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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 79 | Line 79
79   #include "math/ParallelRandNumGen.hpp"
80   #endif
81  
82 < namespace oopse {
82 > namespace OpenMD {
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);
114                  
115 <                  char* buf = new char[streamSize];
116 <                  assert(buf);
115 >        //receive file content
116 >        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117                  
118 <                  //receive file content
119 <                  commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117 <                
118 <                  ppStream.str(buf);
119 <                  delete buf;
118 >        ppStream.str(buf);
119 >        delete [] buf;
120  
121 <            }
121 >      }
122   #endif            
123 <            // Create a scanner that reads from the input stream
124 <            MDLexer lexer(ppStream);
125 <            lexer.setFilename(mdFileName);
126 <            lexer.initDeferredLineCount();
123 >      // Create a scanner that reads from the input stream
124 >      MDLexer lexer(ppStream);
125 >      lexer.setFilename(filename);
126 >      lexer.initDeferredLineCount();
127      
128 <            // Create a parser that reads from the scanner
129 <            MDParser parser(lexer);
130 <            parser.setFilename(mdFileName);
128 >      // Create a parser that reads from the scanner
129 >      MDParser parser(lexer);
130 >      parser.setFilename(filename);
131  
132 <            // Create an observer that synchorizes file name change
133 <            FilenameObserver observer;
134 <            observer.setLexer(&lexer);
135 <            observer.setParser(&parser);
136 <            lexer.setObserver(&observer);
132 >      // Create an observer that synchorizes file name change
133 >      FilenameObserver observer;
134 >      observer.setLexer(&lexer);
135 >      observer.setParser(&parser);
136 >      lexer.setObserver(&observer);
137      
138 <            antlr::ASTFactory factory;
139 <            parser.initializeASTFactory(factory);
140 <            parser.setASTFactory(&factory);
141 <            parser.mdfile();
138 >      antlr::ASTFactory factory;
139 >      parser.initializeASTFactory(factory);
140 >      parser.setASTFactory(&factory);
141 >      parser.mdfile();
142  
143 <            // Create a tree parser that reads information into Globals
144 <            MDTreeParser treeParser;
145 <            treeParser.initializeASTFactory(factory);
146 <            treeParser.setASTFactory(&factory);
147 <             simParams = treeParser.walkTree(parser.getAST());
143 >      // Create a tree parser that reads information into Globals
144 >      MDTreeParser treeParser;
145 >      treeParser.initializeASTFactory(factory);
146 >      treeParser.setASTFactory(&factory);
147 >      simParams = treeParser.walkTree(parser.getAST());
148 >    }
149  
149 –        }
150 –
150        
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 <      }
151 >    catch(antlr::MismatchedCharException& e) {
152 >      sprintf(painCave.errMsg,
153 >              "parser exception: %s %s:%d:%d\n",
154 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
155 >      painCave.isFatal = 1;
156 >      simError();          
157 >    }
158 >    catch(antlr::MismatchedTokenException &e) {
159 >      sprintf(painCave.errMsg,
160 >              "parser exception: %s %s:%d:%d\n",
161 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
162 >      painCave.isFatal = 1;
163 >      simError();  
164 >    }
165 >    catch(antlr::NoViableAltForCharException &e) {
166 >      sprintf(painCave.errMsg,
167 >              "parser exception: %s %s:%d:%d\n",
168 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
169 >      painCave.isFatal = 1;
170 >      simError();  
171 >    }
172 >    catch(antlr::NoViableAltException &e) {
173 >      sprintf(painCave.errMsg,
174 >              "parser exception: %s %s:%d:%d\n",
175 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
176 >      painCave.isFatal = 1;
