src/io/SectionParserManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 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.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * 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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include <algorithm> 
#include <stack>
#include <cstdio>
#include "io/SectionParserManager.hpp"
#include "utils/Trim.hpp"
#include "utils/simError.h"

namespace OpenMD {

  SectionParserManager::~SectionParserManager() {
    SectionParserManager::iterator i;
    for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
      delete (i->sectionParser);
    }
    sectionParsers_.clear();
  }

  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;
    }

    const int bufferSize = 65535;
    char buffer[bufferSize];
    int lineNo = 0;
    std::stack<std::string> sectionNameStack;
    //scan through the input stream and find section names        
    while(input.getline(buffer, bufferSize)) {
      ++lineNo;
        
      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") {
            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);
        (i->sectionParser)->validateSection();
      }
    }
    
  }
  
  void SectionParserManager::push_front(SectionParser* sp) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
      return;
    }
    
    SectionParserContext context;
    
    if (sectionParsers_.empty()) {
      context.priority = beginPriority_;
    } else {
      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) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
      return;
    }

    SectionParserContext context;    
    if (sectionParsers_.empty()) {
      context.priority = beginPriority_;
    } else {
      context.priority = sectionParsers_.back().priority + priorityDifference_;
    }

    context.sectionParser = sp;
    context.lineNo = 0;
    context.offset = 0;
    context.isActive = false;

    sectionParsers_.push_back(context);

  }

  void SectionParserManager::insert(SectionParser* sp, int priority) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
    }

    SectionParserContext context;    
    context.priority = priority;
    context.sectionParser = sp;
    context.lineNo = 0;
    context.offset = 0;
    context.isActive = false;

    if (sectionParsers_.empty()) {
      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;
        }
            
