| 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 |
|
|
| 109 |
|
Globals* simParams_ = info_->getSimParams(); |
| 110 |
|
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 111 |
+ |
int mdFileVersion; |
| 112 |
|
|
| 113 |
+ |
if (simParams_->haveMDfileVersion()) |
| 114 |
+ |
mdFileVersion = simParams_->getMDfileVersion(); |
| 115 |
+ |
else |
| 116 |
+ |
mdFileVersion = 0; |
| 117 |
+ |
|
| 118 |
|
if (simParams_->haveCutoffRadius()) { |
| 119 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 120 |
|
} else { |
| 147 |
|
} |
| 148 |
|
|
| 149 |
|
fDecomp_->setUserCutoff(rCut_); |
| 150 |
+ |
interactionMan_->setCutoffRadius(rCut_); |
| 151 |
|
|
| 152 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 153 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 172 |
|
cutoffMethod_ = i->second; |
| 173 |
|
} |
| 174 |
|
} else { |
| 175 |
< |
sprintf(painCave.errMsg, |
| 176 |
< |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 177 |
< |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 178 |
< |
painCave.isFatal = 0; |
| 179 |
< |
painCave.severity = OPENMD_INFO; |
| 180 |
< |
simError(); |
| 181 |
< |
cutoffMethod_ = SHIFTED_FORCE; |
| 175 |
> |
if (mdFileVersion > 1) { |
| 176 |
> |
sprintf(painCave.errMsg, |
| 177 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 178 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 179 |
> |
painCave.isFatal = 0; |
| 180 |
> |
painCave.severity = OPENMD_INFO; |
| 181 |
> |
simError(); |
| 182 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 183 |
> |
} else { |
| 184 |
> |
// handle the case where the old file version was in play |
| 185 |
> |
// (there should be no cutoffMethod, so we have to deduce it |
| 186 |
> |
// from other data). |
| 187 |
> |
|
| 188 |
> |
sprintf(painCave.errMsg, |
| 189 |
> |
"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n" |
| 190 |
> |
"\tOpenMD found a file which does not set a cutoffMethod.\n" |
| 191 |
> |
"\tOpenMD will attempt to deduce a cutoffMethod using the\n" |
| 192 |
> |
"\tbehavior of the older (version 1) code. To remove this\n" |
| 193 |
> |
"\twarning, add an explicit cutoffMethod and change the top\n" |
| 194 |
> |
"\tof the file so that it begins with <OpenMD version=2>\n"); |
| 195 |
> |
painCave.isFatal = 0; |
| 196 |
> |
painCave.severity = OPENMD_WARNING; |
| 197 |
> |
simError(); |
| 198 |
> |
|
| 199 |
> |
// The old file version tethered the shifting behavior to the |
| 200 |
> |
// electrostaticSummationMethod keyword. |
| 201 |
> |
|
| 202 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 203 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 204 |
> |
toUpper(myMethod); |
| 205 |
> |
|
| 206 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 207 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 208 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 209 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
if (simParams_->haveSwitchingRadius()) |
| 213 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 214 |
> |
|
| 215 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 216 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 217 |
> |
sprintf(painCave.errMsg, |
| 218 |
> |
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 219 |
> |
"\tA value was set for the switchingRadius\n" |
| 220 |
> |
"\teven though the electrostaticSummationMethod was\n" |
| 221 |
> |
"\tset to %s\n", myMethod.c_str()); |
| 222 |
> |
painCave.severity = OPENMD_WARNING; |
| 223 |
> |
painCave.isFatal = 1; |
| 224 |
> |
simError(); |
| 225 |
> |
} |
| 226 |
> |
} |
| 227 |
> |
if (abs(rCut_ - rSwitch_) < 0.0001) { |
| 228 |
> |
if (cutoffMethod_ == SHIFTED_FORCE) { |
| 229 |
> |
sprintf(painCave.errMsg, |
| 230 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 231 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 232 |
> |
"\tsame value. OpenMD will use shifted force\n" |
| 233 |
> |
"\tpotentials instead of switching functions.\n"); |
| 234 |
> |
painCave.isFatal = 0; |
| 235 |
> |
painCave.severity = OPENMD_WARNING; |
| 236 |
> |
simError(); |
| 237 |
> |
} else { |
| 238 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 239 |
> |
sprintf(painCave.errMsg, |
| 240 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 241 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 242 |
> |
"\tsame value. OpenMD will use shifted potentials\n" |
| 243 |
> |
"\tinstead of switching functions.\n"); |
| 244 |
> |
painCave.isFatal = 0; |
| 245 |
> |
painCave.severity = OPENMD_WARNING; |
| 246 |
> |
simError(); |
| 247 |
> |
} |
| 248 |
> |
} |
| 249 |
> |
} |
| 250 |
> |
} |
| 251 |
|
} |
| 252 |
|
|
| 253 |
|
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 288 |
