| 56 |
|
#include "brains/SimCreator.hpp" |
| 57 |
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#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 |
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#include "utils/StringUtils.hpp" |
| 62 |
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#include "math/SeqRandNumGen.hpp" |
| 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 |
| 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, |
| 425 |
|
//find the storage layout |
| 426 |
|
|
| 427 |
|
int storageLayout = computeStorageLayout(info); |
| 428 |
– |
|
| 429 |
– |
cerr << "computed Storage Layout = " << storageLayout << "\n"; |
| 428 |
|
|
| 429 |
|
//allocate memory for DataStorage(circular reference, need to |
| 430 |
|
//break it) |
| 720 |
|
if (storageLayout & DataStorage::dslForce) { |
| 721 |
|
storageLayout |= DataStorage::dslTorque; |
| 722 |
|
} |
| 725 |
– |
} |
| 726 |
– |
if (hasMultipoles) { |
| 727 |
– |
storageLayout |= DataStorage::dslElectroFrame; |
| 723 |
|
} |
| 724 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
| 725 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
| 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 |
|
|
| 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++) { |
| 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 |
|
} |
