--- trunk/src/io/StatWriter.cpp 2008/11/14 15:44:34 1316 +++ branches/development/src/io/StatWriter.cpp 2012/07/03 18:32:27 1764 @@ -1,24 +1,15 @@ /* - * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * 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. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 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. @@ -37,42 +28,35 @@ * 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 "io/StatWriter.hpp" +#include "brains/Stats.hpp" #include "utils/simError.h" -namespace oopse { - 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 = OOPSE_ERROR; - simError(); - } - } - - return mask; - } - - StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){ +using namespace std; +namespace OpenMD { + + StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){ + #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - + statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); if( !statfile_ ){ @@ -109,8 +93,10 @@ namespace oopse { #endif // is_mpi } + void StatWriter::writeTitle() { + Stats::StatsBitSet mask = stats_->getStatsMask(); #ifdef IS_MPI if(worldRank == 0 ){ @@ -118,9 +104,10 @@ namespace oopse { //write title statfile_ << "#"; - for (int i =0; i < mask_.size(); ++i) { - if (mask_[i]) { - statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")"; + for (int i = 0; i getTitle(i) << + "(" << stats_->getUnits(i) << ")"; } } statfile_ << std::endl; @@ -130,25 +117,88 @@ namespace oopse { #endif // is_mpi } - void StatWriter::writeStat(const Stats& s){ - + void StatWriter::writeStat() { + #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi + Stats::StatsBitSet mask = stats_->getStatsMask(); statfile_.precision(8); - for (int i =0; i < mask_.size(); ++i) { - if (mask_[i]) { - statfile_ << "\t" << s[i]; - } + 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(); #ifdef IS_MPI } + errorCheckPoint(); #endif // is_mpi } + void StatWriter::writeReal(int i) { + + RealType s = stats_->getRealData(i); + + 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(); + } + } + + void StatWriter::writeVector(int i) { + + 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]; + } + } + + 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); + } + } + } + } }