| 458 |
atomData[12]); |
| 459 |
} |
| 460 |
|
| 461 |
|
| 462 |
os << writeLine; |
| 463 |
|
| 464 |
} //end for(iter = integrableObject.begin()) |
| 465 |
} |
| 466 |
} //end for(i = 0; i < mpiSim->getNmol()) |
| 467 |
|
| 468 |
os.flush(); |
| 469 |
|
| 470 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 471 |
MPIcheckPoint(); |
| 472 |
|
| 473 |
delete [] potatoes; |
| 474 |
} else { |
| 475 |
|
| 476 |
// worldRank != 0, so I'm a remote node. |
| 477 |
|
| 478 |
// Set my magic potato to 0: |
| 479 |
|
| 480 |
myPotato = 0; |
| 481 |
|
| 482 |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 483 |
|
| 484 |
// Am I the node which has this integrableObject? |
| 485 |
int whichNode = info_->getMolToProc(i); |
| 486 |
if (whichNode == worldRank) { |
| 487 |
if (myPotato + 1 >= MAXTAG) { |
| 488 |
|
| 489 |
// The potato was going to exceed the maximum value, |
| 490 |
// so wrap this processor potato back to 0 (and block until |
| 491 |
// node 0 says we can go: |
| 492 |
|
| 493 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 494 |
&istatus); |
| 495 |
} |
| 496 |
|
| 497 |
mol = info_->getMoleculeByGlobalIndex(i); |
| 498 |
|
| 499 |
|
| 500 |
nCurObj = mol->getNIntegrableObjects(); |
| 501 |
|
| 502 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
| 503 |
myPotato++; |
| 504 |
|
| 505 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 506 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 507 |
|
| 508 |
if (myPotato + 2 >= MAXTAG) { |
| 509 |
|
| 510 |
// The potato was going to exceed the maximum value, |
| 511 |
// so wrap this processor potato back to 0 (and block until |
| 512 |
// node 0 says we can go: |
| 513 |
|
| 514 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 515 |
&istatus); |
| 516 |
} |
| 517 |
|
| 518 |
atomTypeString = integrableObject->getType().c_str(); |
| 519 |
|
| 520 |
pos = integrableObject->getPos(); |
| 521 |
vel = integrableObject->getVel(); |
| 522 |
|
| 523 |
atomData[0] = pos[0]; |
| 524 |
atomData[1] = pos[1]; |
| 525 |
atomData[2] = pos[2]; |
| 526 |
|
| 527 |
atomData[3] = vel[0]; |
| 528 |
atomData[4] = vel[1]; |
| 529 |
atomData[5] = vel[2]; |
| 530 |
|
| 531 |
isDirectional = 0; |
| 532 |
|
| 533 |
if (integrableObject->isDirectional()) { |
| 534 |
isDirectional = 1; |
| 535 |
|
| 536 |
q = integrableObject->getQ(); |
| 537 |
ji = integrableObject->getJ(); |
| 538 |
|
| 539 |
atomData[6] = q[0]; |
| 540 |
atomData[7] = q[1]; |
| 541 |
atomData[8] = q[2]; |
| 542 |
atomData[9] = q[3]; |
| 543 |
|
| 544 |
atomData[10] = ji[0]; |
| 545 |
atomData[11] = ji[1]; |
| 546 |
atomData[12] = ji[2]; |
| 547 |
} |
| 548 |
|
| 549 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 550 |
|
| 551 |
// null terminate the std::string before sending (just in case): |
| 552 |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
| 553 |
|
| 554 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 555 |
myPotato, MPI_COMM_WORLD); |
| 556 |
|
| 557 |
myPotato++; |
| 558 |
|
| 559 |
if (isDirectional) { |
| 560 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
| 561 |
MPI_COMM_WORLD); |
| 562 |
} else { |
| 563 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
| 564 |
MPI_COMM_WORLD); |
| 565 |
} |
| 566 |
|
| 567 |
myPotato++; |
| 568 |
} |
| 569 |
|
| 570 |
} |
| 571 |
|
| 572 |
} |
| 573 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 574 |
MPIcheckPoint(); |
| 575 |
} |
| 576 |
|
| 577 |
#endif // is_mpi |
| 578 |
|
| 579 |
} |
| 580 |
|
| 581 |
void DumpWriter::writeDump() { |
| 582 |
writeFrame(dumpFile_); |
| 583 |
|
| 584 |
} |
| 585 |
|
| 586 |
void DumpWriter::writeEor() { |
| 587 |
std::ofstream eorStream; |
| 588 |
|
| 589 |
#ifdef IS_MPI |
| 590 |
if (worldRank == 0) { |
| 591 |
#endif // is_mpi |
| 592 |
|
| 593 |
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 |
} |
| 600 |
|
| 601 |
#ifdef IS_MPI |
| 602 |
} |
| 603 |
#endif // is_mpi |
| 604 |
|
| 605 |
writeFrame(eorStream); |
| 606 |
} |
| 607 |
|
| 608 |
|
| 609 |
void DumpWriter::writeDumpAndEor() { |
| 610 |
std::ofstream eorStream; |
| 611 |
std::vector<std::streambuf*> buffers; |
| 612 |
#ifdef IS_MPI |
| 613 |
if (worldRank == 0) { |
| 614 |
#endif // is_mpi |
| 615 |
|
| 616 |
buffers.push_back(dumpFile_.rdbuf()); |
| 617 |
|
| 618 |
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 |
} |
| 625 |
|
| 626 |
buffers.push_back(eorStream.rdbuf()); |
| 627 |
|
| 628 |
#ifdef IS_MPI |
| 629 |
} |
| 630 |
#endif // is_mpi |
| 631 |
|
| 632 |
TeeBuf tbuf(buffers.begin(), buffers.end()); |
| 633 |
std::ostream os(&tbuf); |
| 634 |
|
| 635 |
writeFrame(os); |
| 636 |
|
| 637 |
} |
| 638 |
|
| 639 |
|
| 640 |
|
| 641 |
}//end namespace oopse |
