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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 845 by tim, Wed Jan 11 19:01:20 2006 UTC vs.
Revision 1136 by chuckv, Sat May 26 17:53:52 2007 UTC

# 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(static_cast<void*>(const_cast<char*>(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);
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);
115 >        //receive file content
116 >        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        
152 <      catch(antlr::MismatchedCharException& e) {
153 <          sprintf(painCave.errMsg,
154 <                  "parser exception: %s %s:%d:%d\n",
155 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
156 <          painCave.isFatal = 1;
157 <          simError();          
158 <      }
159 <      catch(antlr::MismatchedTokenException &e) {
160 <          sprintf(painCave.errMsg,
161 <                  "parser exception: %s %s:%d:%d\n",
162 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163 <          painCave.isFatal = 1;
164 <          simError();  
165 <      }
166 <      catch(antlr::NoViableAltForCharException &e) {
167 <          sprintf(painCave.errMsg,
168 <                  "parser exception: %s %s:%d:%d\n",
169 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170 <          painCave.isFatal = 1;
171 <          simError();  
172 <      }
173 <      catch(antlr::NoViableAltException &e) {
174 <          sprintf(painCave.errMsg,
175 <                  "parser exception: %s %s:%d:%d\n",
176 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177 <          painCave.isFatal = 1;
178 <          simError();  
179 <      }
152 >    catch(antlr::MismatchedCharException& e) {
153 >      sprintf(painCave.errMsg,
154 >              "parser exception: %s %s:%d:%d\n",
155 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
156 >      painCave.isFatal = 1;
157 >      simError();          
158 >    }
159 >    catch(antlr::MismatchedTokenException &e) {
160 >      sprintf(painCave.errMsg,
161 >              "parser exception: %s %s:%d:%d\n",
162 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163 >      painCave.isFatal = 1;
164 >      simError();  
165 >    }
166 >    catch(antlr::NoViableAltForCharException &e) {
167 >      sprintf(painCave.errMsg,
168 >              "parser exception: %s %s:%d:%d\n",
169 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170 >      painCave.isFatal = 1;
171 >      simError();  
172 >    }
173 >    catch(antlr::NoViableAltException &e) {
174 >      sprintf(painCave.errMsg,
175 >              "parser exception: %s %s:%d:%d\n",
176 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177 >      painCave.isFatal = 1;
178 >      simError();  
179 >    }
180        
181 <        catch(antlr::TokenStreamRecognitionException& e) {
182 <          sprintf(painCave.errMsg,
183 <                  "parser exception: %s %s:%d:%d\n",
184 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185 <          painCave.isFatal = 1;
186 <          simError();  
187 <        }
181 >    catch(antlr::TokenStreamRecognitionException& e) {
182 >      sprintf(painCave.errMsg,
183 >              "parser exception: %s %s:%d:%d\n",
184 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185 >      painCave.isFatal = 1;
186 >      simError();  
187 >    }
188          
189 <        catch(antlr::TokenStreamIOException& e) {
190 <          sprintf(painCave.errMsg,
191 <                  "parser exception: %s\n",
192 <                  e.getMessage().c_str());
193 <          painCave.isFatal = 1;
194 <          simError();
195 <        }
189 >    catch(antlr::TokenStreamIOException& e) {
190 >      sprintf(painCave.errMsg,
191 >              "parser exception: %s\n",
192 >              e.getMessage().c_str());
193 >      painCave.isFatal = 1;
194 >      simError();
195 >    }
196          
197 <        catch(antlr::TokenStreamException& e) {
