| 57 |
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#include "primitives/Bend.hpp" |
| 58 |
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#include "primitives/Torsion.hpp" |
| 59 |
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#include "primitives/Inversion.hpp" |
| 60 |
– |
namespace OpenMD { |
| 60 |
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|
| 61 |
+ |
namespace OpenMD { |
| 62 |
+ |
|
| 63 |
+ |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
| 64 |
+ |
NBforcesInitialized_(false) { |
| 65 |
+ |
} |
| 66 |
+ |
|
| 67 |
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void ForceManager::calcForces() { |
| 68 |
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|
| 69 |
+ |
|
| 70 |
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if (!info_->isFortranInitialized()) { |
| 71 |
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info_->update(); |
| 72 |
+ |
nbiMan_->setSimInfo(info_); |
| 73 |
+ |
nbiMan_->initialize(); |
| 74 |
+ |
info_->setupFortran(); |
| 75 |
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} |
| 76 |
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|
| 77 |
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preCalculation(); |
| 91 |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
| 93 |
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RigidBody* rb; |
| 94 |
+ |
Molecule::CutoffGroupIterator ci; |
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+ |
CutoffGroup* cg; |
| 96 |
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|
| 97 |
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// forces are zeroed here, before any are accumulated. |
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// NOTE: do not rezero the forces in Fortran. |
| 108 |
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rb = mol->nextRigidBody(rbIter)) { |
| 109 |
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rb->zeroForcesAndTorques(); |
| 110 |
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} |
| 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 |
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> |
cg->updateCOM(); |
| 118 |
> |
} |
| 119 |
> |
} |
| 120 |
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} |
| 121 |
< |
|
| 121 |
> |
|
| 122 |
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// Zero out the stress tensor |
| 123 |
|
tau *= 0.0; |
| 124 |
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|
| 245 |
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void ForceManager::calcLongRangeInteraction() { |
| 246 |
|
Snapshot* curSnapshot; |
| 247 |
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DataStorage* config; |
| 248 |
+ |
DataStorage* cgConfig; |
| 249 |
|
RealType* frc; |
| 250 |
|
RealType* pos; |
| 251 |
|
RealType* trq; |
| 259 |
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|
| 260 |
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//get array pointers |
| 261 |
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config = &(curSnapshot->atomData); |
| 262 |
+ |
cgConfig = &(curSnapshot->cgData); |
| 263 |
|
frc = config->getArrayPointer(DataStorage::dslForce); |
| 264 |
|
pos = config->getArrayPointer(DataStorage::dslPosition); |
| 265 |
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trq = config->getArrayPointer(DataStorage::dslTorque); |
| 267 |
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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; |
| 252 |
< |
Molecule::CutoffGroupIterator ci; |
| 253 |
< |
CutoffGroup* cg; |
| 254 |
< |
Vector3d com; |
| 255 |
< |
std::vector<Vector3d> rcGroup; |
| 256 |
< |
|
| 257 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 258 |
< |
|
| 259 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 260 |
< |
mol = info_->nextMolecule(mi)) { |
| 261 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 262 |
< |
cg = mol->nextCutoffGroup(ci)) { |
| 263 |
< |
cg->getCOM(com); |
| 264 |
< |
rcGroup.push_back(com); |
| 265 |
< |
} |
| 266 |
< |
}// end for (mol) |
| 267 |
< |
|
| 268 |
< |
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; |
| 278 |
– |
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 |
< |
|
| 306 |
< |
// grab the simulation box dipole moment if specified |
| 307 |
< |
if (info_->getCalcBoxDipole()){ |
| 308 |
< |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 309 |
< |
|
| 310 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 311 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 312 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 313 |
< |
} |
| 314 |
< |
|
| 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]; |
