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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC

# Line 46 | Line 46
46   * @time 13:51am
47   * @version 1.0
48   */
49 <
49 > #include <exception>
50   #include <iostream>
51   #include <sstream>
52   #include <string>
# Line 81 | Line 81 | namespace oopse {
81  
82   namespace oopse {
83    
84 < Globals* SimCreator::parseFile(const std::string mdFileName){
85 <        Globals* simParams = NULL;
86 <        try {
84 >  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85 >    Globals* simParams = NULL;
86 >    try {
87  
88 <            // Create a preprocessor that preprocesses md file into an ostringstream
89 <            std::stringstream ppStream;
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) {
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);
97 >        SimplePreprocessor preprocessor;
98 >        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, 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);                  
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);
105 >        commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(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);  
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 <                  char* buf = new char[streamSize];
116 <                  assert(buf);
115 >        //receive file content
116 >        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117                  
118 <                  //receive file content
119 <                  commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117 <                
118 <                  ppStream.str(buf);
119 <                  delete buf;
118 >        ppStream.str(buf);
119 >        delete [] buf;
120  
121 <            }
121 >      }
122   #endif            
123 <            // Create a scanner that reads from the input stream
124 <            MDLexer lexer(ppStream);
125 <            lexer.setFilename(mdFileName);
126 <            lexer.initDeferredLineCount();
123 >      // Create a scanner that reads from the input stream
124 >      MDLexer lexer(ppStream);
125 >      lexer.setFilename(filename);
126 >      lexer.initDeferredLineCount();
127      
128 <            // Create a parser that reads from the scanner
129 <            MDParser parser(lexer);
130 <            parser.setFilename(mdFileName);
128 >      // Create a parser that reads from the scanner
129 >      MDParser parser(lexer);
130 >      parser.setFilename(filename);
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);
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 <            antlr::ASTFactory factory;
139 <            parser.initializeASTFactory(factory);
140 <            parser.setASTFactory(&factory);
141 <            parser.mdfile();
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());
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  
149 –        }
150        
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 <        }
151 >    catch(antlr::MismatchedCharException& e) {
152 >      sprintf(painCave.errMsg,
153 >              "parser exception: %s %s:%d:%d\n",
154 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
155 >      painCave.isFatal = 1;
156 >      simError();          
157 >    }
158 >    catch(antlr::MismatchedTokenException &e) {
159 >      sprintf(painCave.errMsg,
160 >              "parser exception: %s %s:%d:%d\n",
161 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
162 >      painCave.isFatal = 1;
163 >      simError();  
164 >    }
165 >    catch(antlr::NoViableAltForCharException &e) {
166 >      sprintf(painCave.errMsg,
167 >              "parser exception: %s %s:%d:%d\n",
168 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
169 >      painCave.isFatal = 1;
170 >      simError();  
171 >    }
172 >    catch(antlr::NoViableAltException &e) {
173 >      sprintf(painCave.errMsg,
174 >              "parser exception: %s %s:%d:%d\n",
175 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
176 >      painCave.isFatal = 1;
177 >      simError();  
178 >    }
179 >      
180 >    catch(antlr::TokenStreamRecognitionException& e) {
181 >      sprintf(painCave.errMsg,
182 >              "parser exception: %s %s:%d:%d\n",
183 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184 >      painCave.isFatal = 1;
185 >      simError();  
186 >    }
187 >        
188 >    catch(antlr::TokenStreamIOException& e) {
189 >      sprintf(painCave.errMsg,
190 >              "parser exception: %s\n",
