| 59 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
|
#include "parallel/ForceMatrixDecomposition.hpp" |
| 61 |
|
|
| 62 |
+ |
#include <cstdio> |
| 63 |
+ |
#include <iostream> |
| 64 |
+ |
#include <iomanip> |
| 65 |
+ |
|
| 66 |
|
using namespace std; |
| 67 |
|
namespace OpenMD { |
| 68 |
|
|
| 69 |
|
ForceManager::ForceManager(SimInfo * info) : info_(info) { |
| 70 |
|
forceField_ = info_->getForceField(); |
| 71 |
< |
fDecomp_ = new ForceMatrixDecomposition(info_); |
| 71 |
> |
interactionMan_ = new InteractionManager(); |
| 72 |
> |
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
/** |
| 76 |
|
* setupCutoffs |
| 77 |
|
* |
| 78 |
< |
* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy |
| 78 |
> |
* Sets the values of cutoffRadius, switchingRadius, cutoffMethod, |
| 79 |
> |
* and cutoffPolicy |
| 80 |
|
* |
| 81 |
|
* cutoffRadius : realType |
| 82 |
|
* If the cutoffRadius was explicitly set, use that value. |
| 86 |
|
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 87 |
|
* Use the maximum suggested value that was found. |
| 88 |
|
* |
| 89 |
< |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 89 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, |
| 90 |
> |
* or SHIFTED_POTENTIAL) |
| 91 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 92 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 93 |
|
* |
| 94 |
|
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 95 |
|
* If cutoffPolicy was explicitly set, use that choice. |
| 96 |
|
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 97 |
+ |
* |
| 98 |
+ |
* switchingRadius : realType |
| 99 |
+ |
* If the cutoffMethod was set to SWITCHED: |
| 100 |
+ |
* If the switchingRadius was explicitly set, use that value |
| 101 |
+ |
* (but do a sanity check first). |
| 102 |
+ |
* If the switchingRadius was not explicitly set: use 0.85 * |
| 103 |
+ |
* cutoffRadius_ |
| 104 |
+ |
* If the cutoffMethod was not set to SWITCHED: |
| 105 |
+ |
* Set switchingRadius equal to cutoffRadius for safety. |
| 106 |
|
*/ |
| 107 |
|
void ForceManager::setupCutoffs() { |
| 108 |
|
|
| 137 |
|
painCave.isFatal = 0; |
| 138 |
|
painCave.severity = OPENMD_INFO; |
| 139 |
|
simError(); |
| 140 |
< |
} |
| 140 |
> |
} |
| 141 |
|
} |
| 142 |
|
|
| 143 |
+ |
fDecomp_->setUserCutoff(rCut_); |
| 144 |
+ |
interactionMan_->setCutoffRadius(rCut_); |
| 145 |
+ |
|
| 146 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 147 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 148 |
|
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 213 |
|
simError(); |
| 214 |
|
cutoffPolicy_ = TRADITIONAL; |
| 215 |
|
} |
| 197 |
– |
} |
| 216 |
|
|
| 217 |
< |
/** |
| 218 |
< |
* setupSwitching |
| 219 |
< |
* |
| 220 |
< |
* Sets the values of switchingRadius and |
| 221 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 222 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 223 |
< |
*/ |
| 224 |
< |
void ForceManager::setupSwitching() { |
| 225 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 226 |
< |
|
| 227 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 228 |
< |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 229 |
< |
if (rSwitch_ > rCut_) { |
| 217 |
> |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 218 |
> |
|
| 219 |
> |
// create the switching function object: |
| 220 |
> |
|
| 221 |
> |
switcher_ = new SwitchingFunction(); |
| 222 |
> |
|
| 223 |
> |
if (cutoffMethod_ == SWITCHED) { |
