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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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/* |
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* Copyright (c) 2005, 2010 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, 234107 (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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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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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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#include "io/StatWriter.hpp" |
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#include "brains/Stats.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){ |
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using namespace std; |
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|
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namespace OpenMD { |
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|
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StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){ |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); |
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|
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statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); |
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|
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if( !statfile_ ){ |
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if( !statfile_ ){ |
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|
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for stat 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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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for stat 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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writeTitle(); |
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writeTitle(); |
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#ifdef IS_MPI |
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} |
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} |
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|
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for stating.\n"); |
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MPIcheckPoint(); |
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for stating.\n"); |
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errorCheckPoint(); |
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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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StatWriter::~StatWriter( ){ |
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StatWriter::~StatWriter( ){ |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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statfile_.close(); |
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statfile_.close(); |
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|
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#ifdef IS_MPI |
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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 StatWriter::writeTitle() { |
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void StatWriter::writeTitle() { |
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|
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Stats::StatsBitSet mask = stats_->getStatsMask(); |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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//write title |
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statfile_ << "#"; |
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for (int i =0; i < mask_.size(); ++i) { |
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if (mask_[i]) { |
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statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")"; |
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} |
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} |
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statfile_ << std::endl; |
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//write title |
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statfile_ << "#"; |
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for (unsigned int i = 0; i <mask.size(); ++i) { |
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if (mask[i]) { |
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statfile_ << "\t" << stats_->getTitle(i) << |
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"(" << stats_->getUnits(i) << ")"; |
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} |
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} |
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statfile_ << std::endl; |
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|
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#ifdef IS_MPI |
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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 StatWriter::writeStat(const Stats& s){ |
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|
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void StatWriter::writeStat() { |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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statfile_.precision(8); |
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|
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for (int i =0; i < mask_.size(); ++i) { |
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if (mask_[i]) { |
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statfile_ << "\t" << s[i]; |
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} |
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Stats::StatsBitSet mask = stats_->getStatsMask(); |
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statfile_.precision(8); |
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for (unsigned int i = 0; i < mask.size(); ++i) { |
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if (mask[i]) { |
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if (stats_->getDataType(i) == "RealType") |
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writeReal(i); |
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else if (stats_->getDataType(i) == "Vector3d") |
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writeVector(i); |
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else if (stats_->getDataType(i) == "Mat3x3d") |
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writeMatrix(i); |
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else { |
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sprintf( painCave.errMsg, |
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"StatWriter found an unknown data type for: %s ", |
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stats_->getTitle(i).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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statfile_ << std::endl; |
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} |
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|
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statfile_ << std::endl; |
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statfile_.flush(); |
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|
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statfile_.flush(); |
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|
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#ifdef IS_MPI |
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} |
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errorCheckPoint(); |
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#endif // is_mpi |
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} |
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} |
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|
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void StatWriter::writeReal(int i) { |
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|
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RealType s = stats_->getRealData(i); |
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|
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if (! isinf(s) && ! isnan(s)) { |
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statfile_ << "\t" << s; |
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} else{ |
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sprintf( painCave.errMsg, |
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"StatWriter detected a numerical error writing: %s ", |
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stats_->getTitle(i).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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|
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void StatWriter::writeVector(int i) { |
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|
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Vector3d s = stats_->getVectorData(i); |
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if (isinf(s[0]) || isnan(s[0]) || |
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isinf(s[1]) || isnan(s[1]) || |
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isinf(s[2]) || isnan(s[2]) ) { |
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sprintf( painCave.errMsg, |
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"StatWriter detected a numerical error writing: %s", |
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stats_->getTitle(i).c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
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} |
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} |
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|
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void StatWriter::writeMatrix(int i) { |
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|
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Mat3x3d s = stats_->getMatrixData(i); |
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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(s(i,j)) || isnan(s(i,j))) { |
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sprintf( painCave.errMsg, |
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"StatWriter detected a numerical error writing: %s", |
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stats_->getTitle(i).c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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statfile_ << "\t" << s(i,j); |
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} |
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} |
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} |
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} |
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} |