191 >              e.getMessage().c_str());
192 >      painCave.isFatal = 1;
193 >      simError();
194 >    }
195 >        
196 >    catch(antlr::TokenStreamException& e) {
197 >      sprintf(painCave.errMsg,
198 >              "parser exception: %s\n",
199 >              e.getMessage().c_str());
200 >      painCave.isFatal = 1;
201 >      simError();
202 >    }        
203 >    catch (antlr::RecognitionException& e) {
204 >      sprintf(painCave.errMsg,
205 >              "parser exception: %s %s:%d:%d\n",
206 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
207 >      painCave.isFatal = 1;
208 >      simError();          
209 >    }
210 >    catch (antlr::CharStreamException& e) {
211 >      sprintf(painCave.errMsg,
212 >              "parser exception: %s\n",
213 >              e.getMessage().c_str());
214 >      painCave.isFatal = 1;
215 >      simError();        
216 >    }
217 >    catch (OOPSEException& e) {
218 >      sprintf(painCave.errMsg,
219 >              "%s\n",
220 >              e.getMessage().c_str());
221 >      painCave.isFatal = 1;
222 >      simError();
223 >    }
224 >    catch (std::exception& e) {
225 >      sprintf(painCave.errMsg,
226 >              "parser exception: %s\n",
227 >              e.what());
228 >      painCave.isFatal = 1;
229 >      simError();
230 >    }
231  
232 <        return simParams;
232 >    return simParams;
233    }
234    
235    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236                                    bool loadInitCoords) {
237  
238 +    const int bufferSize = 65535;
239 +    char buffer[bufferSize];
240 +    int lineNo = 0;
241 +    std::string mdRawData;
242 +    int metaDataBlockStart = -1;
243 +    int metaDataBlockEnd = -1;
244 +    int i;
245 +    int mdOffset;
246 +
247 + #ifdef IS_MPI            
248 +    const int masterNode = 0;
249 +    if (worldRank == masterNode) {
250 + #endif
251 +
252 +      std::ifstream mdFile_(mdFileName.c_str());
253 +      
254 +      if (mdFile_.fail()) {
255 +        sprintf(painCave.errMsg,
256 +                "SimCreator: Cannot open file: %s\n",
257 +                mdFileName.c_str());
258 +        painCave.isFatal = 1;
259 +        simError();
260 +      }
261 +
262 +      mdFile_.getline(buffer, bufferSize);
263 +      ++lineNo;
264 +      std::string line = trimLeftCopy(buffer);
265 +      i = CaseInsensitiveFind(line, "<OOPSE");
266 +      if (static_cast<size_t>(i) == string::npos) {
267 +        sprintf(painCave.errMsg,
268 +                "SimCreator: File: %s is not an OOPSE file!\n",
269 +                mdFileName.c_str());
270 +        painCave.isFatal = 1;
271 +        simError();
272 +      }
273 +
274 +      //scan through the input stream and find MetaData tag        
275 +      while(mdFile_.getline(buffer, bufferSize)) {
276 +        ++lineNo;
277 +        
278 +        std::string line = trimLeftCopy(buffer);
279 +        if (metaDataBlockStart == -1) {
280 +          i = CaseInsensitiveFind(line, "<MetaData>");
281 +          if (i != string::npos) {
282 +            metaDataBlockStart = lineNo;
283 +            mdOffset = mdFile_.tellg();
284 +          }
285 +        } else {
286 +          i = CaseInsensitiveFind(line, "</MetaData>");
287 +          if (i != string::npos) {
288 +            metaDataBlockEnd = lineNo;
289 +          }
290 +        }
291 +      }
292 +
293 +      if (metaDataBlockStart == -1) {
294 +        sprintf(painCave.errMsg,
295 +                "SimCreator: File: %s did not contain a <MetaData> tag!\n",
296 +                mdFileName.c_str());
297 +        painCave.isFatal = 1;
298 +        simError();
299 +      }
300 +      if (metaDataBlockEnd == -1) {
301 +        sprintf(painCave.errMsg,
302 +                "SimCreator: File: %s did not contain a closed MetaData block!\n",
303 +                mdFileName.c_str());
304 +        painCave.isFatal = 1;
305 +        simError();
306 +      }
307 +        
308 +      mdFile_.clear();
309 +      mdFile_.seekg(0);
310 +      mdFile_.seekg(mdOffset);
311 +
312 +      mdRawData.clear();
313 +
314 +      for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
315 +        mdFile_.getline(buffer, bufferSize);
316 +        mdRawData += buffer;
317 +        mdRawData += "\n";
318 +      }
319 +
320 +      mdFile_.close();
321 +
322 + #ifdef IS_MPI
323 +    }
324 + #endif
325 +
326 +    std::stringstream rawMetaDataStream(mdRawData);
327 +
328      //parse meta-data file
329 <    Globals* simParams = parseFile(mdFileName);
