| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 44 |
|
* @file ForceManager.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/09/2004 |
| 47 |
– |
* @time 10:39am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 57 |
|
#include "primitives/Torsion.hpp" |
| 58 |
|
#include "primitives/Inversion.hpp" |
| 59 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
< |
#include "perturbations/ElectricField.hpp" |
| 60 |
> |
#include "perturbations/UniformField.hpp" |
| 61 |
> |
#include "perturbations/UniformGradient.hpp" |
| 62 |
|
#include "parallel/ForceMatrixDecomposition.hpp" |
| 63 |
|
|
| 64 |
|
#include <cstdio> |
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 70 |
|
|
| 71 |
< |
ForceManager::ForceManager(SimInfo * info) : info_(info) { |
| 71 |
> |
ForceManager::ForceManager(SimInfo * info) : initialized_(false), info_(info), |
| 72 |
> |
switcher_(NULL) { |
| 73 |
|
forceField_ = info_->getForceField(); |
| 74 |
|
interactionMan_ = new InteractionManager(); |
| 75 |
|
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 76 |
+ |
thermo = new Thermo(info_); |
| 77 |
|
} |
| 78 |
|
|
| 79 |
+ |
ForceManager::~ForceManager() { |
| 80 |
+ |
perturbations_.clear(); |
| 81 |
+ |
|
| 82 |
+ |
delete switcher_; |
| 83 |
+ |
delete interactionMan_; |
| 84 |
+ |
delete fDecomp_; |
| 85 |
+ |
delete thermo; |
| 86 |
+ |
} |
| 87 |
+ |
|
| 88 |
|
/** |
| 89 |
|
* setupCutoffs |
| 90 |
|
* |
| 91 |
< |
* Sets the values of cutoffRadius, switchingRadius, cutoffMethod, |
| 81 |
< |
* and cutoffPolicy |
| 91 |
> |
* Sets the values of cutoffRadius, switchingRadius, and cutoffMethod |
| 92 |
|
* |
| 93 |
|
* cutoffRadius : realType |
| 94 |
|
* If the cutoffRadius was explicitly set, use that value. |
| 98 |
|
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 99 |
|
* Use the maximum suggested value that was found. |
| 100 |
|
* |
| 101 |
< |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, |
| 102 |
< |
* or SHIFTED_POTENTIAL) |
| 101 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED, |
| 102 |
> |
* SHIFTED_POTENTIAL, or EWALD_FULL) |
| 103 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 104 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 105 |
|
* |
| 96 |
– |
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 97 |
– |
* If cutoffPolicy was explicitly set, use that choice. |
| 98 |
– |
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 99 |
– |
* |
| 106 |
|
* switchingRadius : realType |
| 107 |
|
* If the cutoffMethod was set to SWITCHED: |
| 108 |
|
* If the switchingRadius was explicitly set, use that value |
| 115 |
|
void ForceManager::setupCutoffs() { |
| 116 |
|
|
| 117 |
|
Globals* simParams_ = info_->getSimParams(); |
| 112 |
– |
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 118 |
|
int mdFileVersion; |
| 119 |
|
rCut_ = 0.0; //Needs a value for a later max() call; |
| 120 |
|
|
| 123 |
|
else |
| 124 |
|
mdFileVersion = 0; |
| 125 |
|
|
| 126 |
+ |
// We need the list of simulated atom types to figure out cutoffs |
| 127 |
+ |
// as well as long range corrections. |
| 128 |
+ |
|
| 129 |
+ |
set<AtomType*>::iterator i; |
| 130 |
+ |
set<AtomType*> atomTypes_; |
| 131 |
+ |
atomTypes_ = info_->getSimulatedAtomTypes(); |
| 132 |
+ |
|
| 133 |
|
if (simParams_->haveCutoffRadius()) { |
| 134 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 135 |
|
} else { |
| 144 |
|
rCut_ = 12.0; |
| 145 |
|
} else { |
| 146 |
|
RealType thisCut; |
| 147 |
< |
set<AtomType*>::iterator i; |
| 136 |
< |
set<AtomType*> atomTypes; |
| 137 |
< |
atomTypes = info_->getSimulatedAtomTypes(); |
| 138 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 147 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 148 |
|
