ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/brains/SimCreator.cpp
(Generate patch)

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 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 + 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);
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();
142  
143 < #ifdef IS_MPI
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 <      mpiEventInit();
149 >        }
150  
151 < #endif
152 <
153 <      yacc_BASS(mdFileName.c_str());
154 <
155 < #ifdef IS_MPI
156 <
157 <      throwMPIEvent(NULL);
158 <    } else {
159 <      set_interface_stamps(stamps, simParams);
160 <      mpiEventInit();
161 <      MPIcheckPoint();
162 <      mpiEventLoop();
163 <    }
164 <
165 < #endif
166 <
167 <  }
168 <
169 <  SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
170 <    
171 <    MakeStamps * stamps = new MakeStamps();
172 <
173 <    Globals * simParams = new Globals();
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 >      }
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 >        }
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 >        }
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 >       }
232  
233 <    //parse meta-data file
234 <    parseFile(mdFileName, stamps, simParams);
233 >        return simParams;
234 >  }
235 >  
236 >  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
237 >                                  bool loadInitCoords) {
238  
239 +    //parse meta-data file
240 +    Globals* simParams = parseFile(mdFileName);
241 +    
242      //create the force field
243 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
244 <                                                                         simParams->getForceField());
243 >    ForceField * ff = ForceFieldFactory::getInstance()
244 >      ->createForceField(simParams->getForceField());
245      
246      if (ff == NULL) {
247 <      sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
248 <              simParams->getForceField());
247 >      sprintf(painCave.errMsg,
248 >              "ForceField Factory can not create %s force field\n",
249 >              simParams->getForceField().c_str());
250        painCave.isFatal = 1;
251        simError();
252      }
253 <
253 >    
254      if (simParams->haveForceFieldFileName()) {
255        ff->setForceFieldFileName(simParams->getForceFieldFileName());
256      }
257      
258      std::string forcefieldFileName;
259      forcefieldFileName = ff->getForceFieldFileName();
260 <
260 >    
261      if (simParams->haveForceFieldVariant()) {
262        //If the force field has variant, the variant force field name will be
263        //Base.variant.frc. For exampel EAM.u6.frc
264 <        
264 >      
265        std::string variant = simParams->getForceFieldVariant();
266 <
266 >      
267        std::string::size_type pos = forcefieldFileName.rfind(".frc");
268        variant = "." + variant;
269        if (pos != std::string::npos) {
# Line 139 | Line 275 | namespace oopse {
275      }
276      
277      ff->parse(forcefieldFileName);
278 <    
143 <    //extract the molecule stamps
144 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145 <    compList(stamps, simParams, moleculeStampPairs);
146 <
278 >    ff->setFortranForceOptions();
279      //create SimInfo
280 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
281 <
282 <    //gather parameters (SimCreator only retrieves part of the parameters)
280 >    SimInfo * info = new SimInfo(ff, simParams);
281 >    
282 >    //gather parameters (SimCreator only retrieves part of the
283 >    //parameters)
284      gatherParameters(info, mdFileName);
285 <
285 >    
286      //divide the molecules and determine the global index of molecules
287   #ifdef IS_MPI
288      divideMolecules(info);
289   #endif
290 <
290 >    
291      //create the molecules
292      createMolecules(info);
293 <
294 <
295 <    //allocate memory for DataStorage(circular reference, need to break it)
293 >    
294 >    
295 >    //allocate memory for DataStorage(circular reference, need to
296 >    //break it)
297      info->setSnapshotManager(new SimSnapshotManager(info));
298      
299 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
300 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
301 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
299 >    //set the global index of atoms, rigidbodies and cutoffgroups
300 >    //(only need to be set once, the global index will never change
301 >    //again). Local indices of atoms and rigidbodies are already set
302 >    //by MoleculeCreator class which actually delegates the
303 >    //responsibility to LocalIndexManager.
304      setGlobalIndex(info);
305 <
306 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
307 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
308 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
309 <    //we can determine the beginning global indices of atoms before they get created.
