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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. 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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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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|
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< |
#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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#include "io/StatWriter.hpp" |
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#include "utils/simError.h" |
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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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> |
using namespace std; |
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|
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namespace OpenMD { |
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StatsBitSet parseStatFileFormat(const std::string& format) { |
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StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
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StatsBitSet mask; |
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while(tokenizer.hasMoreTokens()) { |
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std::string token(tokenizer.nextToken()); |
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toUpper(token); |
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Stats::StatsMapType::iterator i = Stats::statsMap.find(token); |
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if (i != Stats::statsMap.end()) { |
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mask.set(i->second); |
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} else { |
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sprintf( painCave.errMsg, |
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"%s is not a valid statFileFormat keyword.\n", token.c_str() ); |
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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} |
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|
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return mask; |
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} |
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|
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StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){ |
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|
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StatWriter::StatWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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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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outName = entry_plug->statusName; |
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|
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//std::cerr << "Opening " << outName << " for stat\n"; |
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|
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outFile.open(outName.c_str(), ios::out | ios::trunc ); |
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statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); |
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|
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if( !outFile ){ |
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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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outName.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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< |
//outFile.setf( ios::scientific ); |
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outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved"; |
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|
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if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) |
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outFile << "\tV_raw"; |
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writeTitle(); |
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|
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if (entry_plug->useSolidThermInt) |
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outFile << "\tV_harm"; |
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|
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outFile << "\n"; |
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|
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|
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#ifdef IS_MPI |
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} |
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} |
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|
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sprintf( checkPointMsg, |
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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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tStats = new Thermo( entry_plug ); |
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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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outFile.close(); |
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delete tStats; |
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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::writeStat( double currentTime ){ |
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void StatWriter::writeTitle() { |
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|
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double totE, potE, kinE, temp, press, vol; |
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double conservedQuantity; |
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totE = tStats->getTotalE(); |
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potE = tStats->getPotential(); |
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kinE = tStats->getKinetic(); |
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temp = tStats->getTemperature(); |
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press = tStats->getPressure(); |
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vol = tStats->getVolume(); |
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conservedQuantity = entry_plug->the_integrator->getConservedQuantity(); |
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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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outFile.precision(8); |
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outFile |
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<< currentTime << "\t" |
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<< totE << "\t" |
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<< potE << "\t" |
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<< kinE << "\t" |
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<< temp << "\t" |
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<< press << "\t" |
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<< vol << "\t" |
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<< conservedQuantity; |
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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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|
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if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) |
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outFile << "\t" << entry_plug->vRaw; |
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|
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if (entry_plug->useSolidThermInt) |
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outFile << "\t" << entry_plug->vHarm; |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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< |
outFile << "\n"; |
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> |
void StatWriter::writeStat(const Stats& s){ |
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|
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< |
outFile.flush(); |
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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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for (int i =0; i < mask_.size(); ++i) { |
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if (mask_[i]) { |
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if (! isinf(s[i]) && ! isnan(s[i])){ |
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statfile_ << "\t" << s[i]; |
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} |
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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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statfile_ << std::endl; |
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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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} |
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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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} |