177 >      simError();  
178 >    }
179        
180 <        catch(antlr::TokenStreamRecognitionException& e) {
181 <          sprintf(painCave.errMsg,
182 <                  "parser exception: %s %s:%d:%d\n",
183 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184 <          painCave.isFatal = 1;
185 <          simError();  
186 <        }
180 >    catch(antlr::TokenStreamRecognitionException& e) {
181 >      sprintf(painCave.errMsg,
182 >              "parser exception: %s %s:%d:%d\n",
183 >              e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184 >      painCave.isFatal = 1;
185 >      simError();  
186 >    }
187          
188 <        catch(antlr::TokenStreamIOException& e) {
189 <          sprintf(painCave.errMsg,
190 <                  "parser exception: %s\n",
191 <                  e.getMessage().c_str());
192 <          painCave.isFatal = 1;
193 <          simError();
194 <        }
195 <        
196 <        catch(antlr::TokenStreamException& e) {
197 <          sprintf(painCave.errMsg,
198 <                  "parser exception: %s\n",
199 <                  e.getMessage().c_str());
200 <          painCave.isFatal = 1;
201 <          simError();
202 <        }        
203 <       catch (antlr::RecognitionException& e) {
204 <          sprintf(painCave.errMsg,
205 <                  "parser exception: %s %s:%d:%d\n",
206 <                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
207 <          painCave.isFatal = 1;
208 <          simError();          
209 <       }
210 <       catch (antlr::CharStreamException& e) {
211 <          sprintf(painCave.errMsg,
212 <                  "parser exception: %s\n",
213 <                  e.getMessage().c_str());
214 <          painCave.isFatal = 1;
215 <          simError();        
216 <       }
217 <       catch (OOPSEException& e) {
218 <          sprintf(painCave.errMsg,
219 <                  "%s\n",
220 <                  e.getMessage().c_str());
221 <          painCave.isFatal = 1;
222 <          simError();
223 <       }
224 <       catch (std::exception& e) {
225 <          sprintf(painCave.errMsg,
226 <                  "parser exception: %s\n",
227 <                  e.what());
228 <          painCave.isFatal = 1;
229 <          simError();
230 <       }
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 (OpenMDException& e) {
218 >      sprintf(painCave.errMsg,
219 >              "%s\n",
220 >              e.getMessage().c_str());
221 >      painCave.isFatal = 1;
222 >      simError();
223 >    }
224 >    catch (std::exception& e) {
225 >      sprintf(painCave.errMsg,
226 >              "parser exception: %s\n",
227 >              e.what());
228 >      painCave.isFatal = 1;
229 >      simError();
230 >    }
231  
232 <        return simParams;
232 >    return simParams;
233    }
234    
235    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236                                    bool loadInitCoords) {
237 +
238 +    const int bufferSize = 65535;
239 +    char buffer[bufferSize];
240 +    int lineNo = 0;
241 +    std::string mdRawData;
242 +    int metaDataBlockStart = -1;
243 +    int metaDataBlockEnd = -1;
244 +    int i;
245 +    int mdOffset;
246 +
247 + #ifdef IS_MPI            
248 +    const int masterNode = 0;
249 +    if (worldRank == masterNode) {
250 + #endif
251 +
252 +      std::ifstream mdFile_(mdFileName.c_str());
253 +      
254 +      if (mdFile_.fail()) {
255 +        sprintf(painCave.errMsg,
256 +                "SimCreator: Cannot open file: %s\n",
257 +                mdFileName.c_str());
258 +        painCave.isFatal = 1;
259 +        simError();
260 +      }
261 +
262 +      mdFile_.getline(buffer, bufferSize);
263 +      ++lineNo;
264 +      std::string line = trimLeftCopy(buffer);
265 +      i = CaseInsensitiveFind(line, "<OpenMD");
266 +      if (static_cast<size_t>(i) == string::npos) {
267 +        // try the older file strings to see if that works:
268 +        i = CaseInsensitiveFind(line, "<OOPSE");
269 +      }
270 +      
271 +      if (static_cast<size_t>(i) == string::npos) {
272 +        // still no luck!