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
| 149 |
|
rCut_ = max(thisCut, rCut_); |
| 150 |
|
} |
| 158 |
|
} |
| 159 |
|
} |
| 160 |
|
|
| 161 |
< |
fDecomp_->setUserCutoff(rCut_); |
| 161 |
> |
fDecomp_->setCutoffRadius(rCut_); |
| 162 |
|
interactionMan_->setCutoffRadius(rCut_); |
| 163 |
+ |
rCutSq_ = rCut_ * rCut_; |
| 164 |
|
|
| 165 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 166 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 167 |
|
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 168 |
|
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 169 |
|
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 170 |
+ |
stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED; |
| 171 |
+ |
stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL; |
| 172 |
|
|
| 173 |
|
if (simParams_->haveCutoffMethod()) { |
| 174 |
|
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 178 |
|
sprintf(painCave.errMsg, |
| 179 |
|
"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 180 |
|
"\tShould be one of: " |
| 181 |
< |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 181 |
> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n" |
| 182 |
> |
"\tSHIFTED_FORCE, or EWALD_FULL\n", |
| 183 |
|
cutMeth.c_str()); |
| 184 |
|
painCave.isFatal = 1; |
| 185 |
|
painCave.severity = OPENMD_ERROR; |
| 223 |
|
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 224 |
|
} else if (myMethod == "SHIFTED_FORCE") { |
| 225 |
|
cutoffMethod_ = SHIFTED_FORCE; |
| 226 |
+ |
} else if (myMethod == "TAYLOR_SHIFTED") { |
| 227 |
+ |
cutoffMethod_ = TAYLOR_SHIFTED; |
| 228 |
+ |
} else if (myMethod == "EWALD_FULL") { |
| 229 |
+ |
cutoffMethod_ = EWALD_FULL; |
| 230 |
|
} |
| 231 |
|
|
| 232 |
|
if (simParams_->haveSwitchingRadius()) |
| 233 |
|
rSwitch_ = simParams_->getSwitchingRadius(); |
| 234 |
|
|
| 235 |
< |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 235 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" || |
| 236 |
> |
myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") { |
| 237 |
|
if (simParams_->haveSwitchingRadius()){ |
| 238 |
|
sprintf(painCave.errMsg, |
| 239 |
|
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 268 |
|
} |
| 269 |
|
} |
| 270 |
|
} |
| 253 |
– |
} |
| 254 |
– |
} |
| 255 |
– |
|
| 256 |
– |
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 257 |
– |
stringToCutoffPolicy["MIX"] = MIX; |
| 258 |
– |
stringToCutoffPolicy["MAX"] = MAX; |
| 259 |
– |
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 260 |
– |
|
| 261 |
– |
string cutPolicy; |
| 262 |
– |
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 263 |
– |
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 264 |
– |
}else if (simParams_->haveCutoffPolicy()) { |
| 265 |
– |
cutPolicy = simParams_->getCutoffPolicy(); |
| 266 |
– |
} |
| 267 |
– |
|
| 268 |
– |
if (!cutPolicy.empty()){ |
| 269 |
– |
toUpper(cutPolicy); |
| 270 |
– |
map<string, CutoffPolicy>::iterator i; |
| 271 |
– |
i = stringToCutoffPolicy.find(cutPolicy); |
| 272 |
– |
|
| 273 |
– |
if (i == stringToCutoffPolicy.end()) { |
| 274 |
– |
sprintf(painCave.errMsg, |
| 275 |
– |
"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n" |
| 276 |
– |
"\tShould be one of: " |
| 277 |
– |
"MIX, MAX, or TRADITIONAL\n", |
| 278 |
– |
cutPolicy.c_str()); |
| 279 |
– |
painCave.isFatal = 1; |
| 280 |
– |
painCave.severity = OPENMD_ERROR; |
| 281 |
– |
simError(); |
| 282 |
– |
} else { |
| 283 |
– |
cutoffPolicy_ = i->second; |
| 271 |
|
} |
| 285 |
– |
} else { |
| 286 |
– |
sprintf(painCave.errMsg, |
| 287 |
– |
"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n" |
| 288 |
– |
"\tOpenMD will use TRADITIONAL.\n"); |
| 289 |
– |
painCave.isFatal = 0; |
| 290 |
– |
painCave.severity = OPENMD_INFO; |
