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root/group/trunk/OOPSE-2.0/src/brains/SimCreator.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimCreator.cpp (file contents):
Revision 2364 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 2522 by chuckv, Thu Dec 29 16:03:11 2005 UTC

# Line 47 | Line 47
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);
144 –    
145 –    //extract the molecule stamps
146 –    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147 –    compList(stamps, simParams, moleculeStampPairs);
225      
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 187 | Line 266 | namespace oopse {
266    
267    void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
268      
269 <    //figure out the ouput file names
269 >    //figure out the output file names
270      std::string prefix;
271      
272   #ifdef IS_MPI
# 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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