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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 1787 by gezelter, Wed Aug 29 18:13:11 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 720 | Line 720 | namespace OpenMD {
720        if (storageLayout & DataStorage::dslForce) {
721          storageLayout |= DataStorage::dslTorque;
722        }
723 –    }
724 –    if (hasMultipoles) {
725 –      storageLayout |= DataStorage::dslElectroFrame;
723      }
724      if (hasFixedCharge || hasFluctuatingCharge) {
725        storageLayout |= DataStorage::dslSkippedCharge;
# Line 761 | Line 758 | namespace OpenMD {
758      if (simParams->getOutputElectricField()) {
759        storageLayout |= DataStorage::dslElectricField;
760      }
761 +
762      if (simParams->getOutputFluctuatingCharges()) {
763        storageLayout |= DataStorage::dslFlucQPosition;
764        storageLayout |= DataStorage::dslFlucQVelocity;
# Line 786 | Line 784 | namespace OpenMD {
784      int nGlobalAtoms = info->getNGlobalAtoms();
785      
786      beginAtomIndex = 0;
787 <    beginRigidBodyIndex = 0;
787 >    //rigidbody's index begins right after atom's
788 >    beginRigidBodyIndex = info->getNGlobalAtoms();
789      beginCutoffGroupIndex = 0;
790  
791      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 904 | Line 903 | namespace OpenMD {
903      for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
904        int myGlobalIndex = mol->getGlobalIndex();
905        int globalIO = startingIOIndexForMol[myGlobalIndex];
906 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
907 <           integrableObject = mol->nextIntegrableObject(ioi)) {
908 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
909 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
906 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
907 >           sd = mol->nextIntegrableObject(ioi)) {
908 >        sd->setGlobalIntegrableObjectIndex(globalIO);
909 >        IOIndexToIntegrableObject[globalIO] = sd;
910          globalIO++;
911        }
912      }

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