| 291 |
– |
simError(); |
| 292 |
– |
cutoffPolicy_ = TRADITIONAL; |
| 272 |
|
} |
| 294 |
– |
|
| 295 |
– |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 273 |
|
|
| 274 |
|
// create the switching function object: |
| 275 |
|
|
| 347 |
|
} |
| 348 |
|
switcher_->setSwitchType(sft_); |
| 349 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 373 |
– |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 350 |
|
} |
| 351 |
|
|
| 376 |
– |
|
| 377 |
– |
|
| 378 |
– |
|
| 352 |
|
void ForceManager::initialize() { |
| 353 |
|
|
| 354 |
|
if (!info_->isTopologyDone()) { |
| 357 |
|
interactionMan_->setSimInfo(info_); |
| 358 |
|
interactionMan_->initialize(); |
| 359 |
|
|
| 360 |
< |
// We want to delay the cutoffs until after the interaction |
| 361 |
< |
// manager has set up the atom-atom interactions so that we can |
| 362 |
< |
// query them for suggested cutoff values |
| 360 |
> |
//! We want to delay the cutoffs until after the interaction |
| 361 |
> |
//! manager has set up the atom-atom interactions so that we can |
| 362 |
> |
//! query them for suggested cutoff values |
| 363 |
|
setupCutoffs(); |
| 364 |
|
|
| 365 |
|
info_->prepareTopology(); |
| 367 |
|
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 368 |
|
doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 369 |
|
if (doHeatFlux_) doParticlePot_ = true; |
| 370 |
+ |
|
| 371 |
+ |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 372 |
+ |
doSitePotential_ = info_->getSimParams()->getOutputSitePotential(); |
| 373 |
|
|
| 374 |
|
} |
| 375 |
|
|
| 376 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 377 |
|
|
| 378 |
< |
// Force fields can set options on how to scale van der Waals and |
| 379 |
< |
// electrostatic interactions for atoms connected via bonds, bends |
| 380 |
< |
// and torsions in this case the topological distance between |
| 381 |
< |
// atoms is: |
| 382 |
< |
// 0 = topologically unconnected |
| 383 |
< |
// 1 = bonded together |
| 384 |
< |
// 2 = connected via a bend |
| 385 |
< |
// 3 = connected via a torsion |
| 378 |
> |
//! Force fields can set options on how to scale van der Waals and |
| 379 |
> |
//! electrostatic interactions for atoms connected via bonds, bends |
| 380 |
> |
//! and torsions in this case the topological distance between |
| 381 |
> |
//! atoms is: |
| 382 |
> |
//! 0 = topologically unconnected |
| 383 |
> |
//! 1 = bonded together |
| 384 |
> |
//! 2 = connected via a bend |
| 385 |
> |
//! 3 = connected via a torsion |
| 386 |
|
|
| 387 |
|
vdwScale_.reserve(4); |
| 388 |
|
fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
| 400 |
|
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 401 |
|
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 402 |
|
|
| 403 |
< |
if (info_->getSimParams()->haveElectricField()) { |
| 404 |
< |
ElectricField* eField = new ElectricField(info_); |
| 403 |
> |
if (info_->getSimParams()->haveUniformField()) { |
| 404 |
> |
UniformField* eField = new UniformField(info_); |
| 405 |
|
perturbations_.push_back(eField); |
| 406 |
|
} |
| 407 |
< |
|
| 408 |
< |
fDecomp_->distributeInitialData(); |
| 409 |
< |
|
| 410 |
< |
initialized_ = true; |
| 411 |
< |
|
| 407 |
> |
if (info_->getSimParams()->haveUniformGradientStrength() || |
| 408 |
> |
info_->getSimParams()->haveUniformGradientDirection1() || |
| 409 |
> |
info_->getSimParams()->haveUniformGradientDirection2() ) { |
| 410 |
> |
UniformGradient* eGrad = new UniformGradient(info_); |
| 411 |
> |
perturbations_.push_back(eGrad); |
| 412 |
> |
} |
| 413 |
> |
|
| 414 |
> |
usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 415 |
> |
|
| 416 |
> |
fDecomp_->distributeInitialData(); |
| 417 |
> |
|
| 418 |
> |
initialized_ = true; |
| 419 |
> |
