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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 832 by tim, Fri Dec 30 15:32:55 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 + Globals* SimCreator::parseFile(const std::string mdFileName){
85 +        Globals* simParams = NULL;
86 +        try {
87  
88 <  void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
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 < #ifdef IS_MPI
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 <    if (worldRank == 0) {
122 < #endif // is_mpi
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 >            // Create a parser that reads from the scanner
129 >            MDParser parser(lexer);
130 >            parser.setFilename(mdFileName);
131  
132 <      simParams->initalize();
133 <      set_interface_stamps(stamps, simParams);
134 <
135 < #ifdef IS_MPI
136 <
78 <      mpiEventInit();
79 <
80 < #endif
81 <
82 <      yacc_BASS(mdFileName.c_str());
83 <
84 < #ifdef IS_MPI
85 <
86 <      throwMPIEvent(NULL);
87 <    } else {
88 <      set_interface_stamps(stamps, simParams);
89 <      mpiEventInit();
90 <      MPIcheckPoint();
91 <      mpiEventLoop();
92 <    }
93 <
94 < #endif
95 <
96 <  }
97 <
98 <  SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
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 <    MakeStamps * stamps = new MakeStamps();
138 >            antlr::ASTFactory factory;
139 >            parser.initializeASTFactory(factory);
140 >            parser.setASTFactory(&factory);
141 >            parser.mdfile();
142  
143 <    Globals * simParams = new Globals();
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 <    //parse meta-data file
150 <    parseFile(mdFileName, stamps, simParams);
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 >        }
181  
182 +        return simParams;
183 +  }
184 +  
185 +  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
186 +                                  bool loadInitCoords) {
187 +
188 +    //parse meta-data file
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      }
202 <
202 >    
203      if (simParams->haveForceFieldFileName()) {
204        ff->setForceFieldFileName(simParams->getForceFieldFileName());
205      }
206      
207      std::string forcefieldFileName;
208      forcefieldFileName = ff->getForceFieldFileName();
209 <
209 >    
210      if (simParams->haveForceFieldVariant()) {
211        //If the force field has variant, the variant force field name will be
212        //Base.variant.frc. For exampel EAM.u6.frc
213 <        
213 >      
214        std::string variant = simParams->getForceFieldVariant();
215 <
215 >      
216        std::string::size_type pos = forcefieldFileName.rfind(".frc");
217        variant = "." + variant;
218        if (pos != std::string::npos) {
# Line 139 | Line 224 | namespace oopse {
224      }
225      
226      ff->parse(forcefieldFileName);
227 <    
143 <    //extract the molecule stamps
144 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145 <    compList(stamps, simParams, moleculeStampPairs);
146 <
227 >    ff->setFortranForceOptions();
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 <
233 >    
234      //divide the molecules and determine the global index of molecules
235   #ifdef IS_MPI
236      divideMolecules(info);
237   #endif
238 <
238 >    
239      //create the molecules
240      createMolecules(info);
241 <
242 <
241 >    
242 >    
243      //allocate memory for DataStorage(circular reference, need to break it)
244      info->setSnapshotManager(new SimSnapshotManager(info));
245      
# Line 166 | Line 247 | namespace oopse {
247      //global index will never change again). Local indices of atoms and rigidbodies are already set by
248      //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
249      setGlobalIndex(info);
250 <
250 >    
251      //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
252      //atoms don't have the global index yet  (their global index are all initialized to -1).
