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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 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 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 {
82 > namespace OpenMD {
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 <      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 <      
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();
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 (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;
233    }
234    
235    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236                                    bool loadInitCoords) {
237 <    
238 <    MakeStamps * stamps = new MakeStamps();
239 <    
240 <    Globals * simParams = new Globals();
241 <    
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 <    parseFile(mdFileName, stamps, simParams);
335 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336      
337      //create the force field
338 <    ForceField * ff = ForceFieldFactory::getInstance()
339 <      ->createForceField(simParams->getForceField());
111 <    
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 141 | Line 369 | namespace oopse {
369      }
370      
371      ff->parse(forcefieldFileName);
372 <    
145 <    //extract the molecule stamps
146 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147 <    compList(stamps, simParams, moleculeStampPairs);
148 <    
372 >    ff->setFortranForceOptions();
373      //create SimInfo
374 <    SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
374 >    SimInfo * info = new SimInfo(ff, simParams);
375 >
376 >    info->setRawMetaData(mdRawData);
377      
378 <    //gather parameters (SimCreator only retrieves part of the parameters)
378 >    //gather parameters (SimCreator only retrieves part of the
379 >    //parameters)
380      gatherParameters(info, mdFileName);
381      
382      //divide the molecules and determine the global index of molecules
# Line 161 | Line 388 | namespace oopse {
388      createMolecules(info);
389      
390      
391 <    //allocate memory for DataStorage(circular reference, need to break it)
391 >    //allocate memory for DataStorage(circular reference, need to
392 >    //break it)
393      info->setSnapshotManager(new SimSnapshotManager(info));
394      
395 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
396 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
397 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
395 >    //set the global index of atoms, rigidbodies and cutoffgroups
396 >    //(only need to be set once, the global index will never change
397 >    //again). Local indices of atoms and rigidbodies are already set
398 >    //by MoleculeCreator class which actually delegates the
399 >    //responsibility to LocalIndexManager.
400      setGlobalIndex(info);
401      
402 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
403 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
404 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
405 <    //we can determine the beginning global indices of atoms before they get created.
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 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 216 | Line 448 | namespace oopse {
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 245 | Line 477 | namespace oopse {
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 333 | Line 565 | namespace oopse {
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 363 | Line 595 | namespace oopse {
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 393 | Line 625 | namespace oopse {
625        
626      } //end for(int i=0)  
627    }
396 –  
397 –  void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398 –                            std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399 –    int i;
400 –    char * id;
401 –    MoleculeStamp * currentStamp;
402 –    Component** the_components = simParams->getComponents();
403 –    int n_components = simParams->getNComponents();
628      
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 –        currentStamp = stamps->getMolStamp(id);
423 –        if (currentStamp == 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 –        moleculeStampPairs.push_back(
433 –                                     std::make_pair(currentStamp, the_components[i]->getNMol()));
434 –      } //end for (i = 0; i < n_components; i++)
435 –    } else {
436 –      sprintf(painCave.errMsg, "SimSetup error.\n"
437 –              "\tSorry, the ability to specify total"
438 –              " nMols and then give molfractions in the components\n"
439 –              "\tis not currently supported."
440 –              " Please give nMol in the components.\n");
441 –      
442 –      painCave.isFatal = 1;
443 –      simError();
444 –    }
445 –    
446 – #ifdef IS_MPI
447 –    
448 –    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
449 –    MPIcheckPoint();
450 –    
451 – #endif // is_mpi
452 –    
453 –  }
454 –  
629    void SimCreator::setGlobalIndex(SimInfo *info) {
630      SimInfo::MoleculeIterator mi;
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 465 | Line 640 | namespace oopse {
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 552 | Line 728 | namespace oopse {
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 564 | Line 740 | namespace oopse {
740      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
741      
742      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
567 –      
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 580 | Line 755 | namespace oopse {
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      
590 –    if (!simParams->haveInitialConfig()) {
591 –      sprintf(painCave.errMsg,
592 –              "Cannot intialize a simulation without an initial configuration file.\n");
593 –      painCave.isFatal = 1;;
594 –      simError();
595 –    }
803      
804 <    DumpReader reader(info, simParams->getInitialConfig());
804 >    DumpReader reader(info, mdFileName);
805      int nframes = reader.getNFrames();
806      
807      if (nframes > 0) {
# Line 603 | Line 810 | namespace oopse {
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 612 | Line 819 | namespace oopse {
819      info->getSnapshotManager()->advance();
820    }
821    
822 < } //end namespace oopse
822 > } //end namespace OpenMD
823  
824  

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