| 224 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 225 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 226 |
> |
if (rSwitch_ > rCut_) { |
| 227 |
> |
sprintf(painCave.errMsg, |
| 228 |
> |
"ForceManager::setupCutoffs: switchingRadius (%f) is larger " |
| 229 |
> |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 230 |
> |
painCave.isFatal = 1; |
| 231 |
> |
painCave.severity = OPENMD_ERROR; |
| 232 |
> |
simError(); |
| 233 |
> |
} |
| 234 |
> |
} else { |
| 235 |
> |
rSwitch_ = 0.85 * rCut_; |
| 236 |
|
sprintf(painCave.errMsg, |
| 237 |
< |
"ForceManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n", |
| 238 |
< |
rSwitch_, rCut_); |
| 239 |
< |
painCave.isFatal = 1; |
| 240 |
< |
painCave.severity = OPENMD_ERROR; |
| 237 |
> |
"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n" |
| 238 |
> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 239 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 240 |
> |
painCave.isFatal = 0; |
| 241 |
> |
painCave.severity = OPENMD_WARNING; |
| 242 |
|
simError(); |
| 243 |
|
} |
| 244 |
< |
} else { |
| 245 |
< |
rSwitch_ = 0.85 * rCut_; |
| 246 |
< |
sprintf(painCave.errMsg, |
| 247 |
< |
"ForceManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 248 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 249 |
< |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 250 |
< |
painCave.isFatal = 0; |
| 251 |
< |
painCave.severity = OPENMD_WARNING; |
| 252 |
< |
simError(); |
| 253 |
< |
} |
| 244 |
> |
} else { |
| 245 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 246 |
> |
map<string, CutoffMethod>::const_iterator it; |
| 247 |
> |
string theMeth; |
| 248 |
> |
for (it = stringToCutoffMethod.begin(); |
| 249 |
> |
it != stringToCutoffMethod.end(); ++it) { |
| 250 |
> |
if (it->second == cutoffMethod_) { |
| 251 |
> |
theMeth = it->first; |
| 252 |
> |
break; |
| 253 |
> |
} |
| 254 |
> |
} |
| 255 |
> |
sprintf(painCave.errMsg, |
| 256 |
> |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 257 |
> |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 258 |
> |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 259 |
> |
painCave.isFatal = 0; |
| 260 |
> |
painCave.severity = OPENMD_WARNING; |
| 261 |
> |
simError(); |
| 262 |
> |
} |
| 263 |
> |
|
| 264 |
> |
rSwitch_ = rCut_; |
| 265 |
> |
} |
| 266 |
|
|
| 267 |
+ |
// Default to cubic switching function. |
| 268 |
+ |
sft_ = cubic; |
| 269 |
|
if (simParams_->haveSwitchingFunctionType()) { |
| 270 |
|
string funcType = simParams_->getSwitchingFunctionType(); |
| 271 |
|
toUpper(funcType); |
| 289 |
|
} |
| 290 |
|
switcher_->setSwitchType(sft_); |
| 291 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 292 |
+ |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 293 |
|
} |
| 294 |
|
|
| 295 |
|
void ForceManager::initialize() { |
| 296 |
|
|
| 297 |
|
if (!info_->isTopologyDone()) { |
| 298 |
+ |
|
| 299 |
|
info_->update(); |
| 300 |
|
interactionMan_->setSimInfo(info_); |
| 301 |
|
interactionMan_->initialize(); |
| 303 |
|
// We want to delay the cutoffs until after the interaction |
| 304 |
|
// manager has set up the atom-atom interactions so that we can |
| 305 |
|
// query them for suggested cutoff values |
| 265 |
– |
|
| 306 |
|
setupCutoffs(); |
| 267 |
– |
setupSwitching(); |
| 307 |
|
|
| 308 |
|
info_->prepareTopology(); |
| 309 |
|
} |
| 310 |
|
|
| 311 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 312 |
|
|
| 313 |
< |
// Force fields can set options on how to scale van der Waals and electrostatic |
| 314 |
< |
// interactions for atoms connected via bonds, bends and torsions |