      }
    }

  }


  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;
      }
    }

    return i;
  }

}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	8158 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42			#include <algorithm>
43	tim	413	#include <stack>
44	jmarr	1401	#include <cstdio>
45	gezelter	246	#include "io/SectionParserManager.hpp"
46			#include "utils/Trim.hpp"
47	tim	413	#include "utils/simError.h"
48	gezelter	246
49	gezelter	1390	namespace OpenMD {
50	gezelter	246
51	gezelter	507	SectionParserManager::~SectionParserManager() {
52	gezelter	246	SectionParserManager::iterator i;
53			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
54	gezelter	507	delete (i->sectionParser);
55	gezelter	246	}
56			sectionParsers_.clear();
57	gezelter	507	}
58	gezelter	246
59	gezelter	507	void SectionParserManager::parse(std::istream& input, ForceField& ff) {
60	gezelter	246
61			//reset active flags
62			SectionParserManager::iterator i;
63			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
64	gezelter	507	i->isActive = false;
65	gezelter	246	}
66
67			const int bufferSize = 65535;
68			char buffer[bufferSize];
69			int lineNo = 0;
70	tim	413	std::stack<std::string> sectionNameStack;
71	gezelter	246	//scan through the input stream and find section names
72			while(input.getline(buffer, bufferSize)) {
73	gezelter	507	++lineNo;
74	gezelter	246
75	gezelter	507	std::string line = trimLeftCopy(buffer);
76			//a line begins with "//" is a comment line
77	chrisfen	514	if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/'
78			&& line[1] == '/') ) {
79	gezelter	507	continue;
80			} else {
81			StringTokenizer tokenizer(line);
82			if (tokenizer.countTokens() < 2) {
83			continue;
84			} else {
85			std::string keyword = tokenizer.nextToken();
86	gezelter	246
87	gezelter	507	if (keyword == "begin") {
88			std::string section = tokenizer.nextToken();
89			sectionNameStack.push(section);
90	chrisfen	514
91			i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
92			SameSectionParserFunctor(section));
93	gezelter	507	if (i == sectionParsers_.end()){
94	chrisfen	514	sprintf(painCave.errMsg,
95			"SectionParserManager Error: Can not find corresponding "
96			"section parser for %s\n",
97			section.c_str());
98	gezelter	507	painCave.isFatal = 1;
99			simError();
100			} else {
101			if (i->isActive) {
102	chrisfen	514	sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s "
103			"section\n",
104			section.c_str());
105			painCave.isFatal = 1;
106			simError();
107	gezelter	507	} else {
108	chrisfen	514	i->isActive = true;
109			i->lineNo = lineNo;
110			i->offset = input.tellg();
111	gezelter	507	}
112			}
113			} else if (keyword == "end") {
114			std::string section = tokenizer.nextToken();
115			if (sectionNameStack.top() == section) {
116			sectionNameStack.pop();
117			} else {
118			sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
119	chrisfen	514	sectionNameStack.top().c_str(), section.c_str(), lineNo);
120	gezelter	507	painCave.isFatal = 1;
121			simError();
122			}
123	chrisfen	514
124	gezelter	507	} else {
125			continue;
126			}
127			}
128			}
129	chrisfen	514
130	gezelter	246	}
131	chrisfen	514
132	tim	413	if (!sectionNameStack.empty()) {
133	gezelter	507	sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
134			painCave.isFatal = 1;
135			simError();
136	tim	413	}
137	chrisfen	514
138	gezelter	246	//invoke parser
139			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
140	gezelter	507	if (i->isActive) {
141	chrisfen	514	//C++ standard does not guarantee seekg reset EOF, in that case, seekg will fail
142			//It is always a good idea to call clear() before seek
143			input.clear();
144			input.seekg(i->offset);
145			(i->sectionParser)->parse(input, ff, i->lineNo);
146	tim	749	(i->sectionParser)->validateSection();
147	gezelter	507	}
148	gezelter	246	}
149
150	gezelter	507	}
151	chrisfen	514
152	gezelter	507	void SectionParserManager::push_front(SectionParser* sp) {
153	gezelter	246	SectionParserManager::iterator i;
154			i = findSectionParser(sp->getSectionName());
155			if (i != sectionParsers_.end()) {
156	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
157	chrisfen	514	<< std::endl;
158	gezelter	507	return;
159	gezelter	246	}
160
161			SectionParserContext context;
162
163			if (sectionParsers_.empty()) {
164	gezelter	507	context.priority = beginPriority_;
165	gezelter	246	} else {
166	gezelter	507	context.priority = sectionParsers_.front().priority - priorityDifference_;
167	gezelter	246	}
168	chrisfen	514
169	gezelter	246	context.sectionParser = sp;
170			context.lineNo = 0;
171			context.offset = 0;
172			context.isActive = false;
173
174			sectionParsers_.push_front(context);
175	gezelter	507	}
176	gezelter	246
177	gezelter	507	void SectionParserManager::push_back(SectionParser* sp) {
178	gezelter	246	SectionParserManager::iterator i;
179			i = findSectionParser(sp->getSectionName());
180			if (i != sectionParsers_.end()) {
181	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
182	chrisfen	514	<< std::endl;
183	gezelter	507	return;
184	gezelter	246	}
185
186			SectionParserContext context;
187			if (sectionParsers_.empty()) {
188	gezelter	507	context.priority = beginPriority_;
189	gezelter	246	} else {
190	gezelter	507	context.priority = sectionParsers_.back().priority + priorityDifference_;
191	gezelter	246	}
192
193			context.sectionParser = sp;
194			context.lineNo = 0;
195			context.offset = 0;
196			context.isActive = false;
197
198			sectionParsers_.push_back(context);
199
200	gezelter	507	}
201	gezelter	246
202	gezelter	507	void SectionParserManager::insert(SectionParser* sp, int priority) {
203	gezelter	246	SectionParserManager::iterator i;
204			i = findSectionParser(sp->getSectionName());
205			if (i != sectionParsers_.end()) {
206	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
207	chrisfen	514	<< std::endl;
208	gezelter	246	}
209
210			SectionParserContext context;
211			context.priority = priority;
212			context.sectionParser = sp;
213			context.lineNo = 0;
214			context.offset = 0;
215			context.isActive = false;
216
217			if (sectionParsers_.empty()) {
218	gezelter	507	sectionParsers_.push_back(context);
219	gezelter	246	} else {
220
221	gezelter	507	for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
222			if (i->priority == priority) {
223			std::cerr << "Priority " << priority << " already used" << std::endl;
224			return;
225			} else if (i->priority > priority) {
226			sectionParsers_.insert(i, context);
227			break;
228			}
229	gezelter	246
230	gezelter	507	}
231	gezelter	246	}
232
233	gezelter	507	}
234	gezelter	246
235
236	gezelter	507	SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
237	gezelter	246	SectionParserManager::iterator i;
238			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
239	gezelter	507	if (i->sectionParser->getSectionName() == sectionName) {
240	chrisfen	514	break;
241	gezelter	507	}
242	gezelter	246	}
243
244			return i;
245	gezelter	507	}
246	gezelter	246
247			}