| 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. |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include <algorithm> |
| 43 |
|
#include <stack> |
| 44 |
+ |
#include <cstdio> |
| 45 |
|
#include "io/SectionParserManager.hpp" |
| 46 |
|
#include "utils/Trim.hpp" |
| 47 |
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#include "utils/simError.h" |
| 48 |
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|
| 49 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
| 50 |
|
|
| 51 |
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SectionParserManager::~SectionParserManager() { |
| 52 |
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SectionParserManager::iterator i; |
| 74 |
|
|
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std::string line = trimLeftCopy(buffer); |
| 76 |
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//a line begins with "//" is a comment line |
| 77 |
< |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
| 77 |
> |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' |
| 78 |
> |
&& line[1] == '/') ) { |
| 79 |
|
continue; |
| 80 |
|
} else { |
| 81 |
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StringTokenizer tokenizer(line); |
| 87 |
|
if (keyword == "begin") { |
| 88 |
|
std::string section = tokenizer.nextToken(); |
| 89 |
|
sectionNameStack.push(section); |
| 90 |
< |
|
| 91 |
< |
i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), SameSectionParserFunctor(section)); |
| 90 |
> |
|
| 91 |
> |
i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(), |
| 92 |
> |
SameSectionParserFunctor(section)); |
| 93 |
|
if (i == sectionParsers_.end()){ |
| 94 |
< |
sprintf(painCave.errMsg, "SectionParserManager Error: Can not find corresponding section parser for %s\n", |
| 95 |
< |
section.c_str()); |
| 94 |
> |
sprintf(painCave.errMsg, |
| 95 |
> |
"SectionParserManager Error: Can not find corresponding " |
| 96 |
> |
"section parser for %s\n", |
| 97 |
> |
section.c_str()); |
| 98 |
|
painCave.isFatal = 1; |
| 99 |
|
simError(); |
| 100 |
|
} else { |
| 101 |
|
if (i->isActive) { |
| 102 |
< |
sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s section\n", |
| 103 |
< |
section.c_str()); |
| 104 |
< |
painCave.isFatal = 1; |
| 105 |
< |
simError(); |
| 102 |
> |
sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s " |
| 103 |
> |
"section\n", |
| 104 |
> |
section.c_str()); |
| 105 |
> |
painCave.isFatal = 1; |
| 106 |
> |
simError(); |
| 107 |
|
} else { |
| 108 |
< |
i->isActive = true; |
| 109 |
< |
i->lineNo = lineNo; |
| 110 |
< |
i->offset = input.tellg(); |
| 108 |
> |
i->isActive = true; |
| 109 |
> |
i->lineNo = lineNo; |
| 110 |
> |
i->offset = input.tellg(); |
| 111 |
|
} |
| 112 |
|
} |
| 113 |
|
} else if (keyword == "end") { |
| 116 |
|
sectionNameStack.pop(); |
| 117 |
|
} else { |
| 118 |
|
sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n", |
| 119 |
< |
sectionNameStack.top().c_str(), section.c_str(), lineNo); |
| 119 |
> |
sectionNameStack.top().c_str(), section.c_str(), lineNo); |
| 120 |
|
painCave.isFatal = 1; |
| 121 |
|
simError(); |
| 122 |
|
} |
| 123 |
< |
|
| 123 |
> |
|
| 124 |
|
} else { |
| 125 |
|
continue; |
| 126 |
|
} |
| 127 |
|
} |
| 128 |
|
} |
| 129 |
< |
|
| 129 |
> |
|
| 130 |
|
} |
| 131 |
< |
|
| 131 |
> |
|
| 132 |
|
if (!sectionNameStack.empty()) { |
| 133 |
|
sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n"); |
| 134 |
|
painCave.isFatal = 1; |
| 135 |
|
simError(); |
| 136 |
|
} |
| 137 |
< |
|
| 137 |
> |
|
| 138 |
|
//invoke parser |
| 139 |
|
for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { |
| 140 |
|
if (i->isActive) { |
| 141 |
< |
//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); |
| 141 |
> |
//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 |
> |
(i->sectionParser)->validateSection(); |
| 147 |
|
} |
| 148 |
|
} |
| 149 |
|
|
| 150 |
|
} |
| 151 |
< |
|
| 151 |
> |
|
| 152 |
|
void SectionParserManager::push_front(SectionParser* sp) { |
| 153 |
|
SectionParserManager::iterator i; |
| 154 |
|
i = findSectionParser(sp->getSectionName()); |
| 155 |
|
if (i != sectionParsers_.end()) { |
| 156 |
< |
std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; |
| 156 |
> |
std::cerr << sp->getSectionName() << " section parser already exists" |
| 157 |
> |
<< std::endl; |
| 158 |
|
return; |
| 159 |
|
} |
| 160 |
|
|
| 165 |
|
} else { |
| 166 |
|
context.priority = sectionParsers_.front().priority - priorityDifference_; |
| 167 |
|
} |
| 168 |
< |
|
| 168 |
> |
|
| 169 |
|
context.sectionParser = sp; |
| 170 |
|
context.lineNo = 0; |
| 171 |
|
context.offset = 0; |
| 178 |
|
SectionParserManager::iterator i; |
| 179 |
|
i = findSectionParser(sp->getSectionName()); |
| 180 |
|
if (i != sectionParsers_.end()) { |
| 181 |
< |
std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; |
| 181 |
> |
std::cerr << sp->getSectionName() << " section parser already exists" |
| 182 |
> |
<< std::endl; |
| 183 |
|
return; |
| 184 |
|
} |
| 185 |
|
|
| 203 |
|
SectionParserManager::iterator i; |
| 204 |
|
i = findSectionParser(sp->getSectionName()); |
| 205 |
|
if (i != sectionParsers_.end()) { |
| 206 |
< |
std::cerr << sp->getSectionName() << " section parser is alway existed" << std::endl; |
| 206 |
> |
std::cerr << sp->getSectionName() << " section parser already exists" |
| 207 |
> |
<< std::endl; |
| 208 |
|
} |
| 209 |
|
|
| 210 |
|
SectionParserContext context; |
| 237 |
|
SectionParserManager::iterator i; |
| 238 |
|
for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) { |
| 239 |
|
if (i->sectionParser->getSectionName() == sectionName) { |
| 240 |
< |
break; |
| 240 |
> |
break; |
| 241 |
|
} |
| 242 |
|
} |
| 243 |
|
|