198 <          sprintf(painCave.errMsg,
199 <                  "parser exception: %s\n",
200 <                  e.getMessage().c_str());
201 <          painCave.isFatal = 1;
202 <          simError();
203 <        }        
204 <       catch (antlr::RecognitionException& e) {
205 <          sprintf(painCave.errMsg,
206 <                  "parser exception: %s %s:%d:%d\n",
207 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
208 <          painCave.isFatal = 1;
209 <          simError();          
210 <       }
211 <       catch (antlr::CharStreamException& e) {
212 <          sprintf(painCave.errMsg,
213 <                  "parser exception: %s\n",
214 <                  e.getMessage().c_str());
215 <          painCave.isFatal = 1;
216 <          simError();        
217 <       }
218 <       catch (OOPSEException& e) {
219 <          sprintf(painCave.errMsg,
220 <                  "%s\n",
221 <                  e.getMessage().c_str());
222 <          painCave.isFatal = 1;
223 <          simError();
224 <       }
225 <       catch (std::exception& e) {
226 <          sprintf(painCave.errMsg,
227 <                  "parser exception: %s\n",
228 <                  e.what());
229 <          painCave.isFatal = 1;
230 <          simError();
231 <       }
197 >    catch(antlr::TokenStreamException& e) {
198 >      sprintf(painCave.errMsg,
199 >              "parser exception: %s\n",
200 >              e.getMessage().c_str());
201 >      painCave.isFatal = 1;
202 >      simError();
203 >    }        
204 >    catch (antlr::RecognitionException& e) {
205 >      sprintf(painCave.errMsg,
206 >              "parser exception: %s %s:%d:%d\n",
207 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
208 >      painCave.isFatal = 1;
209 >      simError();          
210 >    }
211 >    catch (antlr::CharStreamException& e) {
212 >      sprintf(painCave.errMsg,
213 >              "parser exception: %s\n",
214 >              e.getMessage().c_str());
215 >      painCave.isFatal = 1;
216 >      simError();        
217 >    }
218 >    catch (OOPSEException& e) {
219 >      sprintf(painCave.errMsg,
220 >              "%s\n",
221 >              e.getMessage().c_str());
222 >      painCave.isFatal = 1;
223 >      simError();
224 >    }
225 >    catch (std::exception& e) {
226 >      sprintf(painCave.errMsg,
227 >              "parser exception: %s\n",
228 >              e.what());
229 >      painCave.isFatal = 1;
230 >      simError();
231 >    }
232  
233 <        return simParams;
233 >    return simParams;
234    }
235    
236    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
237                                    bool loadInitCoords) {
238  
239 +    const int bufferSize = 65535;
240 +    char buffer[bufferSize];
241 +    int lineNo = 0;
242 +    std::string mdRawData;
243 +    int metaDataBlockStart = -1;
244 +    int metaDataBlockEnd = -1;
245 +    int i;
246 +    int mdOffset;
247 +
248 + #ifdef IS_MPI            
249 +    const int masterNode = 0;
250 +    if (worldRank == masterNode) {
251 + #endif
252 +
253 +      std::ifstream mdFile_(mdFileName.c_str());
254 +      
255 +      if (mdFile_.fail()) {
256 +        sprintf(painCave.errMsg,
257 +                "SimCreator: Cannot open file: %s\n",
258 +                mdFileName.c_str());
259 +        painCave.isFatal = 1;
260 +        simError();
261 +      }
262 +
263 +      mdFile_.getline(buffer, bufferSize);
264 +      ++lineNo;
265 +      std::string line = trimLeftCopy(buffer);
266 +      i = CaseInsensitiveFind(line, "<OOPSE");
267 +      if (i == string::npos) {
268 +        sprintf(painCave.errMsg,
269 +                "SimCreator: File: %s is not an OOPSE file!\n",
270 +                mdFileName.c_str());
271 +        painCave.isFatal = 1;
272 +        simError();
273 +      }
274 +
275 +      //scan through the input stream and find MetaData tag        
276 +      while(mdFile_.getline(buffer, bufferSize)) {
277 +        ++lineNo;
278 +        