|
| 420 |
|
} |
| 421 |
< |
|
| 421 |
> |
|
| 422 |
|
void ForceManager::calcForces() { |
| 423 |
|
|
| 424 |
|
if (!initialized_) initialize(); |
| 425 |
< |
|
| 425 |
> |
|
| 426 |
|
preCalculation(); |
| 427 |
|
shortRangeInteractions(); |
| 428 |
|
longRangeInteractions(); |
| 596 |
|
// Collect from all nodes. This should eventually be moved into a |
| 597 |
|
// SystemDecomposition, but this is a better place than in |
| 598 |
|
// Thermo to do the collection. |
| 599 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 600 |
< |
MPI::SUM); |
| 601 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 602 |
< |
MPI::SUM); |
| 603 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 604 |
< |
MPI::REALTYPE, MPI::SUM); |
| 605 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 606 |
< |
MPI::REALTYPE, MPI::SUM); |
| 599 |
> |
|
| 600 |
> |
MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE, |
| 601 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 602 |
> |
MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE, |
| 603 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 604 |
> |
MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1, |
| 605 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 606 |
> |
MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1, |
| 607 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 608 |
|
#endif |
| 609 |
|
|
| 610 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 622 |
|
|
| 623 |
|
void ForceManager::longRangeInteractions() { |
| 624 |
|
|
| 640 |
– |
|
| 625 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 626 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 627 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 632 |
|
Molecule* mol; |
| 633 |
|
Molecule::CutoffGroupIterator ci; |
| 634 |
|
CutoffGroup* cg; |
| 635 |
< |
|
| 636 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 635 |
> |
|
| 636 |
> |
if(info_->getNCutoffGroups() != info_->getNAtoms()){ |
| 637 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 638 |
|
mol = info_->nextMolecule(mi)) { |
| 639 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 657 |
|
RealType electroMult, vdwMult; |
| 658 |
|
RealType vij; |
| 659 |
|
Vector3d fij, fg, f1; |
| 676 |
– |
tuple3<RealType, RealType, RealType> cuts; |
| 677 |
– |
RealType rCutSq; |
| 660 |
|
bool in_switching_region; |
| 661 |
|
RealType sw, dswdr, swderiv; |
| 662 |
< |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 662 |
> |
vector<int> atomListColumn, atomListRow; |
| 663 |
|
InteractionData idat; |
| 664 |
|
SelfData sdat; |
| 665 |
|
RealType mf; |
| 666 |
|
RealType vpair; |
| 667 |
|
RealType dVdFQ1(0.0); |
| 668 |
|
RealType dVdFQ2(0.0); |
| 687 |
– |
Vector3d eField1(0.0); |
| 688 |
– |
Vector3d eField2(0.0); |
| 669 |
|
potVec longRangePotential(0.0); |
| 670 |
+ |
RealType reciprocalPotential(0.0); |
| 671 |
|
potVec workPot(0.0); |
| 672 |
|
potVec exPot(0.0); |
| 673 |
+ |
Vector3d eField1(0.0); |
| 674 |
+ |
Vector3d eField2(0.0); |
| 675 |
+ |
RealType sPot1(0.0); |
| 676 |
+ |
RealType sPot2(0.0); |
| 677 |
+ |
bool newAtom1; |
| 678 |
+ |
|
| 679 |
|
vector<int>::iterator ia, jb; |
| 680 |
|
|
| 681 |
|
int loopStart, loopEnd; |
| 682 |
< |
|
| 682 |
> |
|
| 683 |
> |
idat.rcut = &rCut_; |
| 684 |
|
idat.vdwMult = &vdwMult; |
| 685 |
|
idat.electroMult = &electroMult; |
| 686 |
|
idat.pot = &workPot; |
| 691 |
|
idat.dVdFQ1 = &dVdFQ1; |
| 692 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 693 |
|
idat.eField1 = &eField1; |
| 694 |
< |
idat.eField2 = &eField2; |
| 694 |
> |
idat.eField2 = &eField2; |
| 695 |
> |
idat.sPot1 = &sPot1; |
| 696 |
> |
idat.sPot2 = &sPot2; |
| 697 |
|
idat.f1 = &f1; |
| 698 |
|
idat.sw = &sw; |
