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root/OpenMD/trunk/src/io/SectionParserManager.cpp
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Comparing trunk/src/io/SectionParserManager.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #include <algorithm>
42   #include <stack>
# Line 44 | Line 44
44   #include "utils/Trim.hpp"
45   #include "utils/simError.h"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49 < SectionParserManager::~SectionParserManager() {
49 >  SectionParserManager::~SectionParserManager() {
50      SectionParserManager::iterator i;
51      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
52 <        delete (i->sectionParser);
52 >      delete (i->sectionParser);
53      }
54      sectionParsers_.clear();
55 < }
55 >  }
56  
57 < void SectionParserManager::parse(std::istream& input, ForceField& ff) {
57 >  void SectionParserManager::parse(std::istream& input, ForceField& ff) {
58  
59      //reset active flags
60      SectionParserManager::iterator i;
61      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
62 <        i->isActive = false;
62 >      i->isActive = false;
63      }
64  
65      const int bufferSize = 65535;
# Line 68 | Line 68 | void SectionParserManager::parse(std::istream& input,
68      std::stack<std::string> sectionNameStack;
69      //scan through the input stream and find section names        
70      while(input.getline(buffer, bufferSize)) {
71 <        ++lineNo;
71 >      ++lineNo;
72          
73 <        std::string line = trimLeftCopy(buffer);
74 <        //a line begins with "//" is a comment line
75 <        if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
76 <            continue;
77 <        } else {        
78 <            StringTokenizer tokenizer(line);
79 <            if (tokenizer.countTokens() < 2) {
80 <                continue;
81 <            } else {
82 <                std::string keyword = tokenizer.nextToken();
73 >      std::string line = trimLeftCopy(buffer);
74 >      //a line begins with "//" is a comment line
75 >      if ( line.empty() || (line.size() >= 2 && line[0] == '/'
76 >                            && line[1] == '/') ) {
77 >        continue;
78 >      } else {        
79 >        StringTokenizer tokenizer(line);
80 >        if (tokenizer.countTokens() < 2) {
81 >          continue;
82 >        } else {
83 >          std::string keyword = tokenizer.nextToken();
84  
85 <                if (keyword == "begin") {
86 <                    std::string section = tokenizer.nextToken();
87 <                    sectionNameStack.push(section);
88 <
89 <                    i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), SameSectionParserFunctor(section));
90 <                    if (i == sectionParsers_.end()){
91 <                        sprintf(painCave.errMsg, "SectionParserManager Error: Can not find corresponding section parser for %s\n",
92 <                                section.c_str());
93 <                        painCave.isFatal = 1;
94 <                        simError();                        
95 <                    } else {
96 <                        if (i->isActive) {
97 <                            sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s section\n",
98 <                                    section.c_str());
99 <                            painCave.isFatal = 1;
100 <                            simError();                        
101 <                        } else {                        
102 <                            i->isActive = true;
103 <                            i->lineNo = lineNo;
104 <                            i->offset = input.tellg();
105 <                        }
106 <                    }
107 <                } else if (keyword == "end") {
108 <                    std::string section = tokenizer.nextToken();
109 <                    if (sectionNameStack.top() == section) {
110 <                        sectionNameStack.pop();
111 <                    } else {
112 <                        sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
113 <                                sectionNameStack.top().c_str(), section.c_str(), lineNo);
114 <                        painCave.isFatal = 1;
115 <                        simError();
116 <                    }
117 <                    
118 <                } else {
119 <                    continue;
120 <                }
121 <            }
122 <        }
123 <        
85 >          if (keyword == "begin") {
86 >            std::string section = tokenizer.nextToken();
87 >            sectionNameStack.push(section);
88 >
89 >            i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
90 >                       SameSectionParserFunctor(section));
91 >            if (i == sectionParsers_.end()){
92 >              sprintf(painCave.errMsg,
93 >                "SectionParserManager Error: Can not find corresponding "
94 >                "section parser for %s\n",
95 >                section.c_str());
96 >              painCave.isFatal = 1;
97 >              simError();                        
98 >            } else {
99 >              if (i->isActive) {
100 >          sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s "
101 >                  "section\n",
102 >                  section.c_str());
103 >          painCave.isFatal = 1;
104 >          simError();                        
105 >              } else {                        
106 >          i->isActive = true;
107 >          i->lineNo = lineNo;
108 >          i->offset = input.tellg();
109 >              }
110 >            }
111 >          } else if (keyword == "end") {
112 >            std::string section = tokenizer.nextToken();
113 >            if (sectionNameStack.top() == section) {
114 >              sectionNameStack.pop();
115 >            } else {
116 >              sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
