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. 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
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#include <algorithm> 
#include <stack>
#include "io/SectionParserManager.hpp"
#include "utils/Trim.hpp"
#include "utils/simError.h"

namespace oopse {

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);
        }
    }
    
}

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;
    }
    
    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 is alway existed" << 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 is alway existed" << 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:	413
Committed:	Wed Mar 9 17:30:29 2005 UTC (20 years, 1 month ago) by tim
File size:	8628 byte(s)
Log Message:	adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
#	User	Rev	Content
1	gezelter	246	/*
2			* 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			* 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include <algorithm>
42	tim	413	#include <stack>
43	gezelter	246	#include "io/SectionParserManager.hpp"
44			#include "utils/Trim.hpp"
45	tim	413	#include "utils/simError.h"
46	gezelter	246
47			namespace oopse {
48
49			SectionParserManager::~SectionParserManager() {
50			SectionParserManager::iterator i;
51			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
52			delete (i->sectionParser);
53			}
54			sectionParsers_.clear();
55			}
56
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;
63			}
64
65			const int bufferSize = 65535;
66			char buffer[bufferSize];
67			int lineNo = 0;
68	tim	413	std::stack<std::string> sectionNameStack;
69	gezelter	246	//scan through the input stream and find section names
70			while(input.getline(buffer, bufferSize)) {
71			++lineNo;
72
73			std::string line = trimLeftCopy(buffer);
74	tim	413	//a line begins with "//" is a comment line
75	gezelter	246	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();
83
84	tim	413	if (keyword == "begin") {
85			std::string section = tokenizer.nextToken();
86			sectionNameStack.push(section);
87	gezelter	246
88	tim	413	i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), SameSectionParserFunctor(section));
89			if (i == sectionParsers_.end()){
90			sprintf(painCave.errMsg, "SectionParserManager Error: Can not find corresponding section parser for %s\n",
91			section.c_str());
92			painCave.isFatal = 1;
93			simError();
94			} else {
95			if (i->isActive) {
96			sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s section\n",
97			section.c_str());
98			painCave.isFatal = 1;
99			simError();
100			} else {
101			i->isActive = true;
102			i->lineNo = lineNo;
103			i->offset = input.tellg();
104			}
105			}
106			} else if (keyword == "end") {
107			std::string section = tokenizer.nextToken();
108			if (sectionNameStack.top() == section) {
109			sectionNameStack.pop();
110			} else {
111			sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
112			sectionNameStack.top().c_str(), section.c_str(), lineNo);
113			painCave.isFatal = 1;
114			simError();
115			}
116
117	gezelter	246	} else {
118	tim	413	continue;
119	gezelter	246	}
120			}
121			}
122
123			}
124
125	tim	413	if (!sectionNameStack.empty()) {
126			sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
127			painCave.isFatal = 1;
128			simError();
129			}
130
131	gezelter	246	//invoke parser
132			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
133			if (i->isActive) {
134			//C++ standard does not guarantee seekg reset EOF, in that case, seekg will fail
135			//It is always a good idea to call clear() before seek
136			input.clear();
137			input.seekg(i->offset);
138			(i->sectionParser)->parse(input, ff, i->lineNo);
139			}
140			}
141
142			}
143
144			void SectionParserManager::push_front(SectionParser* sp) {
145			SectionParserManager::iterator i;
146			i = findSectionParser(sp->getSectionName());
147			if (i != sectionParsers_.end()) {
148			std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
149			return;
150			}
151
152			SectionParserContext context;
153
154			if (sectionParsers_.empty()) {
155			context.priority = beginPriority_;
156			} else {
157			context.priority = sectionParsers_.front().priority - priorityDifference_;
158			}
159
160			context.sectionParser = sp;
161			context.lineNo = 0;
162			context.offset = 0;
163			context.isActive = false;
164
165			sectionParsers_.push_front(context);
166			}
167
168			void SectionParserManager::push_back(SectionParser* sp) {
169			SectionParserManager::iterator i;
170			i = findSectionParser(sp->getSectionName());
171			if (i != sectionParsers_.end()) {
172			std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
173			return;
174			}
175
176			SectionParserContext context;
177			if (sectionParsers_.empty()) {
178			context.priority = beginPriority_;
179			} else {
180			context.priority = sectionParsers_.back().priority + priorityDifference_;
181			}
182
183			context.sectionParser = sp;
184			context.lineNo = 0;
185			context.offset = 0;
186			context.isActive = false;
187
188			sectionParsers_.push_back(context);
189
190			}
191
192			void SectionParserManager::insert(SectionParser* sp, int priority) {
193			SectionParserManager::iterator i;
194			i = findSectionParser(sp->getSectionName());
195			if (i != sectionParsers_.end()) {
196			std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl;
197			}
198
199			SectionParserContext context;
200			context.priority = priority;
201			context.sectionParser = sp;
202			context.lineNo = 0;
203			context.offset = 0;
204			context.isActive = false;
205
206			if (sectionParsers_.empty()) {
207			sectionParsers_.push_back(context);
208			} else {
209
210			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
211			if (i->priority == priority) {
212			std::cerr << "Priority " << priority << " already used" << std::endl;
213			return;
214			} else if (i->priority > priority) {
215			sectionParsers_.insert(i, context);
216			break;
217			}
218
219			}
220			}
221
222			}
223
224
225			SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
226			SectionParserManager::iterator i;
227			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
228			if (i->sectionParser->getSectionName() == sectionName) {
229			break;
230			}
231			}
232
233			return i;
234			}
235
236			}