--- trunk/src/io/StatWriter.cpp 2004/09/24 16:27:58 3 +++ trunk/src/io/StatWriter.cpp 2010/04/21 14:59:18 1437 @@ -1,114 +1,166 @@ +/* + * 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] Vardeman & Gezelter, in progress (2009). + */ + #define _LARGEFILE_SOURCE64 #define _FILE_OFFSET_BITS 64 -#include -#include -#include - -#include "io/ReadWrite.hpp" +#include "io/StatWriter.hpp" #include "utils/simError.h" +using namespace std; -StatWriter::StatWriter( SimInfo* the_entry_plug ){ +namespace OpenMD { + StatsBitSet parseStatFileFormat(const std::string& format) { + StringTokenizer tokenizer(format, " ,;|\t\n\r"); + StatsBitSet mask; + while(tokenizer.hasMoreTokens()) { + std::string token(tokenizer.nextToken()); + toUpper(token); + Stats::StatsMapType::iterator i = Stats::statsMap.find(token); + if (i != Stats::statsMap.end()) { + mask.set(i->second); + } else { + sprintf( painCave.errMsg, + "%s is not a valid statFileFormat keyword.\n", token.c_str() ); + painCave.isFatal = 0; + painCave.severity = OPENMD_ERROR; + simError(); + } + } + + return mask; + } + + StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){ - entry_plug = the_entry_plug; - #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(); + } - //outFile.setf( ios::scientific ); - outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved"; - - if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) - outFile << "\tV_raw"; + writeTitle(); - if (entry_plug->useSolidThermInt) - outFile << "\tV_harm"; - - outFile << "\n"; - - #ifdef IS_MPI - } + } - sprintf( checkPointMsg, - "Sucessfully opened output file for stating.\n"); - MPIcheckPoint(); + sprintf( checkPointMsg, + "Sucessfully opened output file for stating.\n"); + errorCheckPoint(); #endif // is_mpi - tStats = new Thermo( entry_plug ); -} + } -StatWriter::~StatWriter( ){ + StatWriter::~StatWriter( ){ #ifdef IS_MPI - if(worldRank == 0 ){ + if(worldRank == 0 ){ #endif // is_mpi - outFile.close(); - delete tStats; + statfile_.close(); #ifdef IS_MPI - } + } #endif // is_mpi -} + } -void StatWriter::writeStat( double currentTime ){ + void StatWriter::writeTitle() { - 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 ){ + if(worldRank == 0 ){ #endif // is_mpi - outFile.precision(8); - outFile - << currentTime << "\t" - << totE << "\t" - << potE << "\t" - << kinE << "\t" - << temp << "\t" - << press << "\t" - << vol << "\t" - << conservedQuantity; + //write title + statfile_ << "#"; + for (int i =0; i < mask_.size(); ++i) { + if (mask_[i]) { + statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")"; + } + } + statfile_ << std::endl; - if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) - outFile << "\t" << entry_plug->vRaw; - - if (entry_plug->useSolidThermInt) - outFile << "\t" << entry_plug->vHarm; +#ifdef IS_MPI + } +#endif // is_mpi + } - outFile << "\n"; + void StatWriter::writeStat(const Stats& s){ - outFile.flush(); +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + statfile_.precision(8); + for (int i =0; i < mask_.size(); ++i) { + if (mask_[i]) { + if (! isinf(s[i]) && ! isnan(s[i])){ + statfile_ << "\t" << s[i]; + } + else{ + sprintf( painCave.errMsg, + "StatWriter detected a numerical error writing: %s ", + Stats::getTitle(i).c_str()); + painCave.isFatal = 1; + simError(); + } + } + } + statfile_ << std::endl; + + statfile_.flush(); + #ifdef IS_MPI - } + } + errorCheckPoint(); #endif // is_mpi -} + } +}