| 315 |
< |
// in this case the topological distance between atoms is: |
| 313 |
> |
// Force fields can set options on how to scale van der Waals and |
| 314 |
> |
// electrostatic interactions for atoms connected via bonds, bends |
| 315 |
> |
// and torsions in this case the topological distance between |
| 316 |
> |
// atoms is: |
| 317 |
|
// 0 = topologically unconnected |
| 318 |
|
// 1 = bonded together |
| 319 |
|
// 2 = connected via a bend |
| 365 |
|
|
| 366 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 367 |
|
mol = info_->nextMolecule(mi)) { |
| 368 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 368 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 369 |
> |
atom = mol->nextAtom(ai)) { |
| 370 |
|
atom->zeroForcesAndTorques(); |
| 371 |
|
} |
| 372 |
< |
|
| 372 |
> |
|
| 373 |
|
//change the positions of atoms which belong to the rigidbodies |
| 374 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 375 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 376 |
|
rb->zeroForcesAndTorques(); |
| 377 |
|
} |
| 378 |
< |
|
| 378 |
> |
|
| 379 |
|
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 380 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 381 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 384 |
|
} |
| 385 |
|
} |
| 386 |
|
} |
| 387 |
< |
|
| 387 |
> |
|
| 388 |
|
// Zero out the stress tensor |
| 389 |
|
tau *= 0.0; |
| 390 |
|
|
| 438 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 439 |
|
dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
| 440 |
|
dataSet.deltaV = 0.0; |
| 441 |
< |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
| 441 |
> |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, |
| 442 |
> |
dataSet)); |
| 443 |
|
}else { |
| 444 |
|
i->second.prev.angle = i->second.curr.angle; |
| 445 |
|
i->second.prev.potential = i->second.curr.potential; |
| 510 |
|
|
| 511 |
|
void ForceManager::longRangeInteractions() { |
| 512 |
|
|
| 471 |
– |
// some of this initial stuff will go away: |
| 513 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 514 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 515 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 475 |
– |
RealType* frc = config->getArrayPointer(DataStorage::dslForce); |
| 476 |
– |
RealType* pos = config->getArrayPointer(DataStorage::dslPosition); |
| 477 |
– |
RealType* trq = config->getArrayPointer(DataStorage::dslTorque); |
| 478 |
– |
RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
| 479 |
– |
RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 480 |
– |
RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 481 |
– |
RealType* rc; |
| 516 |
|
|
| 517 |
< |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 518 |
< |
rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
| 517 |
> |
//calculate the center of mass of cutoff group |
| 518 |
> |
|
| 519 |
> |
SimInfo::MoleculeIterator mi; |
| 520 |
> |
Molecule* mol; |
| 521 |
> |
Molecule::CutoffGroupIterator ci; |
| 522 |
> |
CutoffGroup* cg; |
| 523 |
> |
|
| 524 |
> |
if(info_->getNCutoffGroups() > 0){ |
| 525 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 526 |
> |
mol = info_->nextMolecule(mi)) { |
| 527 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 528 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 529 |
> |
cg->updateCOM(); |
| 530 |
> |
} |
| 531 |
> |
} |
| 532 |
|
} else { |
| 533 |
|
// center of mass of the group is the same as position of the atom |
| 534 |
|
