--- trunk/src/io/SectionParserManager.cpp 2005/01/12 22:41:40 246 +++ branches/development/src/io/SectionParserManager.cpp 2011/11/22 20:38:56 1665 @@ -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. @@ -37,119 +28,166 @@ * 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). */ #include +#include +#include #include "io/SectionParserManager.hpp" #include "utils/Trim.hpp" +#include "utils/simError.h" -namespace oopse { +namespace OpenMD { -SectionParserManager::~SectionParserManager() { + SectionParserManager::~SectionParserManager() { SectionParserManager::iterator i; for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { - delete (i->sectionParser); + delete (i->sectionParser); } sectionParsers_.clear(); -} + } -void SectionParserManager::parse(std::istream& input, ForceField& ff) { + void SectionParserManager::parse(std::istream& input, ForceField& ff) { //reset active flags SectionParserManager::iterator i; for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { - i->isActive = false; + i->isActive = false; } const int bufferSize = 65535; char buffer[bufferSize]; int lineNo = 0; + std::stack sectionNameStack; //scan through the input stream and find section names while(input.getline(buffer, bufferSize)) { - ++lineNo; + ++lineNo; - std::string line = trimLeftCopy(buffer); - //a line begins with "//" is comment - if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { - continue; - } else { - StringTokenizer tokenizer(line); - if (tokenizer.countTokens() < 2) { - continue; - } else { - std::string keyword = tokenizer.nextToken(); + std::string line = trimLeftCopy(buffer); + //a line begins with "//" is a comment line + if ( line.empty() || (line.size() >= 2 && line[0] == '/' + && line[1] == '/') ) { + continue; + } else { + StringTokenizer tokenizer(line); + if (tokenizer.countTokens() < 2) { + continue; + } else { + std::string keyword = tokenizer.nextToken(); - if (keyword != "begin") { - continue; - } - - std::string section = tokenizer.nextToken(); - - i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), SameSectionParserFunctor(section)); - if (i == sectionParsers_.end()){ - //can not find corresponding section parser - std::cerr << "Can not find corresponding section parser for section: " << section << std::endl; - } else { - i->isActive = true; - i->lineNo = lineNo; - i->offset = input.tellg(); - } - - } - } - - + if (keyword == "begin") { + std::string section = tokenizer.nextToken(); + sectionNameStack.push(section); + + i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), + SameSectionParserFunctor(section)); + if (i == sectionParsers_.end()){ + sprintf(painCave.errMsg, + "SectionParserManager Error: Can not find corresponding " + "section parser for %s\n", + section.c_str()); + painCave.isFatal = 1; + simError(); + } else { + if (i->isActive) { + sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s " + "section\n", + section.c_str()); + painCave.isFatal = 1; + simError(); + } else { + i->isActive = true; + i->lineNo = lineNo; + i->offset = input.tellg(); + } + } + } else if (keyword == "end") { + std::string section = tokenizer.nextToken(); + if (sectionNameStack.top() == section) { + sectionNameStack.pop(); + } else { + sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n", + sectionNameStack.top().c_str(), section.c_str(), lineNo); + painCave.isFatal = 1; + simError(); + } + + } else { + continue; + } + } + } + } - + + if (!sectionNameStack.empty()) { + sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n"); + painCave.isFatal = 1; + simError(); + } + //invoke parser for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { - if (i->isActive) { - //C++ standard does not guarantee seekg reset EOF, in that case, seekg will fail - //It is always a good idea to call clear() before seek - input.clear(); - input.seekg(i->offset); - (i->sectionParser)->parse(input, ff, i->lineNo); - } + if (i->isActive) { + //C++ standard does not guarantee seekg reset EOF, in that case, seekg will fail + //It is always a good idea to call clear() before seek + input.clear(); + input.seekg(i->offset); + (i->sectionParser)->parse(input, ff, i->lineNo); + (i->sectionParser)->validateSection(); + } } -} - -void SectionParserManager::push_front(SectionParser* sp) { + } + + void SectionParserManager::push_front(SectionParser* sp) { SectionParserManager::iterator i; i = findSectionParser(sp->getSectionName()); if (i != sectionParsers_.end()) { - std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; - return; + std::cerr << sp->getSectionName() << " section parser already exists" + << std::endl; + return; } SectionParserContext context; if (sectionParsers_.empty()) { - context.priority = beginPriority_; + context.priority = beginPriority_; } else { - context.priority = sectionParsers_.front().priority - priorityDifference_; + context.priority = sectionParsers_.front().priority - priorityDifference_; } - + context.sectionParser = sp; context.lineNo = 0; context.offset = 0; context.isActive = false; sectionParsers_.push_front(context); -} + } -void SectionParserManager::push_back(SectionParser* sp) { + void SectionParserManager::push_back(SectionParser* sp) { SectionParserManager::iterator i; i = findSectionParser(sp->getSectionName()); if (i != sectionParsers_.end()) { - std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; - return; + std::cerr << sp->getSectionName() << " section parser already exists" + << std::endl; + return; } SectionParserContext context; if (sectionParsers_.empty()) { - context.priority = beginPriority_; + context.priority = beginPriority_; } else { - context.priority = sectionParsers_.back().priority + priorityDifference_; + context.priority = sectionParsers_.back().priority + priorityDifference_; } context.sectionParser = sp; @@ -159,13 +197,14 @@ void SectionParserManager::push_back(SectionParser* sp sectionParsers_.push_back(context); -} + } -void SectionParserManager::insert(SectionParser* sp, int priority) { + void SectionParserManager::insert(SectionParser* sp, int priority) { SectionParserManager::iterator i; i = findSectionParser(sp->getSectionName()); if (i != sectionParsers_.end()) { - std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; + std::cerr << sp->getSectionName() << " section parser already exists" + << std::endl; } SectionParserContext context; @@ -176,33 +215,33 @@ void SectionParserManager::insert(SectionParser* sp, i context.isActive = false; if (sectionParsers_.empty()) { - sectionParsers_.push_back(context); + sectionParsers_.push_back(context); } else { - for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { - if (i->priority == priority) { - std::cerr << "Priority " << priority << " already used" << std::endl; - return; - } else if (i->priority > priority) { - sectionParsers_.insert(i, context); - break; - } + for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { + if (i->priority == priority) { + std::cerr << "Priority " << priority << " already used" << std::endl; + return; + } else if (i->priority > priority) { + sectionParsers_.insert(i, context); + break; + } - } + } } -} + } -SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) { + SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) { SectionParserManager::iterator i; for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { - if (i->sectionParser->getSectionName() == sectionName) { - break; - } + if (i->sectionParser->getSectionName() == sectionName) { + break; + } } return i; -} + } }