329 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
330      
331      //create the force field
332 <    ForceField * ff = ForceFieldFactory::getInstance()
333 <      ->createForceField(simParams->getForceField());
194 <    
332 >    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
333 >
334      if (ff == NULL) {
335        sprintf(painCave.errMsg,
336                "ForceField Factory can not create %s force field\n",
# Line 227 | Line 366 | Globals* SimCreator::parseFile(const std::string mdFil
366      ff->setFortranForceOptions();
367      //create SimInfo
368      SimInfo * info = new SimInfo(ff, simParams);
369 +
370 +    info->setRawMetaData(mdRawData);
371      
372 <    //gather parameters (SimCreator only retrieves part of the parameters)
372 >    //gather parameters (SimCreator only retrieves part of the
373 >    //parameters)
374      gatherParameters(info, mdFileName);
375      
376      //divide the molecules and determine the global index of molecules
# Line 240 | Line 382 | Globals* SimCreator::parseFile(const std::string mdFil
382      createMolecules(info);
383      
384      
385 <    //allocate memory for DataStorage(circular reference, need to break it)
385 >    //allocate memory for DataStorage(circular reference, need to
386 >    //break it)
387      info->setSnapshotManager(new SimSnapshotManager(info));
388      
389 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
390 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
391 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
389 >    //set the global index of atoms, rigidbodies and cutoffgroups
390 >    //(only need to be set once, the global index will never change
391 >    //again). Local indices of atoms and rigidbodies are already set
392 >    //by MoleculeCreator class which actually delegates the
393 >    //responsibility to LocalIndexManager.
394      setGlobalIndex(info);
395      
396 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
397 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
398 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
399 <    //we can determine the beginning global indices of atoms before they get created.
396 >    //Although addInteractionPairs is called inside SimInfo's addMolecule
397 >    //method, at that point atoms don't have the global index yet
398 >    //(their global index are all initialized to -1).  Therefore we
399 >    //have to call addInteractionPairs explicitly here. A way to work
400 >    //around is that we can determine the beginning global indices of
401 >    //atoms before they get created.
402      SimInfo::MoleculeIterator mi;
403      Molecule* mol;
404      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
405 <      info->addExcludePairs(mol);
405 >      info->addInteractionPairs(mol);
406      }
407      
408      if (loadInitCoords)
409 <      loadCoordinates(info);    
409 >      loadCoordinates(info, mdFileName);    
410      
411      return info;
412    }
# Line 295 | Line 442 | Globals* SimCreator::parseFile(const std::string mdFil
442    
443   #ifdef IS_MPI
444    void SimCreator::divideMolecules(SimInfo *info) {
445 <    double numerator;
446 <    double denominator;
447 <    double precast;
448 <    double x;
449 <    double y;
450 <    double a;
445 >    RealType numerator;
446 >    RealType denominator;
447 >    RealType precast;
448 >    RealType x;
449 >    RealType y;
450 >    RealType a;
451      int old_atoms;
452      int add_atoms;
453      int new_atoms;
# Line 412 | Line 559 | Globals* SimCreator::parseFile(const std::string mdFil
559            //           Pacc(x) = exp(- a * x)
560            // where a = penalty / (average atoms per molecule)
561            
562 <          x = (double)(new_atoms - nTarget);
562 >          x = (RealType)(new_atoms - nTarget);
563            y = myRandom->rand();
564            
565            if (y < exp(- a * x)) {
# Line 442 | Line 589 | Globals* SimCreator::parseFile(const std::string mdFil
589      info->setMolToProcMap(molToProcMap);
590      sprintf(checkPointMsg,
591              "Successfully divided the molecules among the processors.\n");
592 <    MPIcheckPoint();
592 >    errorCheckPoint();
593    }
594    
595   #endif
# Line 478 | Line 625 | Globals* SimCreator::parseFile(const std::string mdFil
625      Molecule::AtomIterator ai;
626      Molecule::RigidBodyIterator ri;
627      Molecule::CutoffGroupIterator ci;
628 +    Molecule::IntegrableObjectIterator  ioi;
629      Molecule * mol;
630      Atom * atom;
