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root/OpenMD/branches/development/src/brains/SimCreator.cpp
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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

# Line 56 | Line 56
56   #include "brains/SimCreator.hpp"
57   #include "brains/SimSnapshotManager.hpp"
58   #include "io/DumpReader.hpp"
59 < #include "UseTheForce/ForceFieldFactory.hpp"
59 > #include "brains/ForceField.hpp"
60   #include "utils/simError.h"
61   #include "utils/StringUtils.hpp"
62   #include "math/SeqRandNumGen.hpp"
# Line 256 | Line 256 | namespace OpenMD {
256      int metaDataBlockStart = -1;
257      int metaDataBlockEnd = -1;
258      int i;
259 <    int mdOffset;
259 >    streamoff mdOffset;
260      int mdFileVersion;
261  
262   #ifdef IS_MPI            
# Line 371 | Line 371 | namespace OpenMD {
371                                     metaDataBlockStart + 1);
372      
373      //create the force field
374 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
374 >    ForceField * ff = new ForceField(simParams->getForceField());
375  
376      if (ff == NULL) {
377        sprintf(painCave.errMsg,
# Line 786 | Line 786 | namespace OpenMD {
786      int nGlobalAtoms = info->getNGlobalAtoms();
787      
788      beginAtomIndex = 0;
789 <    beginRigidBodyIndex = 0;
789 >    //rigidbody's index begins right after atom's
790 >    beginRigidBodyIndex = info->getNGlobalAtoms();
791      beginCutoffGroupIndex = 0;
792  
793      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 904 | Line 905 | namespace OpenMD {
905      for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906        int myGlobalIndex = mol->getGlobalIndex();
907        int globalIO = startingIOIndexForMol[myGlobalIndex];
908 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
909 <           integrableObject = mol->nextIntegrableObject(ioi)) {
910 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
911 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
908 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
909 >           sd = mol->nextIntegrableObject(ioi)) {
910 >        sd->setGlobalIntegrableObjectIndex(globalIO);
911 >        IOIndexToIntegrableObject[globalIO] = sd;
912          globalIO++;
913        }
914      }

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