| 699 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 700 |
< |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 700 |
> |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || |
| 701 |
> |
cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 702 |
|
idat.doParticlePot = doParticlePot_; |
| 703 |
+ |
idat.doElectricField = doElectricField_; |
| 704 |
+ |
idat.doSitePotential = doSitePotential_; |
| 705 |
|
sdat.doParticlePot = doParticlePot_; |
| 706 |
|
|
| 707 |
|
loopEnd = PAIR_LOOP; |
| 714 |
|
|
| 715 |
|
if (iLoop == loopStart) { |
| 716 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 717 |
< |
if (update_nlist) |
| 718 |
< |
neighborList = fDecomp_->buildNeighborList(); |
| 719 |
< |
} |
| 720 |
< |
|
| 721 |
< |
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 722 |
< |
it != neighborList.end(); ++it) { |
| 723 |
< |
|
| 724 |
< |
cg1 = (*it).first; |
| 732 |
< |
cg2 = (*it).second; |
| 717 |
> |
if (update_nlist) { |
| 718 |
> |
if (!usePeriodicBoundaryConditions_) |
| 719 |
> |
Mat3x3d bbox = thermo->getBoundingBox(); |
| 720 |
> |
fDecomp_->buildNeighborList(neighborList_, point_); |
| 721 |
> |
} |
| 722 |
> |
} |
| 723 |
> |
|
| 724 |
> |
for (cg1 = 0; cg1 < int(point_.size()) - 1; cg1++) { |
| 725 |
|
|
| 726 |
< |
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 726 |
> |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 727 |
> |
newAtom1 = true; |
| 728 |
> |
|
| 729 |
> |
for (int m2 = point_[cg1]; m2 < point_[cg1+1]; m2++) { |
| 730 |
|
|
| 731 |
< |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 737 |
< |
|
| 738 |
< |
curSnapshot->wrapVector(d_grp); |
| 739 |
< |
rgrpsq = d_grp.lengthSquare(); |
| 740 |
< |
rCutSq = cuts.second; |
| 741 |
< |
|
| 742 |
< |
if (rgrpsq < rCutSq) { |
| 743 |
< |
idat.rcut = &cuts.first; |
| 744 |
< |
if (iLoop == PAIR_LOOP) { |
| 745 |
< |
vij = 0.0; |
| 746 |
< |
fij = V3Zero; |
| 747 |
< |
} |
| 731 |
> |
cg2 = neighborList_[m2]; |
| 732 |
|
|
| 733 |
< |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 734 |
< |
rgrp); |
| 735 |
< |
|
| 736 |
< |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 737 |
< |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 738 |
< |
|
| 739 |
< |
if (doHeatFlux_) |
| 740 |
< |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 741 |
< |
|
| 742 |
< |
for (ia = atomListRow.begin(); |
| 743 |
< |
ia != atomListRow.end(); ++ia) { |
| 744 |
< |
atom1 = (*ia); |
| 745 |
< |
|
| 746 |
< |
for (jb = atomListColumn.begin(); |
| 747 |
< |
jb != atomListColumn.end(); ++jb) { |
| 748 |
< |
atom2 = (*jb); |
| 749 |
< |
|
| 750 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 751 |
< |
|
| 752 |
< |
vpair = 0.0; |
| 753 |
< |
workPot = 0.0; |
| 754 |
< |
exPot = 0.0; |
| 755 |
< |
f1 = V3Zero; |
| 756 |
< |
dVdFQ1 = 0.0; |
| 757 |
< |
dVdFQ2 = 0.0; |
| 758 |
< |
|
| 759 |
< |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 760 |
< |
|
| 761 |
< |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 762 |
< |
vdwMult = vdwScale_[topoDist]; |
| 763 |
< |
electroMult = electrostaticScale_[topoDist]; |
| 764 |
< |
|
| 765 |
< |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 766 |
< |
idat.d = &d_grp; |
| 767 |
< |
idat.r2 = &rgrpsq; |
| 768 |
< |
if (doHeatFlux_) |
| 769 |
< |
vel2 = gvel2; |
| 770 |
< |
} else { |
| 771 |
< |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 772 |
< |
curSnapshot->wrapVector( d ); |
| 773 |
< |
r2 = d.lengthSquare(); |
| 774 |
< |
idat.d = &d; |
| 775 |
< |
idat.r2 = &r2; |
| 776 |
< |
if (doHeatFlux_) |
| 777 |
< |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 733 |
> |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 734 |
> |
|
| 735 |
> |
// already wrapped in the getIntergroupVector call: |
| 736 |
> |