// if cutoff group does not exist |
| 535 |
< |
rc = pos; |
| 535 |
> |
cgConfig->position = config->position; |
| 536 |
|
} |
| 537 |
< |
|
| 491 |
< |
// new stuff starts here: |
| 537 |
> |
|
| 538 |
|
fDecomp_->zeroWorkArrays(); |
| 539 |
|
fDecomp_->distributeData(); |
| 540 |
< |
|
| 541 |
< |
int cg1, cg2, atom1, atom2; |
| 542 |
< |
Vector3d d_grp, dag; |
| 543 |
< |
RealType rgrpsq, rgrp; |
| 540 |
> |
|
| 541 |
> |
int cg1, cg2, atom1, atom2, topoDist; |
| 542 |
> |
Vector3d d_grp, dag, d; |
| 543 |
> |
RealType rgrpsq, rgrp, r2, r; |
| 544 |
> |
RealType electroMult, vdwMult; |
| 545 |
|
RealType vij; |
| 546 |
< |
Vector3d fij, fg; |
| 546 |
> |
Vector3d fij, fg, f1; |
| 547 |
|
tuple3<RealType, RealType, RealType> cuts; |
| 548 |
|
RealType rCutSq; |
| 549 |
|
bool in_switching_region; |
| 552 |
|
InteractionData idat; |
| 553 |
|
SelfData sdat; |
| 554 |
|
RealType mf; |
| 508 |
– |
potVec pot(0.0); |
| 509 |
– |
potVec longRangePotential(0.0); |
| 555 |
|
RealType lrPot; |
| 556 |
+ |
RealType vpair; |
| 557 |
+ |
potVec longRangePotential(0.0); |
| 558 |
+ |
potVec workPot(0.0); |
| 559 |
|
|
| 560 |
|
int loopStart, loopEnd; |
| 561 |
|
|
| 562 |
+ |
idat.vdwMult = &vdwMult; |
| 563 |
+ |
idat.electroMult = &electroMult; |
| 564 |
+ |
idat.pot = &workPot; |
| 565 |
+ |
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 566 |
+ |
idat.vpair = &vpair; |
| 567 |
+ |
idat.f1 = &f1; |
| 568 |
+ |
idat.sw = &sw; |
| 569 |
+ |
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 570 |
+ |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 571 |
+ |
|
| 572 |
|
loopEnd = PAIR_LOOP; |
| 573 |
|
if (info_->requiresPrepair() ) { |
| 574 |
|
loopStart = PREPAIR_LOOP; |
| 575 |
|
} else { |
| 576 |
|
loopStart = PAIR_LOOP; |
| 577 |
|
} |
| 578 |
< |
|
| 579 |
< |
for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) { |
| 580 |
< |
|
| 578 |
> |
|
| 579 |
> |
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 580 |
> |
|
| 581 |
|
if (iLoop == loopStart) { |
| 582 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 583 |
|
if (update_nlist) |
| 584 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 585 |
< |
} |
| 585 |
> |
} |
| 586 |
|
|
| 587 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 588 |
|
it != neighborList.end(); ++it) { |
| 589 |
< |
|
| 589 |
> |
|
| 590 |
|
cg1 = (*it).first; |
| 591 |
|
cg2 = (*it).second; |
| 592 |
|
|
| 599 |
|
rCutSq = cuts.second; |
| 600 |
|
|
| 601 |
|
if (rgrpsq < rCutSq) { |
| 602 |
< |
*(idat.rcut) = cuts.first; |
| 602 |
> |
idat.rcut = &cuts.first; |
| 603 |
|
if (iLoop == PAIR_LOOP) { |
| 604 |
< |
vij *= 0.0; |
| 604 |
> |
vij = 0.0; |
| 605 |
|
fij = V3Zero; |
| 606 |
|
} |
| 607 |
|
|
| 608 |
< |
in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr, |
| 608 |
> |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 609 |
|
rgrp); |
| 610 |
|
|
| 611 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 618 |
|
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 619 |
|
jb != atomListColumn.end(); ++jb) { |
| 620 |
|
atom2 = (*jb); |
| 621 |
< |
|
| 621 |
> |
|
| 622 |
|
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 623 |
+ |
vpair = 0.0; |
| 624 |
+ |
workPot = 0.0; |
| 625 |
+ |
f1 = V3Zero; |
| 626 |
+ |
|
| 627 |
+ |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 628 |
|
|
| 629 |
< |
pot *= 0.0; |
| 629 |
> |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 630 |
> |
vdwMult = vdwScale_[topoDist]; |
| 631 |
> |
electroMult = electrostaticScale_[topoDist]; |
| 632 |
|
|
| 568 |
– |
idat = fDecomp_->fillInteractionData(atom1, atom2); |
| 569 |
– |
*(idat.pot) = pot; |
| 570 |
– |
|
| 633 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 634 |
< |
*(idat.d) = d_grp; |
| 635 |
< |
*(idat.r2) = rgrpsq; |
| 634 |
> |
idat.d = &d_grp; |
| 635 |
> |
idat.r2 = &rgrpsq; |
| 636 |
|
} else { |
| 637 |
< |
*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2); |
| 638 |
< |
curSnapshot->wrapVector( *(idat.d) ); |
| 639 |
< |
*(idat.r2) = idat.d->lengthSquare(); |
| 637 |
> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 638 |
> |
curSnapshot->wrapVector( d ); |
| 639 |
> |
r2 = d.lengthSquare(); |
| 640 |
> |
idat.d = &d; |
| 641 |
> |
idat.r2 = &r2; |
| 642 |
|
} |
| 579 |
– |
|
| 580 |
– |
*(idat.rij) = sqrt( *(idat.r2) ); |
| 643 |
|
|
| 644 |
+ |
r = sqrt( *(idat.r2) ); |
| 645 |
+ |
idat.rij = &r; |
| 646 |
+ |
|
| 647 |
|
if (iLoop == PREPAIR_LOOP) { |
| 648 |
|
interactionMan_->doPrePair(idat); |
| 649 |
|
} else { |
| 650 |
|
interactionMan_->doPair(idat); |
| 651 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 652 |
< |
vij += *(idat.vpair); |
| 653 |
< |
fij += *(idat.f1); |
| 654 |
< |
tau -= outProduct( *(idat.d), *(idat.f1)); |
| 652 |
> |
|
| 653 |
> |
vij += vpair; |
| 654 |
> |
fij += f1; |
| 655 |
> |
tau -= outProduct( *(idat.d), f1); |
| 656 |
|
} |
| 657 |
|
} |
| 658 |
|
} |
| 662 |
|
if (in_switching_region) { |
| 663 |
|
swderiv = vij * dswdr / rgrp; |
| 664 |
|
fg = swderiv * d_grp; |
| 599 |
– |
|
| 665 |
|
fij += fg; |
| 666 |
|
|
| 667 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 713 |
|
} |
| 714 |
|
|
| 715 |
|
if (iLoop == PREPAIR_LOOP) { |
| 716 |
< |
if (info_->requiresPrepair()) { |
| 716 |
> |
if (info_->requiresPrepair()) { |
| 717 |
> |
|
| 718 |
|
fDecomp_->collectIntermediateData(); |
| 719 |
|
|
| 720 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 721 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 721 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 722 |
|
interactionMan_->doPreForce(sdat); |
| 723 |
|
} |
| 724 |
|
|
| 725 |
< |
fDecomp_->distributeIntermediateData(); |
| 725 |
> |
fDecomp_->distributeIntermediateData(); |
| 726 |
> |
|
| 727 |
|
} |
| 728 |
|
} |
| 729 |
|
|
| 730 |
|
} |
| 731 |
|
|
| 732 |
|
fDecomp_->collectData(); |
| 666 |
– |
|
| 667 |
– |
if ( info_->requiresSkipCorrection() ) { |
| 668 |
– |
|
| 669 |
– |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 670 |
– |
|
| 671 |
– |
vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 ); |
| 733 |
|
|
| 673 |
– |
for (vector<int>::iterator jb = skipList.begin(); |
| 674 |
– |
jb != skipList.end(); ++jb) { |
| 675 |
– |
|
| 676 |
– |
atom2 = (*jb); |
| 677 |
– |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 678 |
– |
interactionMan_->doSkipCorrection(idat); |
| 679 |
– |
|
| 680 |
– |
} |
| 681 |
– |
} |
| 682 |
– |
} |
| 683 |
– |
|
| 734 |
|
if (info_->requiresSelfCorrection()) { |
| 735 |
|
|
| 736 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 737 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 737 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 738 |
|
interactionMan_->doSelfCorrection(sdat); |
| 739 |
|
} |
| 740 |
|
|
| 741 |
|
} |
| 742 |
|
|
| 743 |
< |
longRangePotential = fDecomp_->getLongRangePotential(); |
| 743 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 744 |
> |
*(fDecomp_->getPairwisePotential()); |
| 745 |
> |
|
| 746 |
|
lrPot = longRangePotential.sum(); |
| 747 |
|
|
| 748 |
|
//store the tau and long range potential |