631      RigidBody * rb;
# Line 486 | Line 634 | Globals* SimCreator::parseFile(const std::string mdFil
634      int beginRigidBodyIndex;
635      int beginCutoffGroupIndex;
636      int nGlobalAtoms = info->getNGlobalAtoms();
637 <    
637 >
638 >    /**@todo fixme */
639   #ifndef IS_MPI
640      
641      beginAtomIndex = 0;
# Line 573 | Line 722 | Globals* SimCreator::parseFile(const std::string mdFil
722      // to get the full globalGroupMembership array (We think).
723      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
724      // docs said we could.
725 <    std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
725 >    std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
726      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
727                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
728      info->setGlobalGroupMembership(tmpGroupMembership);
# Line 585 | Line 734 | Globals* SimCreator::parseFile(const std::string mdFil
734      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
735      
736      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
588 –      
737        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
738          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
739        }
740      }
741      
742   #ifdef IS_MPI
743 <    std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
743 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
744      
745      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
746                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 601 | Line 749 | Globals* SimCreator::parseFile(const std::string mdFil
749   #else
750      info->setGlobalMolMembership(globalMolMembership);
751   #endif
752 +
753 +    // nIOPerMol holds the number of integrable objects per molecule
754 +    // here the molecules are listed by their global indices.
755 +
756 +    std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
757 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
758 +      nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
759 +    }
760      
761 + #ifdef IS_MPI
762 +    std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
763 +    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
764 +                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
765 + #else
766 +    std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
767 + #endif    
768 +
769 +    std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
770 +    
771 +    int startingIndex = 0;
772 +    for (int i = 0; i < info->getNGlobalMolecules(); i++) {
773 +      startingIOIndexForMol[i] = startingIndex;
774 +      startingIndex += numIntegrableObjectsPerMol[i];
775 +    }
776 +    
777 +    std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
778 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
779 +      int myGlobalIndex = mol->getGlobalIndex();
780 +      int globalIO = startingIOIndexForMol[myGlobalIndex];
781 +      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
782 +           integrableObject = mol->nextIntegrableObject(ioi)) {
783 +        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
784 +        IOIndexToIntegrableObject[globalIO] = integrableObject;
785 +        globalIO++;
786 +      }
787 +    }
788 +    
789 +    info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
790 +    
791    }
792    
793 <  void SimCreator::loadCoordinates(SimInfo* info) {
793 >  void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
794      Globals* simParams;
795      simParams = info->getSimParams();
796      
611 –    if (!simParams->haveInitialConfig()) {
612 –      sprintf(painCave.errMsg,
613 –              "Cannot intialize a simulation without an initial configuration file.\n");
614 –      painCave.isFatal = 1;;
615 –      simError();
616 –    }
797      
798 <    DumpReader reader(info, simParams->getInitialConfig());
798 >    DumpReader reader(info, mdFileName);
799      int nframes = reader.getNFrames();
800      
801      if (nframes > 0) {
# Line 624 | Line 804 | Globals* SimCreator::parseFile(const std::string mdFil
804        //invalid initial coordinate file
805        sprintf(painCave.errMsg,
806                "Initial configuration file %s should at least contain one frame\n",
807 <              simParams->getInitialConfig().c_str());
807 >              mdFileName.c_str());
808        painCave.isFatal = 1;
809        simError();
810      }

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