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Comparing trunk/src/io/SectionParserManager.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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() {
50      SectionParserManager::iterator i;
# Line 72 | Line 72 | namespace oopse {
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] == '/')) {
75 >      if ( line.empty() || (line.size() >= 2 && line[0] == '/'
76 >                            && line[1] == '/') ) {
77          continue;
78        } else {        
79          StringTokenizer tokenizer(line);
# Line 84 | Line 85 | namespace oopse {
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));
88 >
89 >            i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
90 >                       SameSectionParserFunctor(section));
91              if (i == sectionParsers_.end()){
92 <              sprintf(painCave.errMsg, "SectionParserManager Error: Can not find corresponding section parser for %s\n",
93 <                      section.c_str());
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 section\n",
101 <                        section.c_str());
102 <                painCave.isFatal = 1;
103 <                simError();                        
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();
106 >          i->isActive = true;
107 >          i->lineNo = lineNo;
108 >          i->offset = input.tellg();
109                }
110              }
111            } else if (keyword == "end") {
# Line 109 | Line 114 | namespace oopse {
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);
117 >                sectionNameStack.top().c_str(), section.c_str(), lineNo);
118                painCave.isFatal = 1;
119                simError();
120              }
121 <                    
121 >      
122            } else {
123              continue;
124            }
125          }
126        }
127 <        
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();
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);
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 <
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;
154 >      std::cerr << sp->getSectionName() << " section parser already exists"
155 >      << std::endl;
156        return;
157      }
158      
# Line 156 | Line 163 | namespace oopse {
163      } else {
164        context.priority = sectionParsers_.front().priority - priorityDifference_;
165      }
166 <
166 >    
167      context.sectionParser = sp;
168      context.lineNo = 0;
169      context.offset = 0;
# Line 169 | Line 176 | namespace oopse {
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;
179 >      std::cerr << sp->getSectionName() << " section parser already exists"
180 >      << std::endl;
181        return;
182      }
183  
# Line 193 | Line 201 | namespace oopse {
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 226 | Line 235 | namespace oopse {
235      SectionParserManager::iterator i;
236      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
237        if (i->sectionParser->getSectionName() == sectionName) {
238 <        break;
238 >        break;
239        }
240      }
241  

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