273 +        sprintf(painCave.errMsg,
274 +                "SimCreator: File: %s is not a valid OpenMD file!\n",
275 +                mdFileName.c_str());
276 +        painCave.isFatal = 1;
277 +        simError();
278 +      }
279 +
280 +      //scan through the input stream and find MetaData tag        
281 +      while(mdFile_.getline(buffer, bufferSize)) {
282 +        ++lineNo;
283 +        
284 +        std::string line = trimLeftCopy(buffer);
285 +        if (metaDataBlockStart == -1) {
286 +          i = CaseInsensitiveFind(line, "<MetaData>");
287 +          if (i != string::npos) {
288 +            metaDataBlockStart = lineNo;
289 +            mdOffset = mdFile_.tellg();
290 +          }
291 +        } else {
292 +          i = CaseInsensitiveFind(line, "</MetaData>");
293 +          if (i != string::npos) {
294 +            metaDataBlockEnd = lineNo;
295 +          }
296 +        }
297 +      }
298 +
299 +      if (metaDataBlockStart == -1) {
300 +        sprintf(painCave.errMsg,
301 +                "SimCreator: File: %s did not contain a <MetaData> tag!\n",
302 +                mdFileName.c_str());
303 +        painCave.isFatal = 1;
304 +        simError();
305 +      }
306 +      if (metaDataBlockEnd == -1) {
307 +        sprintf(painCave.errMsg,
308 +                "SimCreator: File: %s did not contain a closed MetaData block!\n",
309 +                mdFileName.c_str());
310 +        painCave.isFatal = 1;
311 +        simError();
312 +      }
313 +        
314 +      mdFile_.clear();
315 +      mdFile_.seekg(0);
316 +      mdFile_.seekg(mdOffset);
317  
318 +      mdRawData.clear();
319 +
320 +      for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
321 +        mdFile_.getline(buffer, bufferSize);
322 +        mdRawData += buffer;
323 +        mdRawData += "\n";
324 +      }
325 +
326 +      mdFile_.close();
327 +
328 + #ifdef IS_MPI
329 +    }
330 + #endif
331 +
332 +    std::stringstream rawMetaDataStream(mdRawData);
333 +
334      //parse meta-data file
335 <    Globals* simParams = parseFile(mdFileName);
335 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336      
337      //create the force field
338 <    ForceField * ff = ForceFieldFactory::getInstance()
339 <      ->createForceField(simParams->getForceField());
245 <    
338 >    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
339 >
340      if (ff == NULL) {
341        sprintf(painCave.errMsg,
342                "ForceField Factory can not create %s force field\n",
# Line 278 | Line 372 | Globals* SimCreator::parseFile(const std::string mdFil
372      ff->setFortranForceOptions();
373      //create SimInfo
374      SimInfo * info = new SimInfo(ff, simParams);
375 +
376 +    info->setRawMetaData(mdRawData);
377      
378      //gather parameters (SimCreator only retrieves part of the
379      //parameters)
# Line 303 | Line 399 | Globals* SimCreator::parseFile(const std::string mdFil
399      //responsibility to LocalIndexManager.
400      setGlobalIndex(info);
401      
402 <    //Although addExcludePairs is called inside SimInfo's addMolecule
402 >    //Although addInteractionPairs is called inside SimInfo's addMolecule
403      //method, at that point atoms don't have the global index yet
404      //(their global index are all initialized to -1).  Therefore we
405 <    //have to call addExcludePairs explicitly here. A way to work
405 >    //have to call addInteractionPairs explicitly here. A way to work
406      //around is that we can determine the beginning global indices of
407      //atoms before they get created.
408      SimInfo::MoleculeIterator mi;
409      Molecule* mol;
410      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
411 <      info->addExcludePairs(mol);
411 >      info->addInteractionPairs(mol);
412      }
413      
414      if (loadInitCoords)
415 <      loadCoordinates(info);    
415 >      loadCoordinates(info, mdFileName);    
416      
417      return info;
418    }
# Line 352 | Line 448 | Globals* SimCreator::parseFile(const std::string mdFil
448    
449   #ifdef IS_MPI
450    void SimCreator::divideMolecules(SimInfo *info) {
451 <    double numerator;
452 <    double denominator;
453 <    double precast;
454 <    double x;
455 <    double y;
456 <    double a;
451 >    RealType numerator;
452 >    RealType denominator;
453 >    RealType precast;
454 >    RealType x;
455 >    RealType y;
456 >    RealType a;
457      int old_atoms;
458      int add_atoms;
459      int new_atoms;
# Line 381 | Line 477 | Globals* SimCreator::parseFile(const std::string mdFil
477                "\tthe number of molecules.  This will not result in a \n"
478                "\tusable division of atoms for force decomposition.\n"
479                "\tEither try a smaller number of processors, or run the\n"
480 <              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
480 >              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
481        
482        painCave.isFatal = 1;
483        simError();
# Line 469 | Line 565 | Globals* SimCreator::parseFile(const std::string mdFil
565            //           Pacc(x) = exp(- a * x)
566            // where a = penalty / (average atoms per molecule)
567            
568 <          x = (double)(new_atoms - nTarget);
568 >          x = (RealType)(new_atoms - nTarget);
569            y = myRandom->rand();
570            
