| 62 |
|
|
| 63 |
|
ForceManager::ForceManager(SimInfo * info) : info_(info), |
| 64 |
|
NBforcesInitialized_(false) { |
| 65 |
– |
lj_ = LJ::Instance(); |
| 66 |
– |
lj_->setForceField(info_->getForceField()); |
| 67 |
– |
|
| 68 |
– |
gb_ = GB::Instance(); |
| 69 |
– |
gb_->setForceField(info_->getForceField()); |
| 70 |
– |
|
| 71 |
– |
sticky_ = Sticky::Instance(); |
| 72 |
– |
sticky_->setForceField(info_->getForceField()); |
| 73 |
– |
|
| 74 |
– |
eam_ = EAM::Instance(); |
| 75 |
– |
eam_->setForceField(info_->getForceField()); |
| 76 |
– |
|
| 77 |
– |
sc_ = SC::Instance(); |
| 78 |
– |
sc_->setForceField(info_->getForceField()); |
| 65 |
|
} |
| 66 |
|
|
| 67 |
|
void ForceManager::calcForces() { |
| 68 |
|
|
| 69 |
+ |
|
| 70 |
|
if (!info_->isFortranInitialized()) { |
| 71 |
|
info_->update(); |
| 72 |
+ |
nbiMan_->setSimInfo(info_); |
| 73 |
+ |
nbiMan_->initialize(); |
| 74 |
+ |
info_->setupFortran(); |
| 75 |
|
} |
| 76 |
|
|
| 77 |
|
preCalculation(); |
| 91 |
|
Atom* atom; |
| 92 |
|
Molecule::RigidBodyIterator rbIter; |
| 93 |
|
RigidBody* rb; |
| 94 |
+ |
Molecule::CutoffGroupIterator ci; |
| 95 |
+ |
CutoffGroup* cg; |
| 96 |
|
|
| 97 |
|
// forces are zeroed here, before any are accumulated. |
| 98 |
|
// NOTE: do not rezero the forces in Fortran. |
| 108 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 109 |
|
rb->zeroForcesAndTorques(); |
| 110 |
|
} |
| 111 |
< |
|
| 111 |
> |
|
| 112 |
> |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 113 |
> |
std::cerr << "should not see me \n"; |
| 114 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 115 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 116 |
> |
//calculate the center of mass of cutoff group |
| 117 |
> |
cg->updateCOM(); |
| 118 |
> |
} |
| 119 |
> |
} |
| 120 |
|
} |
| 121 |
< |
|
| 121 |
> |
|
| 122 |
|
// Zero out the stress tensor |
| 123 |
|
tau *= 0.0; |
| 124 |
|
|
| 245 |
|
void ForceManager::calcLongRangeInteraction() { |
| 246 |
|
Snapshot* curSnapshot; |
| 247 |
|
DataStorage* config; |
| 248 |
+ |
DataStorage* cgConfig; |
| 249 |
|
RealType* frc; |
| 250 |
|
RealType* pos; |
| 251 |
|
RealType* trq; |
| 259 |
|
|
| 260 |
|
//get array pointers |
| 261 |
|
config = &(curSnapshot->atomData); |
| 262 |
+ |
cgConfig = &(curSnapshot->cgData); |
| 263 |
|
frc = config->getArrayPointer(DataStorage::dslForce); |
| 264 |
|
pos = config->getArrayPointer(DataStorage::dslPosition); |
| 265 |
|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 267 |
|
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 268 |
|
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 269 |
|
|
| 270 |
< |
//calculate the center of mass of cutoff group |
| 271 |
< |
SimInfo::MoleculeIterator mi; |
| 272 |
< |
Molecule* mol; |
| 271 |
< |
Molecule::CutoffGroupIterator ci; |
| 272 |
< |
CutoffGroup* cg; |
| 273 |
< |
Vector3d com; |
| 274 |
< |
std::vector<Vector3d> rcGroup; |
| 275 |
< |
|
| 276 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 277 |
< |
|
| 278 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 279 |
< |
mol = info_->nextMolecule(mi)) { |
| 280 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 281 |
< |
cg = mol->nextCutoffGroup(ci)) { |
| 282 |
< |
cg->getCOM(com); |
| 283 |
< |
rcGroup.push_back(com); |
| 284 |
< |
} |
| 285 |
< |
}// end for (mol) |
| 286 |
< |
|
| 287 |
< |
rc = rcGroup[0].getArrayPointer(); |
| 270 |
> |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 271 |
> |
std::cerr << "should not see me \n"; |
| 272 |
> |
rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
| 273 |
|
} else { |
| 274 |
|
// center of mass of the group is the same as position of the atom |
| 275 |
|
// if cutoff group does not exist |
| 279 |
|
//initialize data before passing to fortran |
| 280 |
|
RealType longRangePotential[LR_POT_TYPES]; |
| 281 |
|
RealType lrPot = 0.0; |
| 297 |
– |
Vector3d totalDipole; |
| 282 |
|
int isError = 0; |
| 283 |
|
|
| 284 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 305 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 306 |
|
lrPot += longRangePotential[i]; //Quick hack |
| 307 |
|
} |
| 308 |
< |
|
| 325 |
< |
// grab the simulation box dipole moment if specified |
| 326 |
< |
if (info_->getCalcBoxDipole()){ |
| 327 |
< |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 328 |
< |
|
| 329 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 330 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 331 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 332 |
< |
} |
| 333 |
< |
|
| 308 |
> |
|
| 309 |
|
//store the tau and long range potential |
| 310 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 311 |
|
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