// curSnapshot->wrapVector(d_grp); |
| 737 |
> |
rgrpsq = d_grp.lengthSquare(); |
| 738 |
> |
|
| 739 |
> |
if (rgrpsq < rCutSq_) { |
| 740 |
> |
if (iLoop == PAIR_LOOP) { |
| 741 |
> |
vij = 0.0; |
| 742 |
> |
fij.zero(); |
| 743 |
> |
eField1.zero(); |
| 744 |
> |
eField2.zero(); |
| 745 |
> |
sPot1 = 0.0; |
| 746 |
> |
sPot2 = 0.0; |
| 747 |
> |
} |
| 748 |
> |
|
| 749 |
> |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 750 |
> |
rgrp); |
| 751 |
> |
|
| 752 |
> |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 753 |
> |
|
| 754 |
> |
if (doHeatFlux_) |
| 755 |
> |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 756 |
> |
|
| 757 |
> |
for (ia = atomListRow.begin(); |
| 758 |
> |
ia != atomListRow.end(); ++ia) { |
| 759 |
> |
atom1 = (*ia); |
| 760 |
> |
|
| 761 |
> |
for (jb = atomListColumn.begin(); |
| 762 |
> |
jb != atomListColumn.end(); ++jb) { |
| 763 |
> |
atom2 = (*jb); |
| 764 |
> |
|
| 765 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 766 |
> |
|
| 767 |
> |
vpair = 0.0; |
| 768 |
> |
workPot = 0.0; |
| 769 |
> |
exPot = 0.0; |
| 770 |
> |
f1.zero(); |
| 771 |
> |
dVdFQ1 = 0.0; |
| 772 |
> |
dVdFQ2 = 0.0; |
| 773 |
> |
|
| 774 |
> |
fDecomp_->fillInteractionData(idat, atom1, atom2, newAtom1); |
| 775 |
> |
|
| 776 |
> |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 777 |
> |
vdwMult = vdwScale_[topoDist]; |
| 778 |
> |
electroMult = electrostaticScale_[topoDist]; |
| 779 |
> |
|
| 780 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 781 |
> |
idat.d = &d_grp; |
| 782 |
> |
idat.r2 = &rgrpsq; |
| 783 |
> |
if (doHeatFlux_) |
| 784 |
> |
vel2 = gvel2; |
| 785 |
> |
} else { |
| 786 |
> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 787 |
> |
curSnapshot->wrapVector( d ); |
| 788 |
> |
r2 = d.lengthSquare(); |
| 789 |
> |
idat.d = &d; |
| 790 |
> |
idat.r2 = &r2; |
| 791 |
> |
if (doHeatFlux_) |
| 792 |
> |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 793 |
> |
} |
| 794 |
> |
|
| 795 |
> |
r = sqrt( *(idat.r2) ); |
| 796 |
> |
idat.rij = &r; |
| 797 |
> |
|
| 798 |
> |
if (iLoop == PREPAIR_LOOP) { |
| 799 |
> |
interactionMan_->doPrePair(idat); |
| 800 |
> |
} else { |
| 801 |
> |
interactionMan_->doPair(idat); |
| 802 |
> |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 803 |
> |
vij += vpair; |
| 804 |
> |
fij += f1; |
| 805 |
> |
stressTensor -= outProduct( *(idat.d), f1); |
| 806 |
> |
if (doHeatFlux_) |
| 807 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 808 |
> |
} |
| 809 |
|
} |
| 795 |
– |
|
| 796 |
– |
r = sqrt( *(idat.r2) ); |
| 797 |
– |
idat.rij = &r; |
| 798 |
– |
|
| 799 |
– |
if (iLoop == PREPAIR_LOOP) { |
| 800 |
– |
interactionMan_->doPrePair(idat); |
| 801 |
– |
} else { |
| 802 |
– |
interactionMan_->doPair(idat); |
| 803 |
– |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 804 |
– |
vij += vpair; |
| 805 |
– |
fij += f1; |
| 806 |
– |
stressTensor -= outProduct( *(idat.d), f1); |
| 807 |
– |
if (doHeatFlux_) |
| 808 |
– |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 809 |
– |
} |
| 810 |
|
} |
| 811 |
|
} |
| 812 |
< |
} |
| 813 |
< |
|
| 814 |
< |
if (iLoop == PAIR_LOOP) { |
| 815 |
< |
if (in_switching_region) { |
| 816 |
< |
swderiv = vij * dswdr / rgrp; |
| 817 |
< |
fg = swderiv * d_grp; |
| 818 |
< |
fij += fg; |
| 819 |
< |
|
| 820 |
< |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 821 |
< |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 822 |
< |
atomListColumn[0], |
| 823 |
< |
cg1, cg2)) { |
| 812 |
> |
|
| 813 |
> |
if (iLoop == PAIR_LOOP) { |
| 814 |
> |
if (in_switching_region) { |
| 815 |
> |
swderiv = vij * dswdr / rgrp; |
| 816 |
> |
fg = swderiv * d_grp; |
| 817 |
> |
fij += fg; |
| 818 |
> |
|
