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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 436 by tim, Fri Mar 11 17:50:11 2005 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

# Line 46 | Line 46
46   * @time 13:51am
47   * @version 1.0
48   */
49 + #include <exception>
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(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;
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(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);                  
104 >
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);  
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(filename);
126 >      lexer.initDeferredLineCount();
127      
128 < #ifdef IS_MPI
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);
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);
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 < #ifdef IS_MPI
181 <      
182 <      mpiEventInit();
183 <      
184 < #endif
185 <      
83 <      yacc_BASS(mdFileName.c_str());
84 <      
85 < #ifdef IS_MPI
86 <      
87 <      throwMPIEvent(NULL);
88 <    } else {
89 <      set_interface_stamps(stamps, simParams);
90 <      mpiEventInit();
91 <      MPIcheckPoint();
92 <      mpiEventLoop();
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 < #endif
189 <    
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;
233    }
234    
235 <  SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
236 <    
237 <    MakeStamps * stamps = new MakeStamps();
238 <    
239 <    Globals * simParams = new Globals();
240 <    
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 (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 <    parseFile(mdFileName, stamps, simParams);
329 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
330      
331      //create the force field
332 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
333 <                                                                         simParams->getForceField());
111 <    
332 >    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
333 >
334      if (ff == NULL) {
335 <      sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
336 <              simParams->getForceField());
335 >      sprintf(painCave.errMsg,
336 >              "ForceField Factory can not create %s force field\n",
337 >              simParams->getForceField().c_str());
338        painCave.isFatal = 1;
339        simError();
340      }
# Line 140 | Line 363 | namespace oopse {
363      }
364      
365      ff->parse(forcefieldFileName);
366 <    
144 <    //extract the molecule stamps
145 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146 <    compList(stamps, simParams, moleculeStampPairs);
147 <    
366 >    ff->setFortranForceOptions();
367      //create SimInfo
368 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
369 <    
370 <    //gather parameters (SimCreator only retrieves part of the parameters)
368 >    SimInfo * info = new SimInfo(ff, simParams);
369 >
370 >    info->setRawMetaData(mdRawData);
371 >    
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 160 | Line 382 | namespace oopse {
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 addExcludePairs 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 addExcludePairs 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)) {
# Line 179 | Line 406 | namespace oopse {
406      }
407      
408      if (loadInitCoords)
409 <      loadCoordinates(info);    
409 >      loadCoordinates(info, mdFileName);    
410      
411      return info;
412    }
413    
414    void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
415      
416 <    //figure out the ouput file names
416 >    //figure out the output file names
417      std::string prefix;
418      
419   #ifdef IS_MPI
# Line 215 | Line 442 | namespace oopse {
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 332 | Line 559 | namespace oopse {
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 362 | Line 589 | namespace oopse {
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 392 | Line 619 | namespace oopse {
619        
620      } //end for(int i=0)  
621    }
395 –  
396 –  void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
397 –                            std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
398 –    int i;
399 –    char * id;
400 –    LinkedMolStamp* extractedStamp = NULL;
401 –    MoleculeStamp * currentStamp;
402 –    Component** the_components = simParams->getComponents();
403 –    int n_components = simParams->getNComponents();
622      
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 –        extractedStamp = stamps->extractMolStamp(id);
423 –        if (extractedStamp == 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 –        currentStamp = extractedStamp->getStamp();
433 –        
434 –        
435 –        moleculeStampPairs.push_back(
436 –                                     std::make_pair(currentStamp, the_components[i]->getNMol()));
437 –      } //end for (i = 0; i < n_components; i++)
438 –    } else {
439 –      sprintf(painCave.errMsg, "SimSetup error.\n"
440 –              "\tSorry, the ability to specify total"
441 –              " nMols and then give molfractions in the components\n"
442 –              "\tis not currently supported."
443 –              " Please give nMol in the components.\n");
444 –      
445 –      painCave.isFatal = 1;
446 –      simError();
447 –    }
448 –    
449 – #ifdef IS_MPI
450 –    
451 –    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
452 –    MPIcheckPoint();
453 –    
454 – #endif // is_mpi
455 –    
456 –  }
457 –  
623    void SimCreator::setGlobalIndex(SimInfo *info) {
624      SimInfo::MoleculeIterator mi;
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 468 | Line 634 | namespace oopse {
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 583 | Line 750 | namespace oopse {
750   #else
751      info->setGlobalMolMembership(globalMolMembership);
752   #endif
753 +
754 +    // nIOPerMol holds the number of integrable objects per molecule
755 +    // here the molecules are listed by their global indices.
756 +
757 +    std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
758 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
759 +      nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
760 +    }
761      
762 + #ifdef IS_MPI
763 +    std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
764 +    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
765 +                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
766 + #else
767 +    std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
768 + #endif    
769 +
770 + std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
771 +
772 + int startingIndex = 0;
773 + for (int i = 0; i < info->getNGlobalMolecules(); i++) {
774 +  startingIOIndexForMol[i] = startingIndex;
775 +  startingIndex += numIntegrableObjectsPerMol[i];
776 + }
777 +
778 + std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
779 + for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
780 +      int myGlobalIndex = mol->getGlobalIndex();
781 +      int globalIO = startingIOIndexForMol[myGlobalIndex];
782 +      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
783 +           integrableObject = mol->nextIntegrableObject(ioi)) {
784 +            integrableObject->setGlobalIntegrableObjectIndex(globalIO);
785 +            IOIndexToIntegrableObject[globalIO] = integrableObject;
786 +            globalIO++;
787 +      }
788 +    }
789 +
790 +  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
791 +  
792    }
793    
794 <  void SimCreator::loadCoordinates(SimInfo* info) {
794 >  void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
795      Globals* simParams;
796      simParams = info->getSimParams();
797      
593 –    if (!simParams->haveInitialConfig()) {
594 –      sprintf(painCave.errMsg,
595 –              "Cannot intialize a simulation without an initial configuration file.\n");
596 –      painCave.isFatal = 1;;
597 –      simError();
598 –    }
798      
799 <    DumpReader reader(info, simParams->getInitialConfig());
799 >    DumpReader reader(info, mdFileName);
800      int nframes = reader.getNFrames();
801      
802      if (nframes > 0) {
# Line 606 | Line 805 | namespace oopse {
805        //invalid initial coordinate file
806        sprintf(painCave.errMsg,
807                "Initial configuration file %s should at least contain one frame\n",
808 <              simParams->getInitialConfig());
808 >              mdFileName.c_str());
809        painCave.isFatal = 1;
810        simError();
811      }

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