279 +        std::string line = trimLeftCopy(buffer);
280 +        if (metaDataBlockStart == -1) {
281 +          i = CaseInsensitiveFind(line, "<MetaData>");
282 +          if (i != string::npos) {
283 +            metaDataBlockStart = lineNo;
284 +            mdOffset = mdFile_.tellg();
285 +          }
286 +        } else {
287 +          i = CaseInsensitiveFind(line, "</MetaData>");
288 +          if (i != string::npos) {
289 +            metaDataBlockEnd = lineNo;
290 +          }
291 +        }
292 +      }
293 +
294 +      if (metaDataBlockStart == -1) {
295 +        sprintf(painCave.errMsg,
296 +                "SimCreator: File: %s did not contain a <MetaData> tag!\n",
297 +                mdFileName.c_str());
298 +        painCave.isFatal = 1;
299 +        simError();
300 +      }
301 +      if (metaDataBlockEnd == -1) {
302 +        sprintf(painCave.errMsg,
303 +                "SimCreator: File: %s did not contain a closed MetaData block!\n",
304 +                mdFileName.c_str());
305 +        painCave.isFatal = 1;
306 +        simError();
307 +      }
308 +        
309 +      mdFile_.clear();
310 +      mdFile_.seekg(0);
311 +      mdFile_.seekg(mdOffset);
312 +
313 +      mdRawData.clear();
314 +
315 +      for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
316 +        mdFile_.getline(buffer, bufferSize);
317 +        mdRawData += buffer;
318 +        mdRawData += "\n";
319 +      }
320 +
321 +      mdFile_.close();
322 +
323 + #ifdef IS_MPI
324 +    }
325 + #endif
326 +
327 +    std::stringstream rawMetaDataStream(mdRawData);
328 +
329      //parse meta-data file
330 <    Globals* simParams = parseFile(mdFileName);
330 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
331      
332      //create the force field
333      ForceField * ff = ForceFieldFactory::getInstance()
# Line 278 | Line 368 | Globals* SimCreator::parseFile(const std::string mdFil
368      ff->setFortranForceOptions();
369      //create SimInfo
370      SimInfo * info = new SimInfo(ff, simParams);
371 +
372 +    info->setRawMetaData(mdRawData);
373      
374 <    //gather parameters (SimCreator only retrieves part of the parameters)
374 >    //gather parameters (SimCreator only retrieves part of the
375 >    //parameters)
376      gatherParameters(info, mdFileName);
377      
378      //divide the molecules and determine the global index of molecules
# Line 291 | Line 384 | Globals* SimCreator::parseFile(const std::string mdFil
384      createMolecules(info);
385      
386      
387 <    //allocate memory for DataStorage(circular reference, need to break it)
387 >    //allocate memory for DataStorage(circular reference, need to
388 >    //break it)
389      info->setSnapshotManager(new SimSnapshotManager(info));
390      
391 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
392 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
393 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
391 >    //set the global index of atoms, rigidbodies and cutoffgroups
392 >    //(only need to be set once, the global index will never change
393 >    //again). Local indices of atoms and rigidbodies are already set
394 >    //by MoleculeCreator class which actually delegates the
395 >    //responsibility to LocalIndexManager.
396      setGlobalIndex(info);
397      
398 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
399 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
400 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
401 <    //we can determine the beginning global indices of atoms before they get created.
398 >    //Although addExcludePairs is called inside SimInfo's addMolecule
399 >    //method, at that point atoms don't have the global index yet
400 >    //(their global index are all initialized to -1).  Therefore we
401 >    //have to call addExcludePairs explicitly here. A way to work
402 >    //around is that we can determine the beginning global indices of
403 >    //atoms before they get created.
