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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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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. 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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#include "io/DumpWriter.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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< |
namespace oopse { |
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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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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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|
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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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|
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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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os << " <FrameData>\n"; |
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|
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RealType currentTime = s->getTime(); |
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< |
sprintf(buffer, " Time: %.10g\n", time); |
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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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|
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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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|
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#ifndef IS_MPI |
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os << " <Snapshot>\n"; |
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< |
|
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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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< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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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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> |
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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> |
|
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os << " </Snapshot>\n"; |
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|
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os.flush(); |
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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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> |
|
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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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> |
buffer += prepareDumpLine(integrableObject); |
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} |
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} |
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|
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const int masterNode = 0; |
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< |
|
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> |
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 << buffer; |
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os << " <StuntDoubles>\n"; |
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|
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< |
int nProc; |
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< |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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> |
os << buffer; |
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> |
|
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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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> |
|
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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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– |
|
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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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> |
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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> |
delete [] recvBuffer; |
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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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os.flush(); |
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} else { |
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< |
int sendBufferLength = buffer.size(); |
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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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> |
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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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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< |
sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g", |
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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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> |
} |
| 390 |
> |
|
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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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Quat4d q; |
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|
Vector3d ji; |
| 400 |
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q = integrableObject->getQ(); |
| 401 |
+ |
|
| 402 |
+ |
if (isinf(q[0]) || isnan(q[0]) || |
| 403 |
+ |
isinf(q[1]) || isnan(q[1]) || |
| 404 |
+ |
isinf(q[2]) || isnan(q[2]) || |
| 405 |
+ |
isinf(q[3]) || isnan(q[3]) ) { |
| 406 |
+ |
sprintf( painCave.errMsg, |
| 407 |
+ |
"DumpWriter detected a numerical error writing the quaternion" |
| 408 |
+ |
" for object %d", index); |
| 409 |
+ |
painCave.isFatal = 1; |
| 410 |
+ |
simError(); |
| 411 |
+ |
} |
| 412 |
+ |
|
| 413 |
|
ji = integrableObject->getJ(); |
| 414 |
< |
sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g", |
| 414 |
> |
|
| 415 |
> |
if (isinf(ji[0]) || isnan(ji[0]) || |
| 416 |
> |
isinf(ji[1]) || isnan(ji[1]) || |
| 417 |
> |
isinf(ji[2]) || isnan(ji[2]) ) { |
| 418 |
> |
sprintf( painCave.errMsg, |
| 419 |
> |
"DumpWriter detected a numerical error writing the angular" |
| 420 |
> |
" momentum for object %d", index); |
| 421 |
> |
painCave.isFatal = 1; |
| 422 |
> |
simError(); |
| 423 |
> |
} |
| 424 |
> |
|
| 425 |
> |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
| 426 |
|
q[0], q[1], q[2], q[3], |
| 427 |
|
ji[0], ji[1], ji[2]); |
| 428 |
|
line += tempBuffer; |
| 429 |
|
} |
| 430 |
|
|
| 431 |
|
if (needForceVector_) { |
| 432 |
< |
type += "ft"; |
| 432 |
> |
type += "f"; |
| 433 |
|
Vector3d frc; |
| 434 |
< |
Vector3d trq; |
| 434 |
> |
|
| 435 |
|
frc = integrableObject->getFrc(); |
| 436 |
< |
trq = integrableObject->getTrq(); |
| 437 |
< |
|
| 438 |
< |
sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g", |
| 439 |
< |
frc[0], frc[1], frc[2], |
| 440 |
< |
trq[0], trq[1], trq[2]); |
| 436 |
> |
|
| 437 |
> |
if (isinf(frc[0]) || isnan(frc[0]) || |
| 438 |
> |
isinf(frc[1]) || isnan(frc[1]) || |
| 439 |
> |
isinf(frc[2]) || isnan(frc[2]) ) { |
| 440 |
> |
sprintf( painCave.errMsg, |
| 441 |
> |
"DumpWriter detected a numerical error writing the force" |
| 442 |
> |
" for object %d", index); |
| 443 |
> |
painCave.isFatal = 1; |
| 444 |
> |
simError(); |
| 445 |
> |
} |
| 446 |
> |
sprintf(tempBuffer, " %13e %13e %13e", |
| 447 |
> |
frc[0], frc[1], frc[2]); |
| 448 |
|
line += tempBuffer; |
| 449 |
+ |
|
| 450 |
+ |
if (integrableObject->isDirectional()) { |
| 451 |
+ |
type += "t"; |
| 452 |
+ |
Vector3d trq; |
| 453 |
+ |
|
| 454 |
+ |
trq = integrableObject->getTrq(); |
| 455 |
+ |
|
| 456 |
+ |
if (isinf(trq[0]) || isnan(trq[0]) || |
| 457 |
+ |
isinf(trq[1]) || isnan(trq[1]) || |
| 458 |
+ |
isinf(trq[2]) || isnan(trq[2]) ) { |
| 459 |
+ |
sprintf( painCave.errMsg, |
| 460 |
+ |
"DumpWriter detected a numerical error writing the torque" |
| 461 |
+ |
" for object %d", index); |
| 462 |
+ |
painCave.isFatal = 1; |
| 463 |
+ |
simError(); |
| 464 |
+ |
} |
| 465 |
+ |
|
| 466 |
+ |
sprintf(tempBuffer, " %13e %13e %13e", |
| 467 |
+ |
trq[0], trq[1], trq[2]); |
| 468 |
+ |
line += tempBuffer; |
| 469 |
+ |
} |
| 470 |
|
} |
| 471 |
< |
|
| 472 |
< |
sprintf(tempBuffer, "%d\t%s\t%s\n", index, type.c_str(), line.c_str()); |
| 471 |
> |
if (needParticlePot_) { |
| 472 |
> |
type += "u"; |
| 473 |
> |
RealType particlePot; |
| 474 |
> |
|
| 475 |
> |
particlePot = integrableObject->getParticlePot(); |
| 476 |
> |
|
| 477 |
> |
if (isinf(particlePot) || isnan(particlePot)) { |
| 478 |
> |
sprintf( painCave.errMsg, |
| 479 |
> |
"DumpWriter detected a numerical error writing the particle " |
| 480 |
> |
" potential for object %d", index); |
| 481 |
> |
painCave.isFatal = 1; |
| 482 |
> |
simError(); |
| 483 |
> |
} |
| 484 |
> |
sprintf(tempBuffer, " %13e", particlePot); |
| 485 |
> |
line += tempBuffer; |
| 486 |
> |
} |
| 487 |
> |
|
| 488 |
> |
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 489 |
|
return std::string(tempBuffer); |
| 490 |
|
} |
| 491 |
|
|
| 566 |
|
newOStream = new std::ofstream(filename.c_str()); |
| 567 |
|
#endif |
| 568 |
|
//write out MetaData first |
| 569 |
< |
(*newOStream) << "<OOPSE version=4>" << std::endl; |
| 569 |
> |
(*newOStream) << "<OpenMD version=1>" << std::endl; |
| 570 |
|
(*newOStream) << " <MetaData>" << std::endl; |
| 571 |
|
(*newOStream) << info_->getRawMetaData(); |
| 572 |
|
(*newOStream) << " </MetaData>" << std::endl; |
| 575 |
|
|
| 576 |
|
void DumpWriter::writeClosing(std::ostream& os) { |
| 577 |
|
|
| 578 |
< |
os << "</OOPSE>\n"; |
| 578 |
> |
os << "</OpenMD>\n"; |
| 579 |
|
os.flush(); |
| 580 |
|
} |
| 581 |
|
|
| 582 |
< |
}//end namespace oopse |
| 582 |
> |
}//end namespace OpenMD |