571            if (y < exp(- a * x)) {
# Line 499 | Line 595 | Globals* SimCreator::parseFile(const std::string mdFil
595      info->setMolToProcMap(molToProcMap);
596      sprintf(checkPointMsg,
597              "Successfully divided the molecules among the processors.\n");
598 <    MPIcheckPoint();
598 >    errorCheckPoint();
599    }
600    
601   #endif
# Line 535 | Line 631 | Globals* SimCreator::parseFile(const std::string mdFil
631      Molecule::AtomIterator ai;
632      Molecule::RigidBodyIterator ri;
633      Molecule::CutoffGroupIterator ci;
634 +    Molecule::IntegrableObjectIterator  ioi;
635      Molecule * mol;
636      Atom * atom;
637      RigidBody * rb;
# Line 543 | Line 640 | Globals* SimCreator::parseFile(const std::string mdFil
640      int beginRigidBodyIndex;
641      int beginCutoffGroupIndex;
642      int nGlobalAtoms = info->getNGlobalAtoms();
643 <    
643 >
644 >    /**@todo fixme */
645   #ifndef IS_MPI
646      
647      beginAtomIndex = 0;
# Line 630 | Line 728 | Globals* SimCreator::parseFile(const std::string mdFil
728      // to get the full globalGroupMembership array (We think).
729      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
730      // docs said we could.
731 <    std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
731 >    std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
732      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
733                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
734      info->setGlobalGroupMembership(tmpGroupMembership);
# Line 642 | Line 740 | Globals* SimCreator::parseFile(const std::string mdFil
740      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
741      
742      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
645 –      
743        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
744          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
745        }
746      }
747      
748   #ifdef IS_MPI
749 <    std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
749 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
750      
751      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
752                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 658 | Line 755 | Globals* SimCreator::parseFile(const std::string mdFil
755   #else
756      info->setGlobalMolMembership(globalMolMembership);
757   #endif
758 +
759 +    // nIOPerMol holds the number of integrable objects per molecule
760 +    // here the molecules are listed by their global indices.
761 +
762 +    std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
763 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
764 +      nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
765 +    }
766      
767 + #ifdef IS_MPI
768 +    std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
769 +    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
770 +                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
771 + #else
772 +    std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
773 + #endif    
774 +
775 +    std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
776 +    
777 +    int startingIndex = 0;
778 +    for (int i = 0; i < info->getNGlobalMolecules(); i++) {
779 +      startingIOIndexForMol[i] = startingIndex;
780 +      startingIndex += numIntegrableObjectsPerMol[i];
781 +    }
782 +    
783 +    std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
784 +    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
785 +      int myGlobalIndex = mol->getGlobalIndex();
786 +      int globalIO = startingIOIndexForMol[myGlobalIndex];
787 +      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
788 +           integrableObject = mol->nextIntegrableObject(ioi)) {
789 +        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
790 +        IOIndexToIntegrableObject[globalIO] = integrableObject;
791 +        globalIO++;
792 +      }
793 +    }
794 +    
795 +    info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
796 +    
797    }
798    
799 <  void SimCreator::loadCoordinates(SimInfo* info) {
799 >  void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
800      Globals* simParams;
801      simParams = info->getSimParams();
802      
668 –    if (!simParams->haveInitialConfig()) {
669 –      sprintf(painCave.errMsg,
670 –              "Cannot intialize a simulation without an initial configuration file.\n");
671 –      painCave.isFatal = 1;;
672 –      simError();
673 –    }
803      
804 <    DumpReader reader(info, simParams->getInitialConfig());
804 >    DumpReader reader(info, mdFileName);
805      int nframes = reader.getNFrames();
806      
807      if (nframes > 0) {
# Line 681 | Line 810 | Globals* SimCreator::parseFile(const std::string mdFil
810        //invalid initial coordinate file
811        sprintf(painCave.errMsg,
812                "Initial configuration file %s should at least contain one frame\n",
813 <              simParams->getInitialConfig().c_str());
813 >              mdFileName.c_str());
814        painCave.isFatal = 1;
815        simError();
816      }
# Line 690 | Line 819 | Globals* SimCreator::parseFile(const std::string mdFil
819      info->getSnapshotManager()->advance();
820    }
821    
822 < } //end namespace oopse
822 > } //end namespace OpenMD
823  
824  

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