305 >    
306 >    //Although addExcludePairs is called inside SimInfo's addMolecule
307 >    //method, at that point atoms don't have the global index yet
308 >    //(their global index are all initialized to -1).  Therefore we
309 >    //have to call addExcludePairs explicitly here. A way to work
310 >    //around is that we can determine the beginning global indices of
311 >    //atoms before they get created.
312      SimInfo::MoleculeIterator mi;
313      Molecule* mol;
314      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
315        info->addExcludePairs(mol);
316      }
317      
180 –
181 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182 –    //eta, chi for NPT integrator)
318      if (loadInitCoords)
319        loadCoordinates(info);    
320      
321      return info;
322    }
323 <
323 >  
324    void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
325 <
326 <    //figure out the ouput file names
325 >    
326 >    //figure out the output file names
327      std::string prefix;
328 <
328 >    
329   #ifdef IS_MPI
330 <
330 >    
331      if (worldRank == 0) {
332   #endif // is_mpi
333        Globals * simParams = info->getSimParams();
# Line 201 | Line 336 | namespace oopse {
336        } else {
337          prefix = getPrefix(mdfile);
338        }
339 <
339 >      
340        info->setFinalConfigFileName(prefix + ".eor");
341        info->setDumpFileName(prefix + ".dump");
342        info->setStatFileName(prefix + ".stat");
343 <
343 >      info->setRestFileName(prefix + ".zang");
344 >      
345   #ifdef IS_MPI
346 <
346 >      
347      }
348 <
348 >    
349   #endif
350 <
350 >    
351    }
352 <
352 >  
353   #ifdef IS_MPI
354    void SimCreator::divideMolecules(SimInfo *info) {
355 <    double numerator;
356 <    double denominator;
357 <    double precast;
358 <    double x;
359 <    double y;
360 <    double a;
355 >    RealType numerator;
356 >    RealType denominator;
357 >    RealType precast;
358 >    RealType x;
359 >    RealType y;
360 >    RealType a;
361      int old_atoms;
362      int add_atoms;
363      int new_atoms;
# Line 237 | Line 373 | namespace oopse {
373      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
374      
375      MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
376 <
376 >    
377      if (nProcessors > nGlobalMols) {
378        sprintf(painCave.errMsg,
379                "nProcessors (%d) > nMol (%d)\n"
# Line 246 | Line 382 | namespace oopse {
382                "\tusable division of atoms for force decomposition.\n"
383                "\tEither try a smaller number of processors, or run the\n"
384                "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
385 <
385 >      
386        painCave.isFatal = 1;
387        simError();
388      }
389 <
389 >    
390      int seedValue;
391      Globals * simParams = info->getSimParams();
392      SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
# Line 260 | Line 396 | namespace oopse {
396      }else {
397        myRandom = new SeqRandNumGen();
398      }  
399 <
400 <
399 >    
400 >    
401      a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
402 <
402 >    
403      //initialize atomsPerProc
404      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
405 <
405 >    
406      if (worldRank == 0) {
407        numerator = info->getNGlobalAtoms();
408        denominator = nProcessors;
409        precast = numerator / denominator;
410        nTarget = (int)(precast + 0.5);
411 <
411 >      
412        for(i = 0; i < nGlobalMols; i++) {
413          done = 0;
414          loops = 0;
415 <
415 >        
416          while (!done) {
417            loops++;
418 <
418 >          
419            // Pick a processor at random
420 <
420 >          
421            which_proc = (int) (myRandom->rand() * nProcessors);
422 <
422 >          
423            //get the molecule stamp first
424            int stampId = info->getMoleculeStampId(i);
425            MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
426 <
426 >          
427            // How many atoms does this processor have so far?
428            old_atoms = atomsPerProc[which_proc];
429            add_atoms = moleculeStamp->getNAtoms();
430            new_atoms = old_atoms + add_atoms;
431 <
431 >          
432            // If we've been through this loop too many times, we need
433            // to just give up and assign the molecule to this processor
434            // and be done with it.
