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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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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 HAVE_ZLIB |
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#include "io/gzstream.hpp" |
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+ |
#endif |
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#include "io/Globals.hpp" |
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|
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+ |
#ifdef _MSC_VER |
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#define isnan(x) _isnan((x)) |
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+ |
#define isinf(x) (!_finite(x) && !_isnan(x)) |
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+ |
#endif |
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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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> |
#endif |
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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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|
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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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> |
needCompression_ = simParams->getCompressDumpFile(); |
| 69 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 70 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 71 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 72 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
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> |
|
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> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
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> |
doSiteData_ = true; |
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> |
} else { |
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> |
doSiteData_ = false; |
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> |
} |
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> |
|
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createDumpFile_ = true; |
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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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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> |
needCompression_ = simParams->getCompressDumpFile(); |
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> |
needForceVector_ = simParams->getOutputForceVector(); |
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> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
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> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
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> |
needElectricField_ = simParams->getOutputElectricField(); |
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> |
|
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> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
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doSiteData_ = true; |
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> |
} else { |
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> |
doSiteData_ = false; |
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> |
} |
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> |
|
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createDumpFile_ = true; |
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#ifdef HAVE_LIBZ |
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if (needCompression_) { |
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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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< |
|
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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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> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
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> |
needElectricField_ = simParams->getOutputElectricField(); |
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> |
|
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> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
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> |
doSiteData_ = true; |
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> |
} else { |
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> |
doSiteData_ = false; |
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> |
} |
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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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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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+ |
} |
| 257 |
+ |
} |
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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(); |
| 267 |
< |
RealType integralOfChiDt = s->getIntegralOfChiDt(); |
| 268 |
< |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
| 266 |
> |
pair<RealType, RealType> thermostat = s->getThermostat(); |
| 267 |
> |
|
| 268 |
> |
if (isinf(thermostat.first) || isnan(thermostat.first) || |
| 269 |
> |
isinf(thermostat.second) || isnan(thermostat.second)) { |
| 270 |
> |
sprintf( painCave.errMsg, |
| 271 |
> |
"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", thermostat.first, |
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> |
thermostat.second); |
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os << buffer; |
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|
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Mat3x3d eta; |
| 280 |
< |
eta = s->getEta(); |
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> |
eta = s->getBarostat(); |
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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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StuntDouble* integrableObject; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ii; |
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+ |
RigidBody::AtomIterator ai; |
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+ |
Atom* atom; |
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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; |
| 323 |
> |
|
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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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< |
|
| 326 |
> |
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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+ |
if (doSiteData_) { |
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+ |
os << " <SiteData>\n"; |
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+ |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 335 |
+ |
|
| 336 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 337 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 338 |
+ |
|
| 339 |
+ |
int ioIndex = integrableObject->getGlobalIntegrableObjectIndex(); |
| 340 |
+ |
// do one for the IO itself |
| 341 |
+ |
os << prepareSiteLine(integrableObject, ioIndex, 0); |
| 342 |
+ |
|
| 343 |
+ |
if (integrableObject->isRigidBody()) { |
| 344 |
+ |
|
| 345 |
+ |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 346 |
+ |
int siteIndex = 0; |
| 347 |
+ |
for (atom = rb->beginAtom(ai); atom != NULL; |
| 348 |
+ |
atom = rb->nextAtom(ai)) { |
| 349 |
+ |
os << prepareSiteLine(atom, ioIndex, siteIndex); |
| 350 |
+ |
siteIndex++; |
| 351 |
+ |
} |
| 352 |
+ |
} |
| 353 |
+ |
} |
| 354 |
+ |
} |
| 355 |