253      //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
# Line 177 | Line 258 | namespace oopse {
258        info->addExcludePairs(mol);
259      }
260      
180 –
181 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182 –    //eta, chi for NPT integrator)
261      if (loadInitCoords)
262        loadCoordinates(info);    
263      
264      return info;
265    }
266 <
266 >  
267    void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
268 <
269 <    //figure out the ouput file names
268 >    
269 >    //figure out the output file names
270      std::string prefix;
271 <
271 >    
272   #ifdef IS_MPI
273 <
273 >    
274      if (worldRank == 0) {
275   #endif // is_mpi
276        Globals * simParams = info->getSimParams();
# Line 201 | Line 279 | namespace oopse {
279        } else {
280          prefix = getPrefix(mdfile);
281        }
282 <
282 >      
283        info->setFinalConfigFileName(prefix + ".eor");
284        info->setDumpFileName(prefix + ".dump");
285        info->setStatFileName(prefix + ".stat");
286 <
286 >      info->setRestFileName(prefix + ".zang");
287 >      
288   #ifdef IS_MPI
289 <
289 >      
290      }
291 <
291 >    
292   #endif
293 <
293 >    
294    }
295 <
295 >  
296   #ifdef IS_MPI
297    void SimCreator::divideMolecules(SimInfo *info) {
298      double numerator;
# Line 237 | Line 316 | namespace oopse {
316      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
317      
318      MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
319 <
319 >    
320      if (nProcessors > nGlobalMols) {
321        sprintf(painCave.errMsg,
322                "nProcessors (%d) > nMol (%d)\n"
# Line 246 | Line 325 | namespace oopse {
325                "\tusable division of atoms for force decomposition.\n"
326                "\tEither try a smaller number of processors, or run the\n"
327                "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
328 <
328 >      
329        painCave.isFatal = 1;
330        simError();
331      }
332 <
332 >    
333      int seedValue;
334      Globals * simParams = info->getSimParams();
335      SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
# Line 260 | Line 339 | namespace oopse {
339      }else {
340        myRandom = new SeqRandNumGen();
341      }  
342 <
343 <
342 >    
343 >    
344      a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
345 <
345 >    
346      //initialize atomsPerProc
347      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
348 <
348 >    
349      if (worldRank == 0) {
350        numerator = info->getNGlobalAtoms();
351        denominator = nProcessors;
352        precast = numerator / denominator;
353        nTarget = (int)(precast + 0.5);
354 <
354 >      
355        for(i = 0; i < nGlobalMols; i++) {
356          done = 0;
357          loops = 0;
358 <
358 >        
359          while (!done) {
360            loops++;
361 <
361 >          
362            // Pick a processor at random
363 <
363 >          
364            which_proc = (int) (myRandom->rand() * nProcessors);
365 <
365 >          
366            //get the molecule stamp first
367            int stampId = info->getMoleculeStampId(i);
368            MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
369 <
369 >          
370            // How many atoms does this processor have so far?
371            old_atoms = atomsPerProc[which_proc];
372            add_atoms = moleculeStamp->getNAtoms();
373            new_atoms = old_atoms + add_atoms;
374 <
374 >          
375            // If we've been through this loop too many times, we need
376            // to just give up and assign the molecule to this processor
377            // and be done with it.
378 <
378 >          
379            if (loops > 100) {
380              sprintf(painCave.errMsg,
381                      "I've tried 100 times to assign molecule %d to a "
382                      " processor, but can't find a good spot.\n"
383                      "I'm assigning it at random to processor %d.\n",
384                      i, which_proc);
385 <
385 >            
386              painCave.isFatal = 0;
387              simError();
388 <
388 >            
389              molToProcMap[i] = which_proc;
390              atomsPerProc[which_proc] += add_atoms;
391 <
391 >            
392              done = 1;
393              continue;
394            }
395 <
395 >          
396            // If we can add this molecule to this processor without sending
397            // it above nTarget, then go ahead and do it:
398 <
398 >          
399            if (new_atoms <= nTarget) {
400              molToProcMap[i] = which_proc;
401              atomsPerProc[which_proc] += add_atoms;
402 <
402 >            
403              done = 1;
404              continue;
405            }
406 <
406 >          
407            // The only situation left is when new_atoms > nTarget.  We
408            // want to accept this with some probability that dies off the
409            // farther we are from nTarget
410 <
410 >          
411            // roughly:  x = new_atoms - nTarget
412            //           Pacc(x) = exp(- a * x)
413            // where a = penalty / (average atoms per molecule)
414 <
414 >          
415            x = (double)(new_atoms - nTarget);
416            y = myRandom->rand();
417 <
417 >          
418            if (y < exp(- a * x)) {
419              molToProcMap[i] = which_proc;
420              atomsPerProc[which_proc] += add_atoms;
421 <
421 >            
422              done = 1;
423              continue;
424            } else {
# Line 347 | Line 426 | namespace oopse {
426            }
427          }
428        }
429 <
429 >      
430        delete myRandom;
431 <        
431 >      
432        // Spray out this nonsense to all other processors:
433 <
433 >      
434        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
435      } else {
436 <
436 >      
437        // Listen to your marching orders from processor 0:
438 <
438 >      
439        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
440      }
441 <
441 >    
442      info->setMolToProcMap(molToProcMap);
443      sprintf(checkPointMsg,
444              "Successfully divided the molecules among the processors.\n");
445      MPIcheckPoint();
446    }
447 <
447 >  
448   #endif
449 <
449 >  
450    void SimCreator::createMolecules(SimInfo *info) {
451      MoleculeCreator molCreator;
452      int stampId;
453 <
453 >    
454      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
455 <
455 >      
456   #ifdef IS_MPI
457 <
457 >      
458        if (info->getMolToProc(i) == worldRank) {
459   #endif
460 <
460 >        
461          stampId = info->getMoleculeStampId(i);
462          Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
463                                                     stampId, i, info->getLocalIndexManager());
464 <
464 >        
465          info->addMolecule(mol);
466 <
466 >        
467   #ifdef IS_MPI
468 <
468 >        
469        }
470 <
470 >      
471   #endif
472 <
472 >      
473      } //end for(int i=0)  
474    }
475 <
397 <  void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398 <                            std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399 <    int i;
400 <    char * id;
401 <    LinkedMolStamp* extractedStamp = NULL;
402 <    MoleculeStamp * currentStamp;
403 <    Component** the_components = simParams->getComponents();
404 <    int n_components = simParams->getNComponents();
405 <
406 <    if (!simParams->haveNMol()) {
407 <      // we don't have the total number of molecules, so we assume it is
408 <      // given in each component
409 <
410 <      for(i = 0; i < n_components; i++) {
411 <        if (!the_components[i]->haveNMol()) {
412 <          // we have a problem
413 <          sprintf(painCave.errMsg,
414 <                  "SimCreator Error. No global NMol or component NMol given.\n"
415 <                  "\tCannot calculate the number of atoms.\n");
416 <
417 <          painCave.isFatal = 1;
418 <          simError();
419 <        }
420 <      
421 <        id = the_components[i]->getType();
422 <
423 <        extractedStamp = stamps->extractMolStamp(id);
424 <        if (extractedStamp == NULL) {
425 <          sprintf(painCave.errMsg,
426 <                  "SimCreator error: Component \"%s\" was not found in the "
427 <                  "list of declared molecules\n", id);
428 <
429 <          painCave.isFatal = 1;
430 <          simError();
431 <        }
432 <
433 <        currentStamp = extractedStamp->getStamp();
434 <
435 <
436 <        moleculeStampPairs.push_back(
437 <                                     std::make_pair(currentStamp, the_components[i]->getNMol()));
438 <      } //end for (i = 0; i < n_components; i++)
439 <    } else {
440 <      sprintf(painCave.errMsg, "SimSetup error.\n"
441 <              "\tSorry, the ability to specify total"
442 <              " nMols and then give molfractions in the components\n"
443 <              "\tis not currently supported."
