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/* |
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* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. 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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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "io/DumpWriter.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_teebuf.hpp" |
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#include "io/gzstream.hpp" |
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#include "io/Globals.hpp" |
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|
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|
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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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using namespace std; |
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namespace OpenMD { |
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|
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DumpWriter::DumpWriter(SimInfo* info) |
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: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
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|
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Globals* simParams = info->getSimParams(); |
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needCompression_ = simParams->getCompressDumpFile(); |
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needForceVector_ = simParams->getOutputForceVector(); |
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needParticlePot_ = simParams->getOutputParticlePotential(); |
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createDumpFile_ = true; |
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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#endif |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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dumpFile_ = createOStream(filename_); |
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|
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if (!dumpFile_) { |
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sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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#endif // is_mpi |
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|
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} |
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|
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|
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DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
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: info_(info), filename_(filename){ |
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|
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Globals* simParams = info->getSimParams(); |
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eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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|
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needCompression_ = simParams->getCompressDumpFile(); |
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needForceVector_ = simParams->getOutputForceVector(); |
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createDumpFile_ = true; |
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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#endif |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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|
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dumpFile_ = createOStream(filename_); |
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|
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if (!dumpFile_) { |
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sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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#endif // is_mpi |
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|
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} |
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|
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DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) |
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: info_(info), filename_(filename){ |
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|
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Globals* simParams = info->getSimParams(); |
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eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
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|
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needCompression_ = simParams->getCompressDumpFile(); |
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needForceVector_ = simParams->getOutputForceVector(); |
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needParticlePot_ = simParams->getOutputParticlePotential(); |
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|
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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#endif |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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createDumpFile_ = writeDumpFile; |
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if (createDumpFile_) { |
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dumpFile_ = createOStream(filename_); |
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|
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if (!dumpFile_) { |
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sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#ifdef IS_MPI |
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|
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} |
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|
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|
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#endif // is_mpi |
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|
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} |
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|
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DumpWriter::~DumpWriter() { |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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if (createDumpFile_){ |
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writeClosing(*dumpFile_); |
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delete dumpFile_; |
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} |
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#ifdef IS_MPI |
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|
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} |
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|
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#endif // is_mpi |
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|
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} |
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|
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void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { |
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|
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char buffer[1024]; |
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|
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os << " <FrameData>\n"; |
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|
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RealType currentTime = s->getTime(); |
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|
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if (isinf(currentTime) || isnan(currentTime)) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the time"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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sprintf(buffer, " Time: %.10g\n", currentTime); |
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os << buffer; |
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|
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Mat3x3d hmat; |
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hmat = s->getHmat(); |
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|
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for (unsigned int i = 0; i < 3; i++) { |
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for (unsigned int j = 0; j < 3; j++) { |