+ |
os << " </SiteData>\n"; |
| 356 |
+ |
} |
| 357 |
|
os << " </Snapshot>\n"; |
| 358 |
|
|
| 359 |
|
os.flush(); |
| 361 |
|
//every node prepares the dump lines for integrable objects belong to itself |
| 362 |
|
std::string buffer; |
| 363 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 364 |
< |
|
| 364 |
> |
|
| 365 |
> |
|
| 366 |
|
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 367 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
| 368 |
< |
buffer += prepareDumpLine(integrableObject); |
| 368 |
> |
buffer += prepareDumpLine(integrableObject); |
| 369 |
|
} |
| 370 |
|
} |
| 371 |
|
|
| 372 |
|
const int masterNode = 0; |
| 373 |
< |
|
| 373 |
> |
int nProc; |
| 374 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 375 |
|
if (worldRank == masterNode) { |
| 376 |
|
os << " <Snapshot>\n"; |
| 377 |
|
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 270 |
– |
os << buffer; |
| 378 |
|
os << " <StuntDoubles>\n"; |
| 379 |
|
|
| 380 |
< |
int nProc; |
| 381 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 380 |
> |
os << buffer; |
| 381 |
> |
|
| 382 |
|
for (int i = 1; i < nProc; ++i) { |
| 383 |
|
|
| 384 |
|
// receive the length of the string buffer that was |
| 385 |
|
// prepared by processor i |
| 386 |
|
|
| 387 |
+ |
MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD); |
| 388 |
|
int recvLength; |
| 389 |
|
MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
| 390 |
|
char* recvBuffer = new char[recvLength]; |
| 391 |
|
if (recvBuffer == NULL) { |
| 284 |
– |
|
| 392 |
|
} else { |
| 393 |
< |
MPI_Recv(&recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
| 393 |
> |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
| 394 |
|
os << recvBuffer; |
| 395 |
< |
delete recvBuffer; |
| 395 |
> |
delete [] recvBuffer; |
| 396 |
|
} |
| 290 |
– |
|
| 397 |
|
} |
| 398 |
|
os << " </StuntDoubles>\n"; |
| 399 |
|
|
| 400 |
|
os << " </Snapshot>\n"; |
| 401 |
|
os.flush(); |
| 402 |
|
} else { |
| 403 |
< |
int sendBufferLength = buffer.size(); |
| 404 |
< |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 405 |
< |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 403 |
> |
int sendBufferLength = buffer.size() + 1; |
| 404 |
> |
int myturn = 0; |
| 405 |
> |
for (int i = 1; i < nProc; ++i){ |
| 406 |
> |
MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD); |
| 407 |
> |
if (myturn == worldRank){ |
| 408 |
> |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 409 |
> |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 410 |
> |
} |
| 411 |
> |
} |
| 412 |
|
} |
| 413 |
|
|
| 414 |
|
#endif // is_mpi |
| 425 |
|
Vector3d pos; |
| 426 |
|
Vector3d vel; |
| 427 |
|
pos = integrableObject->getPos(); |
| 428 |
+ |
|
| 429 |
+ |
if (isinf(pos[0]) || isnan(pos[0]) || |
| 430 |
+ |
isinf(pos[1]) || isnan(pos[1]) || |
| 431 |
+ |
isinf(pos[2]) || isnan(pos[2]) ) { |
| 432 |
+ |
sprintf( painCave.errMsg, |
| 433 |
+ |
"DumpWriter detected a numerical error writing the position" |
| 434 |
+ |
" for object %d", index); |
| 435 |
+ |
painCave.isFatal = 1; |
| 436 |
+ |
simError(); |
| 437 |
+ |
} |
| 438 |
+ |
|
| 439 |
|
vel = integrableObject->getVel(); |
| 440 |
< |
sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g", |
| 440 |
> |
|
| 441 |
> |
if (isinf(vel[0]) || isnan(vel[0]) || |
| 442 |
> |
isinf(vel[1]) || isnan(vel[1]) || |
| 443 |
> |
isinf(vel[2]) || isnan(vel[2]) ) { |
| 444 |
> |
sprintf( painCave.errMsg, |
| 445 |
> |
"DumpWriter detected a numerical error writing the velocity" |
| 446 |
> |
" for object %d", index); |
| 447 |
> |
painCave.isFatal = 1; |
| 448 |
> |
simError(); |
| 449 |
> |
} |
| 450 |
> |
|
| 451 |
> |
sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
| 452 |
|
pos[0], pos[1], pos[2], |
| 453 |
|
vel[0], vel[1], vel[2]); |
| 454 |
|
line += tempBuffer; |
| 458 |
|
Quat4d q; |