435 <
435 >          
436            if (loops > 100) {
437              sprintf(painCave.errMsg,
438                      "I've tried 100 times to assign molecule %d to a "
439                      " processor, but can't find a good spot.\n"
440                      "I'm assigning it at random to processor %d.\n",
441                      i, which_proc);
442 <
442 >            
443              painCave.isFatal = 0;
444              simError();
445 <
445 >            
446              molToProcMap[i] = which_proc;
447              atomsPerProc[which_proc] += add_atoms;
448 <
448 >            
449              done = 1;
450              continue;
451            }
452 <
452 >          
453            // If we can add this molecule to this processor without sending
454            // it above nTarget, then go ahead and do it:
455 <
455 >          
456            if (new_atoms <= nTarget) {
457              molToProcMap[i] = which_proc;
458              atomsPerProc[which_proc] += add_atoms;
459 <
459 >            
460              done = 1;
461              continue;
462            }
463 <
463 >          
464            // The only situation left is when new_atoms > nTarget.  We
465            // want to accept this with some probability that dies off the
466            // farther we are from nTarget
467 <
467 >          
468            // roughly:  x = new_atoms - nTarget
469            //           Pacc(x) = exp(- a * x)
470            // where a = penalty / (average atoms per molecule)
471 <
472 <          x = (double)(new_atoms - nTarget);
471 >          
472 >          x = (RealType)(new_atoms - nTarget);
473            y = myRandom->rand();
474 <
474 >          
475            if (y < exp(- a * x)) {
476              molToProcMap[i] = which_proc;
477              atomsPerProc[which_proc] += add_atoms;
478 <
478 >            
479              done = 1;
480              continue;
481            } else {
# Line 347 | Line 483 | namespace oopse {
483            }
484          }
485        }
486 <
486 >      
487        delete myRandom;
488 <        
488 >      
489        // Spray out this nonsense to all other processors:
490 <
490 >      
491        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
492      } else {
493 <
493 >      
494        // Listen to your marching orders from processor 0:
495 <
495 >      
496        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
497      }
498 <
498 >    
499      info->setMolToProcMap(molToProcMap);
500      sprintf(checkPointMsg,
501              "Successfully divided the molecules among the processors.\n");
502      MPIcheckPoint();
503    }
504 <
504 >  
505   #endif
506 <
506 >  
507    void SimCreator::createMolecules(SimInfo *info) {
508      MoleculeCreator molCreator;
509      int stampId;
510 <
510 >    
511      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
512 <
512 >      
513   #ifdef IS_MPI
514 <
514 >      
515        if (info->getMolToProc(i) == worldRank) {
516   #endif
517 <
517 >        
518          stampId = info->getMoleculeStampId(i);
519          Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
520                                                     stampId, i, info->getLocalIndexManager());
521 <
521 >        
522          info->addMolecule(mol);
523 <
523 >        
524   #ifdef IS_MPI
525 <
525 >        
526        }
527 <
527 >      
528   #endif
529 <
529 >      
530      } //end for(int i=0)  
531    }
532 <
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 <
532 >    
533    void SimCreator::setGlobalIndex(SimInfo *info) {
534      SimInfo::MoleculeIterator mi;
535      Molecule::AtomIterator ai;
# Line 471 | Line 545 | namespace oopse {
545      int nGlobalAtoms = info->getNGlobalAtoms();
546      
547   #ifndef IS_MPI
548 <
548 >    
549      beginAtomIndex = 0;
550      beginRigidBodyIndex = 0;
551      beginCutoffGroupIndex = 0;
552 <
552 >    
553   #else
554 <
554 >    
555      int nproc;
556      int myNode;
557 <
557 >    
558      myNode = worldRank;
559      MPI_Comm_size(MPI_COMM_WORLD, &nproc);
560 <
560 >    
561      std::vector < int > tmpAtomsInProc(nproc, 0);
562      std::vector < int > tmpRigidBodiesInProc(nproc, 0);
563      std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
564      std::vector < int > NumAtomsInProc(nproc, 0);
565      std::vector < int > NumRigidBodiesInProc(nproc, 0);
566      std::vector < int > NumCutoffGroupsInProc(nproc, 0);
567 <
567 >    
568      tmpAtomsInProc[myNode] = info->getNAtoms();
569      tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
