| 56 |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimSnapshotManager.hpp" |
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#include "io/DumpReader.hpp" |
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< |
#include "UseTheForce/ForceFieldFactory.hpp" |
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> |
#include "brains/ForceField.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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metaDataBlockStart + 1); |
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|
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//create the force field |
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< |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField()); |
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> |
ForceField * ff = new ForceField(simParams->getForceField()); |
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|
| 376 |
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if (ff == NULL) { |
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sprintf(painCave.errMsg, |
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//find the storage layout |
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|
| 427 |
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int storageLayout = computeStorageLayout(info); |
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– |
|
| 429 |
– |
cerr << "computed Storage Layout = " << storageLayout << "\n"; |
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|
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//allocate memory for DataStorage(circular reference, need to |
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//break it) |
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|
| 668 |
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int SimCreator::computeStorageLayout(SimInfo* info) { |
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|
| 670 |
+ |
Globals* simParams = info->getSimParams(); |
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int nRigidBodies = info->getNGlobalRigidBodies(); |
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set<AtomType*> atomTypes = info->getSimulatedAtomTypes(); |
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set<AtomType*>::iterator i; |
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if (storageLayout & DataStorage::dslForce) { |
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storageLayout |= DataStorage::dslFlucQForce; |
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} |
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+ |
} |
| 747 |
+ |
|
| 748 |
+ |
// if the user has asked for them, make sure we've got the memory for the |
| 749 |
+ |
// objects defined. |
| 750 |
+ |
|
| 751 |
+ |
if (simParams->getOutputParticlePotential()) { |
| 752 |
+ |
storageLayout |= DataStorage::dslParticlePot; |
| 753 |
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} |
| 754 |
+ |
|
| 755 |
+ |
if (simParams->havePrintHeatFlux()) { |
| 756 |
+ |
if (simParams->getPrintHeatFlux()) { |
| 757 |
+ |
storageLayout |= DataStorage::dslParticlePot; |
| 758 |
+ |
} |
| 759 |
+ |
} |
| 760 |
+ |
|
| 761 |
+ |
if (simParams->getOutputElectricField()) { |
| 762 |
+ |
storageLayout |= DataStorage::dslElectricField; |
| 763 |
+ |
} |
| 764 |
+ |
if (simParams->getOutputFluctuatingCharges()) { |
| 765 |
+ |
storageLayout |= DataStorage::dslFlucQPosition; |
| 766 |
+ |
storageLayout |= DataStorage::dslFlucQVelocity; |
| 767 |
+ |
storageLayout |= DataStorage::dslFlucQForce; |
| 768 |
+ |
} |
| 769 |
+ |
|
| 770 |
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return storageLayout; |
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} |
| 772 |
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|
| 786 |
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int nGlobalAtoms = info->getNGlobalAtoms(); |
| 787 |
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|
| 788 |
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beginAtomIndex = 0; |
| 789 |
< |
beginRigidBodyIndex = 0; |
| 789 |
> |
//rigidbody's index begins right after atom's |
| 790 |
> |
beginRigidBodyIndex = info->getNGlobalAtoms(); |
| 791 |
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beginCutoffGroupIndex = 0; |
| 792 |
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|
| 793 |
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for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