117 >                sectionNameStack.top().c_str(), section.c_str(), lineNo);
118 >              painCave.isFatal = 1;
119 >              simError();
120 >            }
121 >      
122 >          } else {
123 >            continue;
124 >          }
125 >        }
126 >      }
127 >      
128      }
129 <
129 >    
130      if (!sectionNameStack.empty()) {
131 <        sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
132 <        painCave.isFatal = 1;
133 <        simError();
131 >      sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
132 >      painCave.isFatal = 1;
133 >      simError();
134      }
135 <
135 >    
136      //invoke parser
137      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
138 <        if (i->isActive) {
139 <            //C++ standard does not guarantee seekg  reset EOF, in that case, seekg will fail
140 <            //It is always a good idea to call clear() before seek
141 <            input.clear();            
142 <            input.seekg(i->offset);
143 <            (i->sectionParser)->parse(input, ff, i->lineNo);
144 <        }
138 >      if (i->isActive) {
139 >        //C++ standard does not guarantee seekg  reset EOF, in that case, seekg will fail
140 >        //It is always a good idea to call clear() before seek
141 >        input.clear();            
142 >        input.seekg(i->offset);
143 >        (i->sectionParser)->parse(input, ff, i->lineNo);
144 >        (i->sectionParser)->validateSection();
145 >      }
146      }
147      
148 < }
149 <
150 < void SectionParserManager::push_front(SectionParser* sp) {
148 >  }
149 >  
150 >  void SectionParserManager::push_front(SectionParser* sp) {
151      SectionParserManager::iterator i;
152      i = findSectionParser(sp->getSectionName());
153      if (i != sectionParsers_.end()) {
154 <        std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
155 <        return;
154 >      std::cerr << sp->getSectionName() << " section parser already exists"
155 >      << std::endl;
156 >      return;
157      }
158      
159      SectionParserContext context;
160      
161      if (sectionParsers_.empty()) {
162 <        context.priority = beginPriority_;
162 >      context.priority = beginPriority_;
163      } else {
164 <        context.priority = sectionParsers_.front().priority - priorityDifference_;
164 >      context.priority = sectionParsers_.front().priority - priorityDifference_;
165      }
166 <
166 >    
167      context.sectionParser = sp;
168      context.lineNo = 0;
169      context.offset = 0;
170      context.isActive = false;
171  
172      sectionParsers_.push_front(context);
173 < }
173 >  }
174  
175 < void SectionParserManager::push_back(SectionParser* sp) {
175 >  void SectionParserManager::push_back(SectionParser* sp) {
176      SectionParserManager::iterator i;
177      i = findSectionParser(sp->getSectionName());
178      if (i != sectionParsers_.end()) {
179 <        std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
180 <        return;
179 >      std::cerr << sp->getSectionName() << " section parser already exists"
180 >      << std::endl;
181 >      return;
182      }
183  
184      SectionParserContext context;    
185      if (sectionParsers_.empty()) {
186 <        context.priority = beginPriority_;
186 >      context.priority = beginPriority_;
187      } else {
188 <        context.priority = sectionParsers_.back().priority + priorityDifference_;
188 >      context.priority = sectionParsers_.back().priority + priorityDifference_;
189      }
190  
191      context.sectionParser = sp;
# Line 187 | Line 195 | void SectionParserManager::push_back(SectionParser* sp
195  
196      sectionParsers_.push_back(context);
197  
198 < }
198 >  }
199  
200 < void SectionParserManager::insert(SectionParser* sp, int priority) {
200 >  void SectionParserManager::insert(SectionParser* sp, int priority) {
201      SectionParserManager::iterator i;
202      i = findSectionParser(sp->getSectionName());
203      if (i != sectionParsers_.end()) {
204 <        std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
204 >      std::cerr << sp->getSectionName() << " section parser already exists"
205 >      << std::endl;
206      }
207  
208      SectionParserContext context;    
# Line 204 | Line 213 | void SectionParserManager::insert(SectionParser* sp, i
213      context.isActive = false;
214  
215      if (sectionParsers_.empty()) {
216 <        sectionParsers_.push_back(context);
216 >      sectionParsers_.push_back(context);
217      } else {
218  
219 <        for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
220 <            if (i->priority == priority) {
221 <                 std::cerr << "Priority " << priority << " already used" << std::endl;
222 <                 return;
223 <            } else if (i->priority > priority) {
224 <                sectionParsers_.insert(i, context);
225 <                break;
226 <            }
219 >      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
220 >        if (i->priority == priority) {
221 >          std::cerr << "Priority " << priority << " already used" << std::endl;
222 >          return;
223 >        } else if (i->priority > priority) {
224 >          sectionParsers_.insert(i, context);
225 >          break;
226 >        }
227              
228 <        }
228 >      }
229      }
230  
231 < }
231 >  }
232  
233  
234 < SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
234 >  SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
235      SectionParserManager::iterator i;
236      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
237 <        if (i->sectionParser->getSectionName() == sectionName) {
238 <            break;
239 <        }
237 >      if (i->sectionParser->getSectionName() == sectionName) {
238 >        break;
239 >      }
240      }
241  
242      return i;
243 < }
243 >  }
244  
245   }

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