570      tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
571 <
571 >    
572      //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
573      MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
574                    MPI_SUM, MPI_COMM_WORLD);
# Line 502 | Line 576 | namespace oopse {
576                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
577      MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
578                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
579 <
579 >    
580      beginAtomIndex = 0;
581      beginRigidBodyIndex = 0;
582      beginCutoffGroupIndex = 0;
583 <
583 >    
584      for(int i = 0; i < myNode; i++) {
585        beginAtomIndex += NumAtomsInProc[i];
586        beginRigidBodyIndex += NumRigidBodiesInProc[i];
587        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
588      }
589 <
589 >    
590   #endif
591 <
591 >    
592      //rigidbody's index begins right after atom's
593      beginRigidBodyIndex += info->getNGlobalAtoms();
594 <
594 >    
595      for(mol = info->beginMolecule(mi); mol != NULL;
596          mol = info->nextMolecule(mi)) {
597 <
597 >      
598        //local index(index in DataStorge) of atom is important
599        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
600          atom->setGlobalIndex(beginAtomIndex++);
601        }
602 <
602 >      
603        for(rb = mol->beginRigidBody(ri); rb != NULL;
604            rb = mol->nextRigidBody(ri)) {
605          rb->setGlobalIndex(beginRigidBodyIndex++);
606        }
607 <
607 >      
608        //local index of cutoff group is trivial, it only depends on the order of travesing
609        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610            cg = mol->nextCutoffGroup(ci)) {
611          cg->setGlobalIndex(beginCutoffGroupIndex++);
612        }
613      }
614 <
614 >    
615      //fill globalGroupMembership
616      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
617      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
618        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
619 <
619 >        
620          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
621            globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
622          }
623 <
623 >        
624        }      
625      }
626 <
626 >    
627   #ifdef IS_MPI    
628      // Since the globalGroupMembership has been zero filled and we've only
629      // poked values into the atoms we know, we can do an Allreduce
# Line 563 | Line 637 | namespace oopse {
637   #else
638      info->setGlobalGroupMembership(globalGroupMembership);
639   #endif
640 <
640 >    
641      //fill molMembership
642      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
643      
644      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
645 <
645 >      
646        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
647          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
648        }
649      }
650 <
650 >    
651   #ifdef IS_MPI
652      std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
653 <
653 >    
654      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
655                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
656      
# Line 584 | Line 658 | namespace oopse {
658   #else
659      info->setGlobalMolMembership(globalMolMembership);
660   #endif
661 <
661 >    
662    }
663 <
663 >  
664    void SimCreator::loadCoordinates(SimInfo* info) {
665      Globals* simParams;
666      simParams = info->getSimParams();
# Line 597 | Line 671 | namespace oopse {
671        painCave.isFatal = 1;;
672        simError();
673      }
674 <        
674 >    
675      DumpReader reader(info, simParams->getInitialConfig());
676      int nframes = reader.getNFrames();
677 <
677 >    
678      if (nframes > 0) {
679        reader.readFrame(nframes - 1);
680      } else {
681        //invalid initial coordinate file
682 <      sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
683 <              simParams->getInitialConfig());
682 >      sprintf(painCave.errMsg,
683 >              "Initial configuration file %s should at least contain one frame\n",
684 >              simParams->getInitialConfig().c_str());
685        painCave.isFatal = 1;
686        simError();
687      }
688 <
688 >    
689      //copy the current snapshot to previous snapshot
690      info->getSnapshotManager()->advance();
691    }
692 <
692 >  
693   } //end namespace oopse
694  
695  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines