# | Line 47 | Line 47 | |
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47 | * @version 1.0 | |
48 | */ | |
49 | ||
50 | + | #include <iostream> |
51 | + | #include <sstream> |
52 | + | #include <string> |
53 | + | |
54 | #include "brains/MoleculeCreator.hpp" | |
55 | #include "brains/SimCreator.hpp" | |
56 | #include "brains/SimSnapshotManager.hpp" | |
57 | #include "io/DumpReader.hpp" | |
54 | – | #include "io/parse_me.h" |
58 | #include "UseTheForce/ForceFieldFactory.hpp" | |
59 | #include "utils/simError.h" | |
60 | #include "utils/StringUtils.hpp" | |
61 | #include "math/SeqRandNumGen.hpp" | |
62 | + | #include "mdParser/MDLexer.hpp" |
63 | + | #include "mdParser/MDParser.hpp" |
64 | + | #include "mdParser/MDTreeParser.hpp" |
65 | + | #include "mdParser/SimplePreprocessor.hpp" |
66 | + | #include "antlr/ANTLRException.hpp" |
67 | + | #include "antlr/TokenStreamRecognitionException.hpp" |
68 | + | #include "antlr/TokenStreamIOException.hpp" |
69 | + | #include "antlr/TokenStreamException.hpp" |
70 | + | #include "antlr/RecognitionException.hpp" |
71 | + | #include "antlr/CharStreamException.hpp" |
72 | + | |
73 | + | #include "antlr/MismatchedCharException.hpp" |
74 | + | #include "antlr/MismatchedTokenException.hpp" |
75 | + | #include "antlr/NoViableAltForCharException.hpp" |
76 | + | #include "antlr/NoViableAltException.hpp" |
77 | + | |
78 | #ifdef IS_MPI | |
60 | – | #include "io/mpiBASS.h" |
79 | #include "math/ParallelRandNumGen.hpp" | |
80 | #endif | |
81 | ||
82 | namespace oopse { | |
83 | ||
84 | < | void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, |
85 | < | Globals* simParams){ |
84 | > | Globals* SimCreator::parseFile(const std::string mdFileName){ |
85 | > | Globals* simParams = NULL; |
86 | > | try { |
87 | > | |
88 | > | // Create a preprocessor that preprocesses md file into an ostringstream |
89 | > | std::stringstream ppStream; |
90 | > | #ifdef IS_MPI |
91 | > | int streamSize; |
92 | > | const int masterNode = 0; |
93 | > | int commStatus; |
94 | > | if (worldRank == masterNode) { |
95 | > | #endif |
96 | > | |
97 | > | SimplePreprocessor preprocessor; |
98 | > | preprocessor.preprocess(mdFileName, ppStream); |
99 | > | |
100 | > | #ifdef IS_MPI |
101 | > | //brocasting the stream size |
102 | > | streamSize = ppStream.str().size() +1; |
103 | > | commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
104 | > | |
105 | > | commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
106 | > | |
107 | > | |
108 | > | } else { |
109 | > | //get stream size |
110 | > | commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
111 | > | |
112 | > | char* buf = new char[streamSize]; |
113 | > | assert(buf); |
114 | > | |
115 | > | //receive file content |
116 | > | commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
117 | > | |
118 | > | ppStream.str(buf); |
119 | > | delete buf; |
120 | > | |
121 | > | } |
122 | > | #endif |
123 | > | // Create a scanner that reads from the input stream |
124 | > | MDLexer lexer(ppStream); |
125 | > | lexer.setFilename(mdFileName); |
126 | > | lexer.initDeferredLineCount(); |
127 | ||
128 | < | #ifdef IS_MPI |
128 | > | // Create a parser that reads from the scanner |
129 | > | MDParser parser(lexer); |
130 | > | parser.setFilename(mdFileName); |
131 | > | |
132 | > | // Create an observer that synchorizes file name change |
133 | > | FilenameObserver observer; |
134 | > | observer.setLexer(&lexer); |
135 | > | observer.setParser(&parser); |
136 | > | lexer.setObserver(&observer); |
137 | ||
138 | < | if (worldRank == 0) { |
139 | < | #endif // is_mpi |
138 | > | antlr::ASTFactory factory; |
139 | > | parser.initializeASTFactory(factory); |
140 | > | parser.setASTFactory(&factory); |
141 | > | parser.mdfile(); |
142 | > | |
143 | > | // Create a tree parser that reads information into Globals |
144 | > | MDTreeParser treeParser; |
145 | > | treeParser.initializeASTFactory(factory); |
146 | > | treeParser.setASTFactory(&factory); |
147 | > | simParams = treeParser.walkTree(parser.getAST()); |
148 | > | |
149 | > | } |
150 | ||
151 | < | set_interface_stamps(stamps, simParams); |
152 | < | |
153 | < | #ifdef IS_MPI |
154 | < | |
155 | < | mpiEventInit(); |
156 | < | |
157 | < | #endif |
158 | < | |
159 | < | yacc_BASS(mdFileName.c_str()); |
160 | < | |
161 | < | #ifdef IS_MPI |
162 | < | |
163 | < | throwMPIEvent(NULL); |
164 | < | } else { |
165 | < | set_interface_stamps(stamps, simParams); |
166 | < | mpiEventInit(); |
167 | < | MPIcheckPoint(); |
168 | < | mpiEventLoop(); |
169 | < | } |
170 | < | |
171 | < | #endif |
172 | < | |
151 | > | catch(antlr::MismatchedCharException& e) { |
152 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
153 | > | } |
154 | > | catch(antlr::MismatchedTokenException &e) { |