| 459 |
|
Vector3d ji; |
| 460 |
|
q = integrableObject->getQ(); |
| 461 |
+ |
|
| 462 |
+ |
if (isinf(q[0]) || isnan(q[0]) || |
| 463 |
+ |
isinf(q[1]) || isnan(q[1]) || |
| 464 |
+ |
isinf(q[2]) || isnan(q[2]) || |
| 465 |
+ |
isinf(q[3]) || isnan(q[3]) ) { |
| 466 |
+ |
sprintf( painCave.errMsg, |
| 467 |
+ |
"DumpWriter detected a numerical error writing the quaternion" |
| 468 |
+ |
" for object %d", index); |
| 469 |
+ |
painCave.isFatal = 1; |
| 470 |
+ |
simError(); |
| 471 |
+ |
} |
| 472 |
+ |
|
| 473 |
|
ji = integrableObject->getJ(); |
| 474 |
< |
sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g", |
| 474 |
> |
|
| 475 |
> |
if (isinf(ji[0]) || isnan(ji[0]) || |
| 476 |
> |
isinf(ji[1]) || isnan(ji[1]) || |
| 477 |
> |
isinf(ji[2]) || isnan(ji[2]) ) { |
| 478 |
> |
sprintf( painCave.errMsg, |
| 479 |
> |
"DumpWriter detected a numerical error writing the angular" |
| 480 |
> |
" momentum for object %d", index); |
| 481 |
> |
painCave.isFatal = 1; |
| 482 |
> |
simError(); |
| 483 |
> |
} |
| 484 |
> |
|
| 485 |
> |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
| 486 |
|
q[0], q[1], q[2], q[3], |
| 487 |
|
ji[0], ji[1], ji[2]); |
| 488 |
|
line += tempBuffer; |
| 489 |
|
} |
| 490 |
|
|
| 491 |
|
if (needForceVector_) { |
| 492 |
< |
type += "ft"; |
| 493 |
< |
Vector3d frc; |
| 494 |
< |
Vector3d trq; |
| 495 |
< |
frc = integrableObject->getFrc(); |
| 496 |
< |
trq = integrableObject->getTrq(); |
| 497 |
< |
|
| 498 |
< |
sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g", |
| 499 |
< |
frc[0], frc[1], frc[2], |
| 500 |
< |
trq[0], trq[1], trq[2]); |
| 492 |
> |
type += "f"; |
| 493 |
> |
Vector3d frc = integrableObject->getFrc(); |
| 494 |
> |
if (isinf(frc[0]) || isnan(frc[0]) || |
| 495 |
> |
isinf(frc[1]) || isnan(frc[1]) || |
| 496 |
> |
isinf(frc[2]) || isnan(frc[2]) ) { |
| 497 |
> |
sprintf( painCave.errMsg, |
| 498 |
> |
"DumpWriter detected a numerical error writing the force" |
| 499 |
> |
" for object %d", index); |
| 500 |
> |
painCave.isFatal = 1; |
| 501 |
> |
simError(); |
| 502 |
> |
} |
| 503 |
> |
sprintf(tempBuffer, " %13e %13e %13e", |
| 504 |
> |
frc[0], frc[1], frc[2]); |
| 505 |
|
line += tempBuffer; |
| 506 |
+ |
|
| 507 |
+ |
if (integrableObject->isDirectional()) { |
| 508 |
+ |
type += "t"; |
| 509 |
+ |
Vector3d trq = integrableObject->getTrq(); |
| 510 |
+ |
if (isinf(trq[0]) || isnan(trq[0]) || |
| 511 |
+ |
isinf(trq[1]) || isnan(trq[1]) || |
| 512 |
+ |
isinf(trq[2]) || isnan(trq[2]) ) { |
| 513 |
+ |
sprintf( painCave.errMsg, |
| 514 |
+ |
"DumpWriter detected a numerical error writing the torque" |
| 515 |
+ |
" for object %d", index); |
| 516 |
+ |
painCave.isFatal = 1; |
| 517 |
+ |
simError(); |
| 518 |
+ |
} |
| 519 |
+ |
sprintf(tempBuffer, " %13e %13e %13e", |
| 520 |
+ |
trq[0], trq[1], trq[2]); |
| 521 |
+ |
line += tempBuffer; |
| 522 |
+ |
} |
| 523 |
|
} |
| 524 |
+ |
|
| 525 |
+ |
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 526 |
+ |
return std::string(tempBuffer); |
| 527 |
+ |
} |
| 528 |
+ |
|
| 529 |
+ |
std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) { |
| 530 |
|
|
| 531 |
< |
sprintf(tempBuffer, "%d\t%s\t%s\n", index, type.c_str(), line.c_str()); |
| 531 |
> |
|
| 532 |
> |
std::string id; |
| 533 |
> |
std::string type; |
| 534 |
> |
std::string line; |
| 535 |
> |
char tempBuffer[4096]; |
| 536 |
> |
|
| 537 |
> |
if (integrableObject->isRigidBody()) { |
| 538 |
> |
sprintf(tempBuffer, "%10d ", ioIndex); |
| 539 |
> |
id = std::string(tempBuffer); |
| 540 |
> |
} else { |
| 541 |
> |
sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex); |
| 542 |
> |
id = std::string(tempBuffer); |
| 543 |
> |
} |
| 544 |
> |
|
| 545 |
> |
if (needFlucQ_) { |
| 546 |
> |
type += "cw"; |
| 547 |
> |
RealType fqPos = integrableObject->getFlucQPos(); |
| 548 |
> |
if (isinf(fqPos) || isnan(fqPos) ) { |