444 <              " Please give nMol in the components.\n");
445 <
446 <      painCave.isFatal = 1;
447 <      simError();
448 <    }
449 <
450 < #ifdef IS_MPI
451 <
452 <    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
453 <    MPIcheckPoint();
454 <
455 < #endif // is_mpi
456 <
457 <  }
458 <
475 >    
476    void SimCreator::setGlobalIndex(SimInfo *info) {
477      SimInfo::MoleculeIterator mi;
478      Molecule::AtomIterator ai;
# Line 471 | Line 488 | namespace oopse {
488      int nGlobalAtoms = info->getNGlobalAtoms();
489      
490   #ifndef IS_MPI
491 <
491 >    
492      beginAtomIndex = 0;
493      beginRigidBodyIndex = 0;
494      beginCutoffGroupIndex = 0;
495 <
495 >    
496   #else
497 <
497 >    
498      int nproc;
499      int myNode;
500 <
500 >    
501      myNode = worldRank;
502      MPI_Comm_size(MPI_COMM_WORLD, &nproc);
503 <
503 >    
504      std::vector < int > tmpAtomsInProc(nproc, 0);
505      std::vector < int > tmpRigidBodiesInProc(nproc, 0);
506      std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
507      std::vector < int > NumAtomsInProc(nproc, 0);
508      std::vector < int > NumRigidBodiesInProc(nproc, 0);
509      std::vector < int > NumCutoffGroupsInProc(nproc, 0);
510 <
510 >    
511      tmpAtomsInProc[myNode] = info->getNAtoms();
512      tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
513      tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
514 <
514 >    
515      //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
516      MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
517                    MPI_SUM, MPI_COMM_WORLD);
# Line 502 | Line 519 | namespace oopse {
519                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
520      MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
521                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
522 <
522 >    
523      beginAtomIndex = 0;
524      beginRigidBodyIndex = 0;
525      beginCutoffGroupIndex = 0;
526 <
526 >    
527      for(int i = 0; i < myNode; i++) {
528        beginAtomIndex += NumAtomsInProc[i];
529        beginRigidBodyIndex += NumRigidBodiesInProc[i];
530        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
531      }
532 <
532 >    
533   #endif
534 <
534 >    
535      //rigidbody's index begins right after atom's
536      beginRigidBodyIndex += info->getNGlobalAtoms();
537 <
537 >    
538      for(mol = info->beginMolecule(mi); mol != NULL;
539          mol = info->nextMolecule(mi)) {
540 <
540 >      
541        //local index(index in DataStorge) of atom is important
542        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
543          atom->setGlobalIndex(beginAtomIndex++);
544        }
545 <
545 >      
546        for(rb = mol->beginRigidBody(ri); rb != NULL;
547            rb = mol->nextRigidBody(ri)) {
548          rb->setGlobalIndex(beginRigidBodyIndex++);
549        }
550 <
550 >      
551        //local index of cutoff group is trivial, it only depends on the order of travesing
552        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
553            cg = mol->nextCutoffGroup(ci)) {
554          cg->setGlobalIndex(beginCutoffGroupIndex++);
555        }
556      }
557 <
557 >    
558      //fill globalGroupMembership
559      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
560      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
561        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
562 <
562 >        
563          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
564            globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
565          }
566 <
566 >        
567        }      
568      }
569 <
569 >    
570   #ifdef IS_MPI    
571      // Since the globalGroupMembership has been zero filled and we've only
572      // poked values into the atoms we know, we can do an Allreduce
# Line 563 | Line 580 | namespace oopse {
580   #else
581      info->setGlobalGroupMembership(globalGroupMembership);
582   #endif
583 <
583 >    
584      //fill molMembership
585      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
586      
587      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
588 <
588 >      
589        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
590          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
591        }
592      }
593 <
593 >    
594   #ifdef IS_MPI
595      std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
596 <
596 >    
597      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
598                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
599      
# Line 584 | Line 601 | namespace oopse {
601   #else
602      info->setGlobalMolMembership(globalMolMembership);
603   #endif
604 <
604 >    
605    }
606 <
606 >  
607    void SimCreator::loadCoordinates(SimInfo* info) {
608      Globals* simParams;
609      simParams = info->getSimParams();
# Line 597 | Line 614 | namespace oopse {
614        painCave.isFatal = 1;;
615        simError();
616      }
617 <        
617 >    
618      DumpReader reader(info, simParams->getInitialConfig());
619      int nframes = reader.getNFrames();
620 <
620 >    
621      if (nframes > 0) {
622        reader.readFrame(nframes - 1);
623      } else {
624        //invalid initial coordinate file
625 <      sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
626 <              simParams->getInitialConfig());
625 >      sprintf(painCave.errMsg,
626 >              "Initial configuration file %s should at least contain one frame\n",
627 >              simParams->getInitialConfig().c_str());
628        painCave.isFatal = 1;
629        simError();
630      }
631 <
631 >    
632      //copy the current snapshot to previous snapshot
633      info->getSnapshotManager()->advance();
634    }
635 <
635 >  
636   } //end namespace oopse
637  
638  

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