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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 1401 by jmarr, Wed Jan 6 21:06:59 2010 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>
43 + #include <cstdio>
44   #include "io/SectionParserManager.hpp"
45   #include "utils/Trim.hpp"
46   #include "utils/simError.h"
47  
48 < namespace oopse {
48 > namespace OpenMD {
49  
50    SectionParserManager::~SectionParserManager() {
51      SectionParserManager::iterator i;
# Line 72 | Line 73 | namespace oopse {
73          
74        std::string line = trimLeftCopy(buffer);
75        //a line begins with "//" is a comment line
76 <      if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
76 >      if ( line.empty() || (line.size() >= 2 && line[0] == '/'
77 >                            && line[1] == '/') ) {
78          continue;
79        } else {        
80          StringTokenizer tokenizer(line);
# Line 84 | Line 86 | namespace oopse {
86            if (keyword == "begin") {
87              std::string section = tokenizer.nextToken();
88              sectionNameStack.push(section);
89 <
90 <            i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), SameSectionParserFunctor(section));
89 >
90 >            i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
91 >                       SameSectionParserFunctor(section));
92              if (i == sectionParsers_.end()){
93 <              sprintf(painCave.errMsg, "SectionParserManager Error: Can not find corresponding section parser for %s\n",
94 <                      section.c_str());
93 >              sprintf(painCave.errMsg,
94 >                "SectionParserManager Error: Can not find corresponding "
95 >                "section parser for %s\n",
96 >                section.c_str());
97                painCave.isFatal = 1;
98                simError();                        
99              } else {
100                if (i->isActive) {
101 <                sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s section\n",
102 <                        section.c_str());
103 <                painCave.isFatal = 1;
104 <                simError();                        
101 >          sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s "
102 >                  "section\n",
103 >                  section.c_str());
104 >          painCave.isFatal = 1;
105 >          simError();                        
106                } else {                        
107 <                i->isActive = true;
108 <                i->lineNo = lineNo;
109 <                i->offset = input.tellg();
107 >          i->isActive = true;
108 >          i->lineNo = lineNo;
109 >          i->offset = input.tellg();
110                }
111              }
112            } else if (keyword == "end") {
# Line 109 | Line 115 | namespace oopse {
115                sectionNameStack.pop();
116              } else {
117                sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
118 <                      sectionNameStack.top().c_str(), section.c_str(), lineNo);
118 >                sectionNameStack.top().c_str(), section.c_str(), lineNo);
119                painCave.isFatal = 1;
120                simError();
121              }
122 <                    
122 >      
123            } else {
124              continue;
125            }
126          }
127        }
128 <        
128 >      
129      }
130 <
130 >    
131      if (!sectionNameStack.empty()) {
132        sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
133        painCave.isFatal = 1;
134        simError();
135      }
136 <
136 >    
137      //invoke parser
138      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
139        if (i->isActive) {
140 <        //C++ standard does not guarantee seekg  reset EOF, in that case, seekg will fail
141 <        //It is always a good idea to call clear() before seek
142 <        input.clear();            
143 <        input.seekg(i->offset);
144 <        (i->sectionParser)->parse(input, ff, i->lineNo);
140 >        //C++ standard does not guarantee seekg  reset EOF, in that case, seekg will fail
141 >        //It is always a good idea to call clear() before seek
142 >        input.clear();            
143 >        input.seekg(i->offset);
144 >        (i->sectionParser)->parse(input, ff, i->lineNo);
145 >        (i->sectionParser)->validateSection();
146        }
147      }
148      
149    }
150 <
150 >  
151    void SectionParserManager::push_front(SectionParser* sp) {
152      SectionParserManager::iterator i;
153      i = findSectionParser(sp->getSectionName());
154      if (i != sectionParsers_.end()) {
155 <      std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
155 >      std::cerr << sp->getSectionName() << " section parser already exists"
156 >      << std::endl;
157        return;
158      }
159      
# Line 156 | Line 164 | namespace oopse {
164      } else {
165        context.priority = sectionParsers_.front().priority - priorityDifference_;
166      }
167 <
167 >    
168      context.sectionParser = sp;
169      context.lineNo = 0;
170      context.offset = 0;
# Line 169 | Line 177 | namespace oopse {
177      SectionParserManager::iterator i;
178      i = findSectionParser(sp->getSectionName());
179      if (i != sectionParsers_.end()) {
180 <      std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
180 >      std::cerr << sp->getSectionName() << " section parser already exists"
181 >      << std::endl;
182        return;
183      }
184  
# Line 193 | Line 202 | namespace oopse {
202      SectionParserManager::iterator i;
203      i = findSectionParser(sp->getSectionName());
204      if (i != sectionParsers_.end()) {
205 <      std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
205 >      std::cerr << sp->getSectionName() << " section parser already exists"
206 >      << std::endl;
207      }
208  
209      SectionParserContext context;    
# Line 226 | Line 236 | namespace oopse {
236      SectionParserManager::iterator i;
237      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
238        if (i->sectionParser->getSectionName() == sectionName) {
239 <        break;
239 >        break;
240        }
241      }
242  

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