| 549 |
> |
sprintf( painCave.errMsg, |
| 550 |
> |
"DumpWriter detected a numerical error writing the" |
| 551 |
> |
" fluctuating charge for object %s", id.c_str()); |
| 552 |
> |
painCave.isFatal = 1; |
| 553 |
> |
simError(); |
| 554 |
> |
} |
| 555 |
> |
sprintf(tempBuffer, " %13e ", fqPos); |
| 556 |
> |
line += tempBuffer; |
| 557 |
> |
|
| 558 |
> |
RealType fqVel = integrableObject->getFlucQVel(); |
| 559 |
> |
if (isinf(fqVel) || isnan(fqVel) ) { |
| 560 |
> |
sprintf( painCave.errMsg, |
| 561 |
> |
"DumpWriter detected a numerical error writing the" |
| 562 |
> |
" fluctuating charge velocity for object %s", id.c_str()); |
| 563 |
> |
painCave.isFatal = 1; |
| 564 |
> |
simError(); |
| 565 |
> |
} |
| 566 |
> |
sprintf(tempBuffer, " %13e ", fqVel); |
| 567 |
> |
line += tempBuffer; |
| 568 |
> |
|
| 569 |
> |
if (needForceVector_) { |
| 570 |
> |
type += "g"; |
| 571 |
> |
RealType fqFrc = integrableObject->getFlucQFrc(); |
| 572 |
> |
if (isinf(fqFrc) || isnan(fqFrc) ) { |
| 573 |
> |
sprintf( painCave.errMsg, |
| 574 |
> |
"DumpWriter detected a numerical error writing the" |
| 575 |
> |
" fluctuating charge force for object %s", id.c_str()); |
| 576 |
> |
painCave.isFatal = 1; |
| 577 |
> |
simError(); |
| 578 |
> |
} |
| 579 |
> |
sprintf(tempBuffer, " %13e ", fqFrc); |
| 580 |
> |
line += tempBuffer; |
| 581 |
> |
} |
| 582 |
> |
} |
| 583 |
> |
|
| 584 |
> |
if (needElectricField_) { |
| 585 |
> |
type += "e"; |
| 586 |
> |
Vector3d eField= integrableObject->getElectricField(); |
| 587 |
> |
if (isinf(eField[0]) || isnan(eField[0]) || |
| 588 |
> |
isinf(eField[1]) || isnan(eField[1]) || |
| 589 |
> |
isinf(eField[2]) || isnan(eField[2]) ) { |
| 590 |
> |
sprintf( painCave.errMsg, |
| 591 |
> |
"DumpWriter detected a numerical error writing the electric" |
| 592 |
> |
" field for object %s", id.c_str()); |
| 593 |
> |
painCave.isFatal = 1; |
| 594 |
> |
simError(); |
| 595 |
> |
} |
| 596 |
> |
sprintf(tempBuffer, " %13e %13e %13e", |
| 597 |
> |
eField[0], eField[1], eField[2]); |
| 598 |
> |
line += tempBuffer; |
| 599 |
> |
} |
| 600 |
> |
|
| 601 |
> |
|
| 602 |
> |
if (needParticlePot_) { |
| 603 |
> |
type += "u"; |
| 604 |
> |
RealType particlePot = integrableObject->getParticlePot(); |
| 605 |
> |
if (isinf(particlePot) || isnan(particlePot)) { |
| 606 |
> |
sprintf( painCave.errMsg, |
| 607 |
> |
"DumpWriter detected a numerical error writing the particle " |
| 608 |
> |
" potential for object %s", id.c_str()); |
| 609 |
> |
painCave.isFatal = 1; |
| 610 |
> |
simError(); |
| 611 |
> |
} |
| 612 |
> |
sprintf(tempBuffer, " %13e", particlePot); |
| 613 |
> |
line += tempBuffer; |
| 614 |
> |
} |
| 615 |
> |
|
| 616 |
> |
|
| 617 |
> |
sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str()); |
| 618 |
|
return std::string(tempBuffer); |
| 619 |
|
} |
| 620 |
|
|
| 685 |
|
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
| 686 |
|
|
| 687 |
|
std::ostream* newOStream; |
| 688 |
< |
#ifdef HAVE_LIBZ |
| 688 |
> |
#ifdef HAVE_ZLIB |
| 689 |
|
if (needCompression_) { |
| 690 |
|
newOStream = new ogzstream(filename.c_str()); |
| 691 |
|
} else { |
| 695 |
|
newOStream = new std::ofstream(filename.c_str()); |
| 696 |
|
#endif |
| 697 |
|
//write out MetaData first |
| 698 |
< |
(*newOStream) << "<OOPSE version=4>" << std::endl; |
| 698 |
> |
(*newOStream) << "<OpenMD version=2>" << std::endl; |
| 699 |
|
(*newOStream) << " <MetaData>" << std::endl; |
| 700 |
|
(*newOStream) << info_->getRawMetaData(); |
| 701 |
|
(*newOStream) << " </MetaData>" << std::endl; |
| 704 |
|
|
| 705 |
|
void DumpWriter::writeClosing(std::ostream& os) { |
| 706 |
|
|
| 707 |
< |
os << "</OOPSE>\n"; |
| 707 |
> |
os << "</OpenMD>\n"; |
| 708 |
|
os.flush(); |
| 709 |
|
} |
| 710 |
|
|
| 711 |
< |
}//end namespace oopse |
| 711 |
> |
}//end namespace OpenMD |