| 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" |
| 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, |
| 750 |
|
|
| 751 |
|
if (simParams->getOutputParticlePotential()) { |
| 752 |
|
storageLayout |= DataStorage::dslParticlePot; |
| 753 |
+ |
} |
| 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 |
|
} |
| 786 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 787 |
|
|
| 788 |
|
beginAtomIndex = 0; |
| 789 |
< |
beginRigidBodyIndex = 0; |
| 789 |
> |
//rigidbody's index begins right after atom's |
| 790 |
> |
beginRigidBodyIndex = info->getNGlobalAtoms(); |
| 791 |
|
beginCutoffGroupIndex = 0; |
| 792 |
|
|
| 793 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