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if (isinf(hmat(i,j)) || isnan(hmat(i,j))) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the box"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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|
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sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
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hmat(0, 0), hmat(1, 0), hmat(2, 0), |
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hmat(0, 1), hmat(1, 1), hmat(2, 1), |
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hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
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os << buffer; |
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|
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RealType chi = s->getChi(); |
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RealType integralOfChiDt = s->getIntegralOfChiDt(); |
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if (isinf(chi) || isnan(chi) || |
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isinf(integralOfChiDt) || isnan(integralOfChiDt)) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the thermostat"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
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os << buffer; |
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|
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Mat3x3d eta; |
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eta = s->getEta(); |
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|
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for (unsigned int i = 0; i < 3; i++) { |
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for (unsigned int j = 0; j < 3; j++) { |
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if (isinf(eta(i,j)) || isnan(eta(i,j))) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the barostat"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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|
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sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
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eta(0, 0), eta(1, 0), eta(2, 0), |
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eta(0, 1), eta(1, 1), eta(2, 1), |
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eta(0, 2), eta(1, 2), eta(2, 2)); |
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os << buffer; |
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|
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os << " </FrameData>\n"; |
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} |
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|
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void DumpWriter::writeFrame(std::ostream& os) { |
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|
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#ifdef IS_MPI |
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MPI_Status istatus; |
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#endif |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ii; |
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|
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#ifndef IS_MPI |
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os << " <Snapshot>\n"; |
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|
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writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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os << " <StuntDoubles>\n"; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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os << prepareDumpLine(integrableObject); |
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|
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} |
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} |
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os << " </StuntDoubles>\n"; |
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|
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os << " </Snapshot>\n"; |
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|
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os.flush(); |
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#else |
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//every node prepares the dump lines for integrable objects belong to itself |
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std::string buffer; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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buffer += prepareDumpLine(integrableObject); |
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} |
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} |
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|
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const int masterNode = 0; |
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int nProc; |
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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if (worldRank == masterNode) { |
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os << " <Snapshot>\n"; |
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writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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os << " <StuntDoubles>\n"; |
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|
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os << buffer; |
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|
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for (int i = 1; i < nProc; ++i) { |
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|
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// receive the length of the string buffer that was |
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// prepared by processor i |
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|
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MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD); |
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int recvLength; |
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MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
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char* recvBuffer = new char[recvLength]; |
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if (recvBuffer == NULL) { |
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} else { |
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MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
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os << recvBuffer; |
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delete [] recvBuffer; |
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} |
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} |
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os << " </StuntDoubles>\n"; |
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|
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os << " </Snapshot>\n"; |
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os.flush(); |
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} else { |
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int sendBufferLength = buffer.size() + 1; |
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int myturn = 0; |
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for (int i = 1; i < nProc; ++i){ |
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MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD); |
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if (myturn == worldRank){ |
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MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
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MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
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} |
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} |
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} |
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|
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#endif // is_mpi |
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|
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} |
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|
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std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