155 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
156 | > | } |
157 | > | catch(antlr::NoViableAltForCharException &e) { |
158 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
159 | > | } |
160 | > | catch(antlr::NoViableAltException &e) { |
161 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
162 | > | } |
163 | > | catch(antlr::TokenStreamRecognitionException& e) { |
164 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
165 | > | } |
166 | > | catch(antlr::TokenStreamIOException& e) { |
167 | > | cerr<< "parser exception: " << e.getMessage() << endl; |
168 | > | } |
169 | > | catch(antlr::TokenStreamException& e) { |
170 | > | cerr<< "parser exception: " << e.getMessage() << endl; |
171 | > | } |
172 | > | catch (antlr::RecognitionException& e) { |
173 | > | cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
174 | > | } |
175 | > | catch (antlr::CharStreamException& e) { |
176 | > | cerr << "parser exception: " << e.getMessage() << endl; |
177 | > | } |
178 | > | catch (exception& e) { |
179 | > | cerr << "parser exception: " << e.what() << endl; |
180 | > | } |
181 | > | |
182 | > | return simParams; |
183 | } | |
184 | ||
185 | SimInfo* SimCreator::createSim(const std::string & mdFileName, | |
186 | bool loadInitCoords) { | |
187 | < | |
101 | < | MakeStamps * stamps = new MakeStamps(); |
102 | < | |
103 | < | Globals * simParams = new Globals(); |
104 | < | |
187 | > | |
188 | //parse meta-data file | |
189 | < | parseFile(mdFileName, stamps, simParams); |
189 | > | Globals* simParams = parseFile(mdFileName); |
190 | ||
191 | //create the force field | |
192 | ForceField * ff = ForceFieldFactory::getInstance() | |
# | Line 139 | Line 222 | namespace oopse { | |
222 | forcefieldFileName.append(variant); | |
223 | } | |
224 | } | |
142 | – | |
143 | – | ff->parse(forcefieldFileName); |
225 | ||
226 | < | //extract the molecule stamps |
227 | < | std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
147 | < | compList(stamps, simParams, moleculeStampPairs); |
148 | < | |
226 | > | ff->parse(forcefieldFileName); |
227 | > | ff->setFortranForceOptions(); |
228 | //create SimInfo | |
229 | < | SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
229 | > | SimInfo * info = new SimInfo(ff, simParams); |
230 | ||
231 | //gather parameters (SimCreator only retrieves part of the parameters) | |
232 | gatherParameters(info, mdFileName); | |
# | Line 393 | Line 472 | namespace oopse { | |
472 | ||
473 | } //end for(int i=0) | |
474 | } | |
396 | – | |
397 | – | void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
398 | – | std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
399 | – | int i; |
400 | – | char * id; |
401 | – | MoleculeStamp * currentStamp; |
402 | – | Component** the_components = simParams->getComponents(); |
403 | – | int n_components = simParams->getNComponents(); |
475 | ||
405 | – | if (!simParams->haveNMol()) { |
406 | – | // we don't have the total number of molecules, so we assume it is |
407 | – | // given in each component |
408 | – | |
409 | – | for(i = 0; i < n_components; i++) { |
410 | – | if (!the_components[i]->haveNMol()) { |
411 | – | // we have a problem |
412 | – | sprintf(painCave.errMsg, |
413 | – | "SimCreator Error. No global NMol or component NMol given.\n" |
414 | – | "\tCannot calculate the number of atoms.\n"); |
415 | – | |
416 | – | painCave.isFatal = 1; |
417 | – | simError(); |
418 | – | } |
419 | – | |
420 | – | id = the_components[i]->getType(); |
421 | – | |
422 | – | currentStamp = stamps->getMolStamp(id); |
423 | – | if (currentStamp == NULL) { |
424 | – | sprintf(painCave.errMsg, |
425 | – | "SimCreator error: Component \"%s\" was not found in the " |
426 | – | "list of declared molecules\n", id); |
427 | – | |
428 | – | painCave.isFatal = 1; |
429 | – | simError(); |
430 | – | } |
431 | – | |
432 | – | moleculeStampPairs.push_back( |
433 | – | std::make_pair(currentStamp, the_components[i]->getNMol())); |
434 | – | } //end for (i = 0; i < n_components; i++) |
435 | – | } else { |
436 | – | sprintf(painCave.errMsg, "SimSetup error.\n" |
437 | – | "\tSorry, the ability to specify total" |
438 | – | " nMols and then give molfractions in the components\n" |
439 | – | "\tis not currently supported." |
440 | – | " Please give nMol in the components.\n"); |
441 | – | |
442 | – | painCave.isFatal = 1; |
443 | – | simError(); |
444 | – | } |
445 | – | |
446 | – | #ifdef IS_MPI |
447 | – | |
448 | – | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
449 | – | MPIcheckPoint(); |
450 | – | |
451 | – | #endif // is_mpi |
452 | – | |
453 | – | } |
454 | – | |
476 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
477 | SimInfo::MoleculeIterator mi; | |
478 | Molecule::AtomIterator ai; |
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