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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 55 | 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 75 | Line 76
76   #include "antlr/NoViableAltForCharException.hpp"
77   #include "antlr/NoViableAltException.hpp"
78  
79 + #include "types/DirectionalAdapter.hpp"
80 + #include "types/MultipoleAdapter.hpp"
81 + #include "types/EAMAdapter.hpp"
82 + #include "types/SuttonChenAdapter.hpp"
83 + #include "types/PolarizableAdapter.hpp"
84 + #include "types/FixedChargeAdapter.hpp"
85 + #include "types/FluctuatingChargeAdapter.hpp"
86 +
87   #ifdef IS_MPI
88   #include "mpi.h"
89   #include "math/ParallelRandNumGen.hpp"
# Line 247 | 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 362 | 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 413 | Line 422 | namespace OpenMD {
422      //create the molecules
423      createMolecules(info);
424      
425 +    //find the storage layout
426 +
427 +    int storageLayout = computeStorageLayout(info);
428 +
429      //allocate memory for DataStorage(circular reference, need to
430      //break it)
431 <    info->setSnapshotManager(new SimSnapshotManager(info));
431 >    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
432      
433      //set the global index of atoms, rigidbodies and cutoffgroups
434      //(only need to be set once, the global index will never change
# Line 652 | Line 665 | namespace OpenMD {
665      } //end for(int i=0)  
666    }
667      
668 +  int SimCreator::computeStorageLayout(SimInfo* info) {
669 +
670 +    Globals* simParams = info->getSimParams();
671 +    int nRigidBodies = info->getNGlobalRigidBodies();
672 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
673 +    set<AtomType*>::iterator i;
674 +    bool hasDirectionalAtoms = false;
675 +    bool hasFixedCharge = false;
676 +    bool hasMultipoles = false;    
677 +    bool hasPolarizable = false;    
678 +    bool hasFluctuatingCharge = false;    
679 +    bool hasMetallic = false;
680 +    int storageLayout = 0;
681 +    storageLayout |= DataStorage::dslPosition;
682 +    storageLayout |= DataStorage::dslVelocity;
683 +    storageLayout |= DataStorage::dslForce;
684 +
685 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
686 +
687 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
688 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
689 +      EAMAdapter ea = EAMAdapter( (*i) );
690 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
691 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
692 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
693 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
694 +
695 +      if (da.isDirectional()){
696 +        hasDirectionalAtoms = true;
697 +      }
698 +      if (ma.isMultipole()){
699 +        hasMultipoles = true;
700 +      }
701 +      if (ea.isEAM() || sca.isSuttonChen()){
702 +        hasMetallic = true;
703 +      }
704 +      if ( fca.isFixedCharge() ){
705 +        hasFixedCharge = true;
706 +      }
707 +      if ( fqa.isFluctuatingCharge() ){
708 +        hasFluctuatingCharge = true;
709 +      }
710 +      if ( pa.isPolarizable() ){
711 +        hasPolarizable = true;
712 +      }
713 +    }
714 +    
715 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
716 +      storageLayout |= DataStorage::dslAmat;
717 +      if(storageLayout & DataStorage::dslVelocity) {
718 +        storageLayout |= DataStorage::dslAngularMomentum;
719 +      }
720 +      if (storageLayout & DataStorage::dslForce) {
721 +        storageLayout |= DataStorage::dslTorque;
722 +      }
723 +    }
724 +    if (hasFixedCharge || hasFluctuatingCharge) {
725 +      storageLayout |= DataStorage::dslSkippedCharge;
726 +    }
727 +    if (hasMetallic) {
728 +      storageLayout |= DataStorage::dslDensity;
729 +      storageLayout |= DataStorage::dslFunctional;
730 +      storageLayout |= DataStorage::dslFunctionalDerivative;
731 +    }
732 +    if (hasPolarizable) {
733 +      storageLayout |= DataStorage::dslElectricField;
734 +    }
735 +    if (hasFluctuatingCharge){
736 +      storageLayout |= DataStorage::dslFlucQPosition;
737 +      if(storageLayout & DataStorage::dslVelocity) {
738 +        storageLayout |= DataStorage::dslFlucQVelocity;
739 +      }
740 +      if (storageLayout & DataStorage::dslForce) {
741 +        storageLayout |= DataStorage::dslFlucQForce;
742 +      }
743 +    }
744 +    
745 +    // if the user has asked for them, make sure we've got the memory for the
746 +    // objects defined.
747 +
748 +    if (simParams->getOutputParticlePotential()) {
749 +      storageLayout |= DataStorage::dslParticlePot;
750 +    }
751 +
752 +    if (simParams->havePrintHeatFlux()) {
753 +      if (simParams->getPrintHeatFlux()) {
754 +        storageLayout |= DataStorage::dslParticlePot;
755 +      }
756 +    }
757 +
758 +    if (simParams->getOutputElectricField()) {
759 +      storageLayout |= DataStorage::dslElectricField;
760 +    }
761 +
762 +    if (simParams->getOutputFluctuatingCharges()) {
763 +      storageLayout |= DataStorage::dslFlucQPosition;
764 +      storageLayout |= DataStorage::dslFlucQVelocity;
765 +      storageLayout |= DataStorage::dslFlucQForce;
766 +    }
767 +
768 +    return storageLayout;
769 +  }
770 +
771    void SimCreator::setGlobalIndex(SimInfo *info) {
772      SimInfo::MoleculeIterator mi;
773      Molecule::AtomIterator ai;
# Line 668 | 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 786 | 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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