| 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 |
|
/** |
| 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" |
| 90 |
|
#endif |
| 91 |
|
|
| 422 |
|
//create the molecules |
| 423 |
|
createMolecules(info); |
| 424 |
|
|
| 425 |
+ |
//find the storage layout |
| 426 |
+ |
|
| 427 |
+ |
int storageLayout = computeStorageLayout(info); |
| 428 |
+ |
|
| 429 |
+ |
cerr << "computed Storage Layout = " << storageLayout << "\n"; |
| 430 |
+ |
|
| 431 |
|
//allocate memory for DataStorage(circular reference, need to |
| 432 |
|
//break it) |
| 433 |
< |
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 433 |
> |
info->setSnapshotManager(new SimSnapshotManager(info, storageLayout)); |
| 434 |
|
|
| 435 |
|
//set the global index of atoms, rigidbodies and cutoffgroups |
| 436 |
|
//(only need to be set once, the global index will never change |
| 667 |
|
} //end for(int i=0) |
| 668 |
|
} |
| 669 |
|
|
| 670 |
+ |
int SimCreator::computeStorageLayout(SimInfo* info) { |
| 671 |
+ |
|
| 672 |
+ |
Globals* simParams = info->getSimParams(); |
| 673 |
+ |
int nRigidBodies = info->getNGlobalRigidBodies(); |
| 674 |
+ |
set<AtomType*> atomTypes = info->getSimulatedAtomTypes(); |
| 675 |
+ |
set<AtomType*>::iterator i; |
| 676 |
+ |
bool hasDirectionalAtoms = false; |
| 677 |
+ |
bool hasFixedCharge = false; |
| 678 |
+ |
bool hasMultipoles = false; |
| 679 |
+ |
bool hasPolarizable = false; |
| 680 |
+ |
bool hasFluctuatingCharge = false; |
| 681 |
+ |
bool hasMetallic = false; |
| 682 |
+ |
int storageLayout = 0; |
| 683 |
+ |
storageLayout |= DataStorage::dslPosition; |
| 684 |
+ |
storageLayout |= DataStorage::dslVelocity; |
| 685 |
+ |
storageLayout |= DataStorage::dslForce; |
| 686 |
+ |
|
| 687 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 688 |
+ |
|
| 689 |
+ |
DirectionalAdapter da = DirectionalAdapter( (*i) ); |
| 690 |
+ |
MultipoleAdapter ma = MultipoleAdapter( (*i) ); |
| 691 |
+ |
EAMAdapter ea = EAMAdapter( (*i) ); |
| 692 |
+ |
SuttonChenAdapter sca = SuttonChenAdapter( (*i) ); |
| 693 |
+ |
PolarizableAdapter pa = PolarizableAdapter( (*i) ); |
| 694 |
+ |
FixedChargeAdapter fca = FixedChargeAdapter( (*i) ); |
| 695 |
+ |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) ); |
| 696 |
+ |
|
| 697 |
+ |
if (da.isDirectional()){ |
| 698 |
+ |
hasDirectionalAtoms = true; |
| 699 |
+ |
} |
| 700 |
+ |
if (ma.isMultipole()){ |
| 701 |
+ |
hasMultipoles = true; |
| 702 |
+ |
} |
| 703 |
+ |
if (ea.isEAM() || sca.isSuttonChen()){ |
| 704 |
+ |
hasMetallic = true; |
| 705 |
+ |
} |
| 706 |
+ |
if ( fca.isFixedCharge() ){ |
| 707 |
+ |
hasFixedCharge = true; |
| 708 |
+ |
} |
| 709 |
+ |
if ( fqa.isFluctuatingCharge() ){ |
| 710 |
+ |
hasFluctuatingCharge = true; |
| 711 |
+ |
} |
| 712 |
+ |
if ( pa.isPolarizable() ){ |
| 713 |
+ |
hasPolarizable = true; |
| 714 |
+ |
} |
| 715 |
+ |
} |
| 716 |
+ |
|
| 717 |
+ |
if (nRigidBodies > 0 || hasDirectionalAtoms) { |
| 718 |
+ |
storageLayout |= DataStorage::dslAmat; |
| 719 |
+ |
if(storageLayout & DataStorage::dslVelocity) { |
| 720 |
+ |
storageLayout |= DataStorage::dslAngularMomentum; |
| 721 |
+ |
} |
| 722 |
+ |
if (storageLayout & DataStorage::dslForce) { |
| 723 |
+ |
storageLayout |= DataStorage::dslTorque; |
| 724 |
+ |
} |
| 725 |
+ |
} |
| 726 |
+ |
if (hasMultipoles) { |
| 727 |
+ |
storageLayout |= DataStorage::dslElectroFrame; |
| 728 |
+ |
} |
| 729 |
+ |
if (hasFixedCharge || hasFluctuatingCharge) { |
| 730 |
+ |
storageLayout |= DataStorage::dslSkippedCharge; |
| 731 |
+ |
} |
| 732 |
+ |
if (hasMetallic) { |
| 733 |
+ |
storageLayout |= DataStorage::dslDensity; |
| 734 |
+ |
storageLayout |= DataStorage::dslFunctional; |
| 735 |
+ |
storageLayout |= DataStorage::dslFunctionalDerivative; |
| 736 |
+ |
} |
| 737 |
+ |
if (hasPolarizable) { |
| 738 |
+ |
storageLayout |= DataStorage::dslElectricField; |
| 739 |
+ |
} |
| 740 |
+ |
if (hasFluctuatingCharge){ |
| 741 |
+ |
storageLayout |= DataStorage::dslFlucQPosition; |
| 742 |
+ |
if(storageLayout & DataStorage::dslVelocity) { |
| 743 |
+ |
storageLayout |= DataStorage::dslFlucQVelocity; |
| 744 |
+ |
} |
| 745 |
+ |
if (storageLayout & DataStorage::dslForce) { |
| 746 |
+ |
storageLayout |= DataStorage::dslFlucQForce; |
| 747 |
+ |
} |
| 748 |
+ |
} |
| 749 |
+ |
|
| 750 |
+ |
if (simParams->getOutputParticlePotential()) { |
| 751 |
+ |
storageLayout |= DataStorage::dslParticlePot; |
| 752 |
+ |
} |
| 753 |
+ |
|
| 754 |
+ |
return storageLayout; |
| 755 |
+ |
} |
| 756 |
+ |
|
| 757 |
|
void SimCreator::setGlobalIndex(SimInfo *info) { |
| 758 |
|
SimInfo::MoleculeIterator mi; |
| 759 |
|
Molecule::AtomIterator ai; |
