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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 2101 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 2515 by tim, Fri Dec 16 18:26:41 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 <      simParams->initalize();
152 <      set_interface_stamps(stamps, simParams);
153 <      
154 < #ifdef IS_MPI
155 <      
156 <      mpiEventInit();
157 <      
158 < #endif
159 <      
160 <      yacc_BASS(mdFileName.c_str());
161 <      
162 < #ifdef IS_MPI
163 <      
164 <      throwMPIEvent(NULL);
165 <    } else {
166 <      set_interface_stamps(stamps, simParams);
167 <      mpiEventInit();
168 <      MPIcheckPoint();
169 <      mpiEventLoop();
170 <    }
171 <    
172 < #endif
173 <    
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, bool loadInitCoords) {
186 <    
187 <    MakeStamps * stamps = new MakeStamps();
102 <    
103 <    Globals * simParams = new Globals();
104 <    
185 >  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
186 >                                  bool loadInitCoords) {
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()->createForceField(
193 <                                                                         simParams->getForceField());
192 >    ForceField * ff = ForceFieldFactory::getInstance()
193 >      ->createForceField(simParams->getForceField());
194      
195      if (ff == NULL) {
196 <      sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
197 <              simParams->getForceField());
196 >      sprintf(painCave.errMsg,
197 >              "ForceField Factory can not create %s force field\n",
198 >              simParams->getForceField().c_str());
199        painCave.isFatal = 1;
200        simError();
201      }
# Line 140 | Line 224 | namespace oopse {
224      }
225      
226      ff->parse(forcefieldFileName);
227 <    
144 <    //extract the molecule stamps
145 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146 <    compList(stamps, simParams, moleculeStampPairs);
147 <    
227 >        
228      //create SimInfo
229 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
230 <    
229 >    SimInfo * info = new SimInfo(ff, simParams);
230 >    
231      //gather parameters (SimCreator only retrieves part of the parameters)
232      gatherParameters(info, mdFileName);
233      
# Line 178 | Line 258 | namespace oopse {
258        info->addExcludePairs(mol);
259      }
260      
181 –    
182 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183 –    //eta, chi for NPT integrator)
261      if (loadInitCoords)
262        loadCoordinates(info);    
263      
# Line 189 | 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 395 | Line 472 | namespace oopse {
472        
473      } //end for(int i=0)  
474    }
398 –  
399 –  void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
400 –                            std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
401 –    int i;
402 –    char * id;
403 –    LinkedMolStamp* extractedStamp = NULL;
404 –    MoleculeStamp * currentStamp;
405 –    Component** the_components = simParams->getComponents();
406 –    int n_components = simParams->getNComponents();
475      
408 –    if (!simParams->haveNMol()) {
409 –      // we don't have the total number of molecules, so we assume it is
410 –      // given in each component
411 –      
412 –      for(i = 0; i < n_components; i++) {
413 –        if (!the_components[i]->haveNMol()) {
414 –          // we have a problem
415 –          sprintf(painCave.errMsg,
416 –                  "SimCreator Error. No global NMol or component NMol given.\n"
417 –                  "\tCannot calculate the number of atoms.\n");
418 –          
419 –          painCave.isFatal = 1;
420 –          simError();
421 –        }
422 –        
423 –        id = the_components[i]->getType();
424 –        
425 –        extractedStamp = stamps->extractMolStamp(id);
426 –        if (extractedStamp == NULL) {
427 –          sprintf(painCave.errMsg,
428 –                  "SimCreator error: Component \"%s\" was not found in the "
429 –                  "list of declared molecules\n", id);
430 –          
431 –          painCave.isFatal = 1;
432 –          simError();
433 –        }
434 –        
435 –        currentStamp = extractedStamp->getStamp();
436 –        
437 –        
438 –        moleculeStampPairs.push_back(
439 –                                     std::make_pair(currentStamp, the_components[i]->getNMol()));
440 –      } //end for (i = 0; i < n_components; i++)
441 –    } else {
442 –      sprintf(painCave.errMsg, "SimSetup error.\n"
443 –              "\tSorry, the ability to specify total"
444 –              " nMols and then give molfractions in the components\n"
445 –              "\tis not currently supported."
446 –              " Please give nMol in the components.\n");
447 –      
448 –      painCave.isFatal = 1;
449 –      simError();
450 –    }
451 –    
452 – #ifdef IS_MPI
453 –    
454 –    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
455 –    MPIcheckPoint();
456 –    
457 – #endif // is_mpi
458 –    
459 –  }
460 –  
476    void SimCreator::setGlobalIndex(SimInfo *info) {
477      SimInfo::MoleculeIterator mi;
478      Molecule::AtomIterator ai;
# Line 609 | Line 624 | namespace oopse {
624        //invalid initial coordinate file
625        sprintf(painCave.errMsg,
626                "Initial configuration file %s should at least contain one frame\n",
627 <              simParams->getInitialConfig());
627 >              simParams->getInitialConfig().c_str());
628        painCave.isFatal = 1;
629        simError();
630      }

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