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|
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int index = integrableObject->getGlobalIntegrableObjectIndex(); |
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std::string type("pv"); |
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std::string line; |
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char tempBuffer[4096]; |
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|
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Vector3d pos; |
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Vector3d vel; |
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pos = integrableObject->getPos(); |
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|
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if (isinf(pos[0]) || isnan(pos[0]) || |
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isinf(pos[1]) || isnan(pos[1]) || |
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isinf(pos[2]) || isnan(pos[2]) ) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the position" |
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" for object %d", index); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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vel = integrableObject->getVel(); |
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|
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if (isinf(vel[0]) || isnan(vel[0]) || |
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isinf(vel[1]) || isnan(vel[1]) || |
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isinf(vel[2]) || isnan(vel[2]) ) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the velocity" |
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" for object %d", index); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
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pos[0], pos[1], pos[2], |
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vel[0], vel[1], vel[2]); |
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line += tempBuffer; |
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|
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if (integrableObject->isDirectional()) { |
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type += "qj"; |
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Quat4d q; |
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Vector3d ji; |
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q = integrableObject->getQ(); |
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|
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if (isinf(q[0]) || isnan(q[0]) || |
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isinf(q[1]) || isnan(q[1]) || |
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isinf(q[2]) || isnan(q[2]) || |
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isinf(q[3]) || isnan(q[3]) ) { |
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sprintf( painCave.errMsg, |
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"DumpWriter detected a numerical error writing the quaternion" |
| 406 |
" for object %d", index); |
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painCave.isFatal = 1; |
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simError(); |
| 409 |
} |
| 410 |
|
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ji = integrableObject->getJ(); |
| 412 |
|
| 413 |
if (isinf(ji[0]) || isnan(ji[0]) || |
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isinf(ji[1]) || isnan(ji[1]) || |
| 415 |
isinf(ji[2]) || isnan(ji[2]) ) { |
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sprintf( painCave.errMsg, |
| 417 |
"DumpWriter detected a numerical error writing the angular" |
| 418 |
" momentum for object %d", index); |
| 419 |
painCave.isFatal = 1; |
| 420 |
simError(); |
| 421 |
} |
| 422 |
|
| 423 |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
| 424 |
q[0], q[1], q[2], q[3], |
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ji[0], ji[1], ji[2]); |
| 426 |
line += tempBuffer; |
| 427 |
} |
| 428 |
|
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if (needForceVector_) { |
| 430 |
type += "f"; |
| 431 |
Vector3d frc; |
| 432 |
|
| 433 |
frc = integrableObject->getFrc(); |
| 434 |
|
| 435 |
if (isinf(frc[0]) || isnan(frc[0]) || |
| 436 |
isinf(frc[1]) || isnan(frc[1]) || |
| 437 |
isinf(frc[2]) || isnan(frc[2]) ) { |
| 438 |
sprintf( painCave.errMsg, |
| 439 |
"DumpWriter detected a numerical error writing the force" |
| 440 |
" for object %d", index); |
| 441 |
painCave.isFatal = 1; |
| 442 |
simError(); |
| 443 |
} |
| 444 |
sprintf(tempBuffer, " %13e %13e %13e", |
| 445 |
frc[0], frc[1], frc[2]); |
| 446 |
line += tempBuffer; |
| 447 |
|
| 448 |
if (integrableObject->isDirectional()) { |
| 449 |
type += "t"; |
| 450 |
Vector3d trq; |
| 451 |
|
| 452 |
trq = integrableObject->getTrq(); |
| 453 |
|
| 454 |
if (isinf(trq[0]) || isnan(trq[0]) || |
| 455 |
isinf(trq[1]) || isnan(trq[1]) || |
| 456 |
isinf(trq[2]) || isnan(trq[2]) ) { |
| 457 |
sprintf( painCave.errMsg, |
| 458 |
"DumpWriter detected a numerical error writing the torque" |
| 459 |
" for object %d", index); |
| 460 |
painCave.isFatal = 1; |
| 461 |
simError(); |
| 462 |
} |
| 463 |
|
| 464 |
sprintf(tempBuffer, " %13e %13e %13e", |
| 465 |
trq[0], trq[1], trq[2]); |
| 466 |
line += tempBuffer; |
| 467 |
} |
| 468 |
} |
| 469 |
if (needParticlePot_) { |
| 470 |
type += "u"; |
| 471 |
RealType particlePot; |
| 472 |
|
| 473 |
particlePot = integrableObject->getParticlePot(); |
| 474 |
|
| 475 |
if (isinf(particlePot) || isnan(particlePot)) { |
| 476 |
sprintf( painCave.errMsg, |
| 477 |
"DumpWriter detected a numerical error writing the particle " |
| 478 |
" potential for object %d", index); |
| 479 |
painCave.isFatal = 1; |
| 480 |
simError(); |
| 481 |
} |
| 482 |
sprintf(tempBuffer, " %13e", particlePot); |
| 483 |
line += tempBuffer; |
| 484 |
} |
| 485 |
|
| 486 |
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 487 |
return std::string(tempBuffer); |
| 488 |
} |
| 489 |
|
| 490 |
void DumpWriter::writeDump() { |
| 491 |
writeFrame(*dumpFile_); |
| 492 |
} |
| 493 |
|
| 494 |
void DumpWriter::writeEor() { |
| 495 |
std::ostream* eorStream; |
| 496 |
|
| 497 |
#ifdef IS_MPI |
| 498 |
if (worldRank == 0) { |
| 499 |
#endif // is_mpi |
| 500 |
|
| 501 |
eorStream = createOStream(eorFilename_); |
| 502 |
|
| 503 |
#ifdef IS_MPI |
| 504 |
} |
| 505 |
#endif // is_mpi |
| 506 |
|
| 507 |
writeFrame(*eorStream); |
| 508 |
|
| 509 |
#ifdef IS_MPI |
| 510 |
if (worldRank == 0) { |
| 511 |
#endif // is_mpi |
| 512 |
writeClosing(*eorStream); |
| 513 |
delete eorStream; |
| 514 |
#ifdef IS_MPI |
| 515 |
} |
| 516 |
#endif // is_mpi |
| 517 |
|
| 518 |
} |
| 519 |
|
| 520 |
|
| 521 |
void DumpWriter::writeDumpAndEor() { |
| 522 |
std::vector<std::streambuf*> buffers; |
| 523 |
std::ostream* eorStream; |
| 524 |
#ifdef IS_MPI |
| 525 |
if (worldRank == 0) { |
| 526 |
#endif // is_mpi |
| 527 |
|
| 528 |
buffers.push_back(dumpFile_->rdbuf()); |
| 529 |
|
| 530 |
eorStream = createOStream(eorFilename_); |
| 531 |
|
| 532 |
buffers.push_back(eorStream->rdbuf()); |
| 533 |
|
| 534 |
#ifdef IS_MPI |
| 535 |
} |
| 536 |
#endif // is_mpi |
| 537 |
|
| 538 |
TeeBuf tbuf(buffers.begin(), buffers.end()); |
| 539 |
std::ostream os(&tbuf); |
| 540 |
|
| 541 |
writeFrame(os); |
| 542 |
|
| 543 |
#ifdef IS_MPI |
| 544 |
if (worldRank == 0) { |
| 545 |
#endif // is_mpi |
| 546 |
writeClosing(*eorStream); |
| 547 |
delete eorStream; |
| 548 |
#ifdef IS_MPI |
| 549 |
} |
| 550 |
#endif // is_mpi |
| 551 |
|
| 552 |
} |
| 553 |
|
| 554 |
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
| 555 |
|
| 556 |
std::ostream* newOStream; |
| 557 |
#ifdef HAVE_LIBZ |
| 558 |
if (needCompression_) { |
| 559 |
newOStream = new ogzstream(filename.c_str()); |
| 560 |
} else { |
| 561 |
newOStream = new std::ofstream(filename.c_str()); |
| 562 |
} |
| 563 |
#else |
| 564 |
newOStream = new std::ofstream(filename.c_str()); |
| 565 |
#endif |
| 566 |
//write out MetaData first |
| 567 |
(*newOStream) << "<OpenMD version=1>" << std::endl; |
| 568 |
(*newOStream) << " <MetaData>" << std::endl; |
| 569 |
(*newOStream) << info_->getRawMetaData(); |
| 570 |
(*newOStream) << " </MetaData>" << std::endl; |
| 571 |
return newOStream; |
| 572 |
} |
| 573 |
|
| 574 |
void DumpWriter::writeClosing(std::ostream& os) { |
| 575 |
|
| 576 |
os << "</OpenMD>\n"; |
| 577 |
os.flush(); |
| 578 |
} |
| 579 |
|
| 580 |
}//end namespace OpenMD |