| 819 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 820 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 821 |
> |
atomListColumn[0], |
| 822 |
> |
cg1, cg2)) { |
| 823 |
|
stressTensor -= outProduct( *(idat.d), fg); |
| 824 |
|
if (doHeatFlux_) |
| 825 |
|
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 826 |
< |
} |
| 827 |
< |
} |
| 828 |
< |
|
| 829 |
< |
for (ia = atomListRow.begin(); |
| 830 |
< |
ia != atomListRow.end(); ++ia) { |
| 831 |
< |
atom1 = (*ia); |
| 832 |
< |
mf = fDecomp_->getMassFactorRow(atom1); |
| 833 |
< |
// fg is the force on atom ia due to cutoff group's |
| 834 |
< |
// presence in switching region |
| 835 |
< |
fg = swderiv * d_grp * mf; |
| 836 |
< |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 837 |
< |
if (atomListRow.size() > 1) { |
| 838 |
< |
if (info_->usesAtomicVirial()) { |
| 839 |
< |
// find the distance between the atom |
| 840 |
< |
// and the center of the cutoff group: |
| 841 |
< |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 842 |
< |
stressTensor -= outProduct(dag, fg); |
| 843 |
< |
if (doHeatFlux_) |
| 844 |
< |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 826 |
> |
} |
| 827 |
> |
} |
| 828 |
> |
|
| 829 |
> |
for (ia = atomListRow.begin(); |
| 830 |
> |
ia != atomListRow.end(); ++ia) { |
| 831 |
> |
atom1 = (*ia); |
| 832 |
> |
mf = fDecomp_->getMassFactorRow(atom1); |
| 833 |
> |
// fg is the force on atom ia due to cutoff group's |
| 834 |
> |
// presence in switching region |
| 835 |
> |
fg = swderiv * d_grp * mf; |
| 836 |
> |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 837 |
> |
if (atomListRow.size() > 1) { |
| 838 |
> |
if (info_->usesAtomicVirial()) { |
| 839 |
> |
// find the distance between the atom |
| 840 |
> |
// and the center of the cutoff group: |
| 841 |
> |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 842 |
> |
stressTensor -= outProduct(dag, fg); |
| 843 |
> |
if (doHeatFlux_) |
| 844 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 845 |
> |
} |
| 846 |
|
} |
| 847 |
|
} |
| 848 |
< |
} |
| 849 |
< |
for (jb = atomListColumn.begin(); |
| 850 |
< |
jb != atomListColumn.end(); ++jb) { |
| 851 |
< |
atom2 = (*jb); |
| 852 |
< |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 853 |
< |
// fg is the force on atom jb due to cutoff group's |
| 854 |
< |
// presence in switching region |
| 855 |
< |
fg = -swderiv * d_grp * mf; |
| 856 |
< |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 857 |
< |
|
| 858 |
< |
if (atomListColumn.size() > 1) { |
| 859 |
< |
if (info_->usesAtomicVirial()) { |
| 860 |
< |
// find the distance between the atom |
| 861 |
< |
// and the center of the cutoff group: |
| 862 |
< |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 863 |
< |
stressTensor -= outProduct(dag, fg); |
| 864 |
< |
if (doHeatFlux_) |
| 865 |
< |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 848 |
> |
for (jb = atomListColumn.begin(); |
| 849 |
> |
jb != atomListColumn.end(); ++jb) { |
| 850 |
> |
atom2 = (*jb); |
| 851 |
> |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 852 |
> |
// fg is the force on atom jb due to cutoff group's |
| 853 |
> |
// presence in switching region |
| 854 |
> |
fg = -swderiv * d_grp * mf; |
| 855 |
> |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 856 |
> |
|
| 857 |
> |
if (atomListColumn.size() > 1) { |
| 858 |
> |
if (info_->usesAtomicVirial()) { |
| 859 |
> |
// find the distance between the atom |
| 860 |
> |
// and the center of the cutoff group: |
| 861 |
> |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 862 |
> |
stressTensor -= outProduct(dag, fg); |
| 863 |
> |
if (doHeatFlux_) |
| 864 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 865 |
> |
} |
| 866 |
|
} |
| 867 |
|
} |
| 868 |
|
} |
| 869 |
+ |
