--- trunk/src/io/StatWriter.cpp 2004/09/24 04:16:43 2 +++ branches/development/src/io/StatWriter.cpp 2012/07/03 18:32:27 1764 @@ -1,114 +1,204 @@ +/* + * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 2. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). + */ + #define _LARGEFILE_SOURCE64 #define _FILE_OFFSET_BITS 64 -#include -#include -#include +#include "io/StatWriter.hpp" +#include "brains/Stats.hpp" +#include "utils/simError.h" -#include "ReadWrite.hpp" -#include "simError.h" +using namespace std; - -StatWriter::StatWriter( SimInfo* the_entry_plug ){ - - entry_plug = the_entry_plug; - +namespace OpenMD { + + StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){ + #ifdef IS_MPI - if(worldRank == 0 ){ + if(worldRank == 0 ){ #endif // is_mpi - - outName = entry_plug->statusName; - - //std::cerr << "Opening " << outName << " for stat\n"; - - outFile.open(outName.c_str(), ios::out | ios::trunc ); + + statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); - if( !outFile ){ + if( !statfile_ ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for stat output.\n", - outName.c_str()); - painCave.isFatal = 1; - simError(); + sprintf( painCave.errMsg, + "Could not open \"%s\" for stat output.\n", + filename.c_str()); + painCave.isFatal = 1; + simError(); + } + + writeTitle(); + +#ifdef IS_MPI } - //outFile.setf( ios::scientific ); - outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved"; + sprintf( checkPointMsg, + "Sucessfully opened output file for stating.\n"); + errorCheckPoint(); +#endif // is_mpi - if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) - outFile << "\tV_raw"; - - if (entry_plug->useSolidThermInt) - outFile << "\tV_harm"; + } - outFile << "\n"; + StatWriter::~StatWriter( ){ - #ifdef IS_MPI - } + if(worldRank == 0 ){ +#endif // is_mpi - sprintf( checkPointMsg, - "Sucessfully opened output file for stating.\n"); - MPIcheckPoint(); + statfile_.close(); + +#ifdef IS_MPI + } #endif // is_mpi + } - tStats = new Thermo( entry_plug ); -} -StatWriter::~StatWriter( ){ + void StatWriter::writeTitle() { + Stats::StatsBitSet mask = stats_->getStatsMask(); + #ifdef IS_MPI - if(worldRank == 0 ){ + if(worldRank == 0 ){ #endif // is_mpi - outFile.close(); - delete tStats; + //write title + statfile_ << "#"; + for (int i = 0; i getTitle(i) << + "(" << stats_->getUnits(i) << ")"; + } + } + statfile_ << std::endl; #ifdef IS_MPI + } +#endif // is_mpi } + + void StatWriter::writeStat() { + +#ifdef IS_MPI + if(worldRank == 0 ){ #endif // is_mpi -} -void StatWriter::writeStat( double currentTime ){ + Stats::StatsBitSet mask = stats_->getStatsMask(); + statfile_.precision(8); + for (int i = 0; i < mask.size(); ++i) { + if (mask[i]) { + if (stats_->getDataType(i) == "RealType") + writeReal(i); + else if (stats_->getDataType(i) == "Vector3d") + writeVector(i); + else if (stats_->getDataType(i) == "Mat3x3d") + writeMatrix(i); + else { + sprintf( painCave.errMsg, + "StatWriter found an unknown data type for: %s ", + stats_->getTitle(i).c_str()); + painCave.isFatal = 1; + simError(); + } + } + } + + statfile_ << std::endl; + statfile_.flush(); - double totE, potE, kinE, temp, press, vol; - double conservedQuantity; - - totE = tStats->getTotalE(); - potE = tStats->getPotential(); - kinE = tStats->getKinetic(); - temp = tStats->getTemperature(); - press = tStats->getPressure(); - vol = tStats->getVolume(); - conservedQuantity = entry_plug->the_integrator->getConservedQuantity(); - #ifdef IS_MPI - if(worldRank == 0 ){ + } + errorCheckPoint(); #endif // is_mpi + } - outFile.precision(8); - outFile - << currentTime << "\t" - << totE << "\t" - << potE << "\t" - << kinE << "\t" - << temp << "\t" - << press << "\t" - << vol << "\t" - << conservedQuantity; + void StatWriter::writeReal(int i) { - if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) - outFile << "\t" << entry_plug->vRaw; - - if (entry_plug->useSolidThermInt) - outFile << "\t" << entry_plug->vHarm; + RealType s = stats_->getRealData(i); - outFile << "\n"; + if (! isinf(s) && ! isnan(s)) { + statfile_ << "\t" << s; + } else{ + sprintf( painCave.errMsg, + "StatWriter detected a numerical error writing: %s ", + stats_->getTitle(i).c_str()); + painCave.isFatal = 1; + simError(); + } + } - outFile.flush(); + void StatWriter::writeVector(int i) { -#ifdef IS_MPI + Vector3d s = stats_->getVectorData(i); + if (isinf(s[0]) || isnan(s[0]) || + isinf(s[1]) || isnan(s[1]) || + isinf(s[2]) || isnan(s[2]) ) { + sprintf( painCave.errMsg, + "StatWriter detected a numerical error writing: %s", + stats_->getTitle(i).c_str()); + painCave.isFatal = 1; + simError(); + } else { + statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; + } } -#endif // is_mpi -} + void StatWriter::writeMatrix(int i) { + + Mat3x3d s = stats_->getMatrixData(i); + + for (unsigned int i = 0; i < 3; i++) { + for (unsigned int j = 0; j < 3; j++) { + if (isinf(s(i,j)) || isnan(s(i,j))) { + sprintf( painCave.errMsg, + "StatWriter detected a numerical error writing: %s", + stats_->getTitle(i).c_str()); + painCave.isFatal = 1; + simError(); + } else { + statfile_ << "\t" << s(i,j); + } + } + } + } +}