| 475 |
|
} |
| 476 |
|
|
| 477 |
|
void ForceManager::longRangeInteractions() { |
| 478 |
< |
// some of this initial stuff will go away: |
| 478 |
> |
|
| 479 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 480 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 481 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 482 |
– |
RealType* frc = config->getArrayPointer(DataStorage::dslForce); |
| 483 |
– |
RealType* pos = config->getArrayPointer(DataStorage::dslPosition); |
| 484 |
– |
RealType* trq = config->getArrayPointer(DataStorage::dslTorque); |
| 485 |
– |
RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
| 486 |
– |
RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 487 |
– |
RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 482 |
|
|
| 483 |
< |
// new stuff starts here: |
| 484 |
< |
|
| 483 |
> |
//calculate the center of mass of cutoff group |
| 484 |
> |
|
| 485 |
> |
SimInfo::MoleculeIterator mi; |
| 486 |
> |
Molecule* mol; |
| 487 |
> |
Molecule::CutoffGroupIterator ci; |
| 488 |
> |
CutoffGroup* cg; |
| 489 |
> |
|
| 490 |
> |
if(info_->getNCutoffGroups() > 0){ |
| 491 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 492 |
> |
mol = info_->nextMolecule(mi)) { |
| 493 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 494 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 495 |
> |
cg->updateCOM(); |
| 496 |
> |
} |
| 497 |
> |
} |
| 498 |
> |
} else { |
| 499 |
> |
// center of mass of the group is the same as position of the atom |
| 500 |
> |
// if cutoff group does not exist |
| 501 |
> |
cgConfig->position = config->position; |
| 502 |
> |
} |
| 503 |
> |
|
| 504 |
|
fDecomp_->zeroWorkArrays(); |
| 505 |
|
fDecomp_->distributeData(); |
| 506 |
|
|
| 509 |
|
RealType rgrpsq, rgrp, r2, r; |
| 510 |
|
RealType electroMult, vdwMult; |
| 511 |
|
RealType vij; |
| 512 |
< |
Vector3d fij, fg; |
| 512 |
> |
Vector3d fij, fg, f1; |
| 513 |
|
tuple3<RealType, RealType, RealType> cuts; |
| 514 |
|
RealType rCutSq; |
| 515 |
|
bool in_switching_region; |
| 525 |
|
|
| 526 |
|
int loopStart, loopEnd; |
| 527 |
|
|
| 528 |
+ |
idat.vdwMult = &vdwMult; |
| 529 |
+ |
idat.electroMult = &electroMult; |
| 530 |
+ |
idat.pot = &pot; |
| 531 |
+ |
idat.vpair = &vpair; |
| 532 |
+ |
idat.f1 = &f1; |
| 533 |
+ |
idat.sw = &sw; |
| 534 |
+ |
|
| 535 |
|
loopEnd = PAIR_LOOP; |
| 536 |
|
if (info_->requiresPrepair() ) { |
| 537 |
|
loopStart = PREPAIR_LOOP; |
| 539 |
|
loopStart = PAIR_LOOP; |
| 540 |
|
} |
| 541 |
|
|
| 522 |
– |
|
| 542 |
|
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 543 |
|
|
| 544 |
|
if (iLoop == loopStart) { |
| 570 |
|
|
| 571 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 572 |
|
rgrp); |
| 554 |
– |
|
| 555 |
– |
idat.sw = &sw; |
| 573 |
|
|
| 574 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 575 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 582 |
|
jb != atomListColumn.end(); ++jb) { |
| 583 |
|
atom2 = (*jb); |
| 584 |
|
|
| 568 |
– |
cerr << "doing atoms " << atom1 << " " << atom2 << "\n"; |
| 585 |
|
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 586 |
|
|
| 587 |
|
vpair = 0.0; |
| 588 |
+ |
f1 = V3Zero; |
| 589 |
|
|
| 590 |
< |
cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n"; |
| 574 |
< |
idat = fDecomp_->fillInteractionData(atom1, atom2); |
| 575 |
< |
cerr << "done with idat\n"; |
| 590 |
> |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 591 |
|
|
| 592 |
|
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 593 |
|
vdwMult = vdwScale_[topoDist]; |
| 594 |
|
electroMult = electrostaticScale_[topoDist]; |
| 595 |
|
|
| 581 |
– |
idat.vdwMult = &vdwMult; |
| 582 |
– |
idat.electroMult = &electroMult; |
| 583 |
– |
idat.pot = &pot; |
| 584 |
– |
idat.vpair = &vpair; |
| 585 |
– |
|
| 596 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 597 |
|
idat.d = &d_grp; |
| 598 |
|
idat.r2 = &rgrpsq; |
| 604 |
|
idat.r2 = &r2; |
| 605 |
|
} |
| 606 |
|
|
| 607 |
< |
cerr << "d = " << d << "\n"; |
| 598 |
< |
cerr << "r2 = " << r2 << "\n"; |
| 599 |
< |
r = sqrt( r2 ); |
| 607 |
> |
r = sqrt( *(idat.r2) ); |
| 608 |
|
idat.rij = &r; |
| 609 |
|
|
| 610 |
|
if (iLoop == PREPAIR_LOOP) { |
| 611 |
|
interactionMan_->doPrePair(idat); |
| 612 |
|
} else { |
| 605 |
– |
cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n"; |
| 613 |
|
interactionMan_->doPair(idat); |
| 614 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 615 |
< |
vij += *(idat.vpair); |
| 616 |
< |
fij += *(idat.f1); |
| 617 |
< |
tau -= outProduct( *(idat.d), *(idat.f1)); |
| 615 |
> |
vij += vpair; |
| 616 |
> |
fij += f1; |
| 617 |
> |
tau -= outProduct( *(idat.d), f1); |
| 618 |
|
} |
| 619 |
|
} |
| 620 |
|
} |
| 680 |
|
fDecomp_->collectIntermediateData(); |
| 681 |
|
|
| 682 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 683 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 683 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 684 |
|
interactionMan_->doPreForce(sdat); |
| 685 |
|
} |
| 686 |
|
|
| 702 |
|
jb != skipList.end(); ++jb) { |
| 703 |
|
|
| 704 |
|
atom2 = (*jb); |
| 705 |
< |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 705 |
> |
fDecomp_->fillSkipData(idat, atom1, atom2); |
| 706 |
|
interactionMan_->doSkipCorrection(idat); |
| 707 |
|
|
| 708 |
|
} |
| 712 |
|
if (info_->requiresSelfCorrection()) { |
| 713 |
|
|
| 714 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 715 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 715 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 716 |
|
interactionMan_->doSelfCorrection(sdat); |
| 717 |
|
} |
| 718 |
|
|