//if (!info_->usesAtomicVirial()) { |
| 870 |
+ |
// stressTensor -= outProduct(d_grp, fij); |
| 871 |
+ |
// if (doHeatFlux_) |
| 872 |
+ |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 873 |
+ |
//} |
| 874 |
|
} |
| 870 |
– |
//if (!info_->usesAtomicVirial()) { |
| 871 |
– |
// stressTensor -= outProduct(d_grp, fij); |
| 872 |
– |
// if (doHeatFlux_) |
| 873 |
– |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 874 |
– |
//} |
| 875 |
|
} |
| 876 |
|
} |
| 877 |
+ |
newAtom1 = false; |
| 878 |
|
} |
| 879 |
< |
|
| 879 |
> |
|
| 880 |
|
if (iLoop == PREPAIR_LOOP) { |
| 881 |
|
if (info_->requiresPrepair()) { |
| 882 |
< |
|
| 882 |
> |
|
| 883 |
|
fDecomp_->collectIntermediateData(); |
| 884 |
< |
|
| 884 |
> |
|
| 885 |
|
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 886 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 887 |
|
interactionMan_->doPreForce(sdat); |
| 888 |
|
} |
| 889 |
< |
|
| 889 |
> |
|
| 890 |
|
fDecomp_->distributeIntermediateData(); |
| 891 |
< |
|
| 891 |
> |
|
| 892 |
|
} |
| 893 |
|
} |
| 894 |
|
} |
| 895 |
< |
|
| 895 |
> |
|
| 896 |
|
// collects pairwise information |
| 897 |
|
fDecomp_->collectData(); |
| 898 |
+ |
if (cutoffMethod_ == EWALD_FULL) { |
| 899 |
+ |
interactionMan_->doReciprocalSpaceSum(reciprocalPotential); |
| 900 |
+ |
|
| 901 |
+ |
curSnapshot->setReciprocalPotential(reciprocalPotential); |
| 902 |
+ |
} |
| 903 |
|
|
| 904 |
|
if (info_->requiresSelfCorrection()) { |
| 905 |
|
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 917 |
|
curSnapshot->setLongRangePotential(longRangePotential); |
| 918 |
|
|
| 919 |
|
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 920 |
< |
*(fDecomp_->getExcludedPotential())); |
| 920 |
> |
*(fDecomp_->getExcludedPotential())); |
| 921 |
|
|
| 922 |
|
} |
| 923 |
|
|
| 918 |
– |
|
| 924 |
|
void ForceManager::postCalculation() { |
| 925 |
|
|
| 926 |
|
vector<Perturbation*>::iterator pi; |
| 946 |
|
} |
| 947 |
|
|
| 948 |
|
#ifdef IS_MPI |
| 949 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 950 |
< |
MPI::REALTYPE, MPI::SUM); |
| 949 |
> |
MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 950 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 951 |
|
#endif |
| 952 |
|
curSnapshot->setStressTensor(stressTensor); |
| 953 |
|
|
| 954 |
+ |
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 955 |
+ |
/* |
| 956 |
+ |
RealType vol = curSnapshot->getVolume(); |
| 957 |
+ |
RealType Elrc(0.0); |
| 958 |
+ |
RealType Wlrc(0.0); |
| 959 |
+ |
|
| 960 |
+ |
set<AtomType*>::iterator i; |
| 961 |
+ |
set<AtomType*>::iterator j; |
| 962 |
+ |
|
| 963 |
+ |
RealType n_i, n_j; |
| 964 |
+ |
RealType rho_i, rho_j; |
| 965 |
+ |
pair<RealType, RealType> LRI; |
| 966 |
+ |
|
| 967 |
+ |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 968 |
+ |
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 969 |
+ |
rho_i = n_i / vol; |
| 970 |
+ |
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 971 |
+ |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 972 |
+ |
rho_j = n_j / vol; |
| 973 |
+ |
|
| 974 |
+ |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 975 |
+ |
|
| 976 |
+ |
Elrc += n_i * rho_j * LRI.first; |
| 977 |
+ |
Wlrc -= rho_i * rho_j * LRI.second; |
| 978 |
+ |
} |
| 979 |
+ |
} |
| 980 |
+ |
Elrc *= 2.0 * NumericConstant::PI; |
| 981 |
+ |
Wlrc *= 2.0 * NumericConstant::PI; |
| 982 |
+ |
|
| 983 |
+ |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 984 |
+ |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 985 |
+ |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 986 |
+ |
curSnapshot->setStressTensor(stressTensor); |
| 987 |
+ |
*/ |
| 988 |
+ |
|
| 989 |
+ |
} |
| 990 |
|
} |
| 991 |
< |
} //end namespace OpenMD |
| 991 |
> |
} |