404      SimInfo::MoleculeIterator mi;
405      Molecule* mol;
406      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
# Line 310 | Line 408 | Globals* SimCreator::parseFile(const std::string mdFil
408      }
409      
410      if (loadInitCoords)
411 <      loadCoordinates(info);    
411 >      loadCoordinates(info, mdFileName);    
412      
413      return info;
414    }
# Line 346 | Line 444 | Globals* SimCreator::parseFile(const std::string mdFil
444    
445   #ifdef IS_MPI
446    void SimCreator::divideMolecules(SimInfo *info) {
447 <    double numerator;
448 <    double denominator;
449 <    double precast;
450 <    double x;
451 <    double y;
452 <    double a;
447 >    RealType numerator;
448 >    RealType denominator;
449 >    RealType precast;
450 >    RealType x;
451 >    RealType y;
452 >    RealType a;
453      int old_atoms;
454      int add_atoms;
455      int new_atoms;
# Line 463 | Line 561 | Globals* SimCreator::parseFile(const std::string mdFil
561            //           Pacc(x) = exp(- a * x)
562            // where a = penalty / (average atoms per molecule)
563            
564 <          x = (double)(new_atoms - nTarget);
564 >          x = (RealType)(new_atoms - nTarget);
565            y = myRandom->rand();
566            
567            if (y < exp(- a * x)) {
# Line 529 | Line 627 | Globals* SimCreator::parseFile(const std::string mdFil
627      Molecule::AtomIterator ai;
628      Molecule::RigidBodyIterator ri;
629      Molecule::CutoffGroupIterator ci;
630 +    Molecule::IntegrableObjectIterator  ioi;
631      Molecule * mol;
632      Atom * atom;
633      RigidBody * rb;
# Line 537 | Line 636 | Globals* SimCreator::parseFile(const std::string mdFil
636      int beginRigidBodyIndex;
637      int beginCutoffGroupIndex;
638      int nGlobalAtoms = info->getNGlobalAtoms();
639 <    
639 >
640 >    /**@todo fixme */
641   #ifndef IS_MPI
642      
643      beginAtomIndex = 0;
# Line 652 | Line 752 | Globals* SimCreator::parseFile(const std::string mdFil
752   #else
753      info->setGlobalMolMembership(globalMolMembership);
754   #endif
755 +
756 +    // nIOPerMol holds the number of integrable objects per molecule
757 +    // here the molecules are listed by their global indices.
758 +
759 +    std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
760 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
761 +      nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
762 +    }
763      
764 + #ifdef IS_MPI
765 +    std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
766 +    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
767 +                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
768 + #else
769 +    std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
770 + #endif    
771 +
772 + std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
773 +
774 + int startingIndex = 0;
775 + for (int i = 0; i < info->getNGlobalMolecules(); i++) {
776 +  startingIOIndexForMol[i] = startingIndex;
777 +  startingIndex += numIntegrableObjectsPerMol[i];
778 + }
779 +
780 + std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
781 + for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
782 +      int myGlobalIndex = mol->getGlobalIndex();
783 +      int globalIO = startingIOIndexForMol[myGlobalIndex];
784 +      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
785 +           integrableObject = mol->nextIntegrableObject(ioi)) {
786 +            integrableObject->setGlobalIntegrableObjectIndex(globalIO);
787 +            IOIndexToIntegrableObject[globalIO] = integrableObject;
788 +            globalIO++;
789 +      }
790 +    }
791 +
792 +  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
793 +  
794    }
795    
796 <  void SimCreator::loadCoordinates(SimInfo* info) {
796 >  void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
797      Globals* simParams;
798      simParams = info->getSimParams();
799      
662 –    if (!simParams->haveInitialConfig()) {
663 –      sprintf(painCave.errMsg,
664 –              "Cannot intialize a simulation without an initial configuration file.\n");
665 –      painCave.isFatal = 1;;
666 –      simError();
667 –    }
800      
801 <    DumpReader reader(info, simParams->getInitialConfig());
801 >    DumpReader reader(info, mdFileName);
802      int nframes = reader.getNFrames();
803      
804      if (nframes > 0) {
# Line 675 | Line 807 | Globals* SimCreator::parseFile(const std::string mdFil
807        //invalid initial coordinate file
808        sprintf(painCave.errMsg,
809                "Initial configuration file %s should at least contain one frame\n",
810 <              simParams->getInitialConfig().c_str());
810 >              mdFileName.c_str());
811        painCave.isFatal = 1;
812        simError();
813      }

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