--- trunk/src/io/SectionParser.cpp 2005/01/12 22:41:40 246 +++ branches/development/src/io/SectionParser.cpp 2010/07/09 23:08:25 1465 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -6,19 +6,10 @@ * 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. @@ -37,51 +28,64 @@ * 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). */ #include "io/SectionParser.hpp" #include "utils/Trim.hpp" -namespace oopse { +namespace OpenMD { -void SectionParser::parse(std::istream& input, ForceField& ff, int lineNo) { + void SectionParser::parse(std::istream& input, ForceField& ff, int lineNo) { const int bufferSize = 65535; char buffer[bufferSize]; std::string line; while(input.getline(buffer, bufferSize)) { - /**@todo */ - line = trimLeftCopy(buffer); - //a line begins with "//" is comment - if (isEndSection(line)) { - break; - } else if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { - continue; - } else { - parseLine(ff, line, lineNo); - } + ++lineNo; + line = trimLeftCopy(buffer); + //a line begins with "//" is comment + // let's also call lines starting with # and ! as comments + if (isEndSection(line)) { + break; + } else if ( line.empty() || + (line.size() >= 2 && line[0] == '/' && line[1] == '/') || + (line.size() >= 1 && line[0] == '#') || + (line.size() >= 1 && line[0] == '!') ) { + continue; + } else { + parseLine(ff, line, lineNo); + } } -} - -bool SectionParser::isEndSection(const std::string& line) { + } + + bool SectionParser::isEndSection(const std::string& line) { StringTokenizer tokenizer(line); - + if (tokenizer.countTokens() >= 2) { - std::string keyword = tokenizer.nextToken(); - - if (keyword != "end"){ - return false; - } - - std::string section = tokenizer.nextToken(); - if (section == sectionName_) { - return true; - }else { - return false; - } - - }else { + std::string keyword = tokenizer.nextToken(); + + if (keyword != "end"){ return false; + } + + std::string section = tokenizer.nextToken(); + if (section == sectionName_) { + return true; + }else { + return false; + } + + }else { + return false; } - -} + + } -}//namespace oopse +}//namespace OpenMD