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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 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(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85      Globals* simParams = NULL;
# Line 108 | Line 108 | namespace oopse {
108        } else {
109          //get stream size
110          commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
111 <                
111 >
112          char* buf = new char[streamSize];
113          assert(buf);
114                  
# Line 116 | Line 116 | namespace oopse {
116          commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117                  
118          ppStream.str(buf);
119 <        delete buf;
119 >        delete [] buf;
120  
121        }
122   #endif            
# Line 145 | Line 145 | namespace oopse {
145        treeParser.initializeASTFactory(factory);
146        treeParser.setASTFactory(&factory);
147        simParams = treeParser.walkTree(parser.getAST());
148 –
148      }
149  
150        
# Line 215 | Line 214 | namespace oopse {
214        painCave.isFatal = 1;
215        simError();        
216      }
217 <    catch (OOPSEException& e) {
217 >    catch (OpenMDException& e) {
218        sprintf(painCave.errMsg,
219                "%s\n",
220                e.getMessage().c_str());
# Line 263 | Line 262 | namespace oopse {
262        mdFile_.getline(buffer, bufferSize);
263        ++lineNo;
264        std::string line = trimLeftCopy(buffer);
265 <      i = CaseInsensitiveFind(line, "<OOPSE");
266 <      if (i == string::npos) {
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 an OOPSE file!\n",
274 >                "SimCreator: File: %s is not a valid OpenMD file!\n",
275                  mdFileName.c_str());
276          painCave.isFatal = 1;
277          simError();
# Line 330 | Line 335 | namespace oopse {
335      Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336      
337      //create the force field
338 <    ForceField * ff = ForceFieldFactory::getInstance()
339 <      ->createForceField(simParams->getForceField());
335 <    
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 395 | Line 399 | namespace oopse {
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)
# Line 473 | 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 724 | 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 736 | 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)) {
739 –      
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 769 | Line 772 | namespace oopse {
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)) {
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++;
789 >        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
790 >        IOIndexToIntegrableObject[globalIO] = integrableObject;
791 >        globalIO++;
792        }
793      }
794 <
795 <  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
796 <  
794 >    
795 >    info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
796 >    
797    }
798    
799    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
# Line 816 | Line 819 | int startingIndex = 0;
819      info->getSnapshotManager()->advance();
820    }
821    
822 < } //end namespace oopse
822 > } //end namespace OpenMD
823  
824  

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