|
simError(); |
| 289 |
|
cutoffPolicy_ = TRADITIONAL; |
| 290 |
|
} |
| 204 |
– |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 205 |
– |
} |
| 291 |
|
|
| 292 |
< |
/** |
| 293 |
< |
* setupSwitching |
| 209 |
< |
* |
| 210 |
< |
* Sets the values of switchingRadius and |
| 211 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 212 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 213 |
< |
*/ |
| 214 |
< |
void ForceManager::setupSwitching() { |
| 215 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 216 |
< |
|
| 292 |
> |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 293 |
> |
|
| 294 |
|
// create the switching function object: |
| 295 |
+ |
|
| 296 |
|
switcher_ = new SwitchingFunction(); |
| 297 |
< |
|
| 298 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 299 |
< |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 300 |
< |
if (rSwitch_ > rCut_) { |
| 297 |
> |
|
| 298 |
> |
if (cutoffMethod_ == SWITCHED) { |
| 299 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 300 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 301 |
> |
if (rSwitch_ > rCut_) { |
| 302 |
> |
sprintf(painCave.errMsg, |
| 303 |
> |
"ForceManager::setupCutoffs: switchingRadius (%f) is larger " |
| 304 |
> |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 305 |
> |
painCave.isFatal = 1; |
| 306 |
> |
painCave.severity = OPENMD_ERROR; |
| 307 |
> |
simError(); |
| 308 |
> |
} |
| 309 |
> |
} else { |
| 310 |
> |
rSwitch_ = 0.85 * rCut_; |
| 311 |
|
sprintf(painCave.errMsg, |
| 312 |
< |
"ForceManager::setupSwitching: switchingRadius (%f) is larger " |
| 313 |
< |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 314 |
< |
painCave.isFatal = 1; |
| 315 |
< |
painCave.severity = OPENMD_ERROR; |
| 312 |
> |
"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n" |
| 313 |
> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 314 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 315 |
> |
painCave.isFatal = 0; |
| 316 |
> |
painCave.severity = OPENMD_WARNING; |
| 317 |
|
simError(); |
| 318 |
|
} |
| 319 |
< |
} else { |
| 320 |
< |
rSwitch_ = 0.85 * rCut_; |
| 321 |
< |
sprintf(painCave.errMsg, |
| 322 |
< |
"ForceManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 323 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 324 |
< |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 325 |
< |
painCave.isFatal = 0; |
| 326 |
< |
painCave.severity = OPENMD_WARNING; |
| 327 |
< |
simError(); |
| 328 |
< |
} |
| 319 |
> |
} else { |
| 320 |
> |
if (mdFileVersion > 1) { |
| 321 |
> |
// throw an error if we define a switching radius and don't need one. |
| 322 |
> |
// older file versions should not do this. |
| 323 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 324 |
> |
map<string, CutoffMethod>::const_iterator it; |
| 325 |
> |
string theMeth; |
| 326 |
> |
for (it = stringToCutoffMethod.begin(); |
| 327 |
> |
it != stringToCutoffMethod.end(); ++it) { |
| 328 |
> |
if (it->second == cutoffMethod_) { |
| 329 |
> |
theMeth = it->first; |
| 330 |
> |
break; |
| 331 |
> |
} |
| 332 |
> |
} |
| 333 |
> |
sprintf(painCave.errMsg, |
| 334 |
> |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 335 |
> |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 336 |
> |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 337 |
> |
painCave.isFatal = 0; |
| 338 |
> |
painCave.severity = OPENMD_WARNING; |
| 339 |
> |
simError(); |
| 340 |
> |
} |
| 341 |
> |
} |
| 342 |
> |
rSwitch_ = rCut_; |
| 343 |
> |
} |
| 344 |
|
|
| 345 |
|
// Default to cubic switching function. |
| 346 |
|
sft_ = cubic; |
| 367 |
|
} |
| 368 |
|
switcher_->setSwitchType(sft_); |
| 369 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 370 |
+ |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 371 |
|
} |
| 372 |
+ |
|
| 373 |
+ |
|
| 374 |
+ |
|
| 375 |
|
|
| 376 |
|
void ForceManager::initialize() { |
| 377 |
|
|
| 378 |
|
if (!info_->isTopologyDone()) { |
| 379 |
+ |
|
| 380 |
|
info_->update(); |
| 381 |
|
interactionMan_->setSimInfo(info_); |
| 382 |
|
interactionMan_->initialize(); |
| 384 |
|
// We want to delay the cutoffs until after the interaction |
| 385 |
|
// manager has set up the atom-atom interactions so that we can |
| 386 |
|
// query them for suggested cutoff values |
| 278 |
– |
|
| 387 |
|
setupCutoffs(); |
| 280 |
– |
setupSwitching(); |
| 388 |
|
|
| 389 |
|
info_->prepareTopology(); |
| 390 |
|
} |
| 391 |
|
|
| 392 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 393 |
|
|
| 394 |
< |
// Force fields can set options on how to scale van der Waals and electrostatic |
| 395 |
< |
// interactions for atoms connected via bonds, bends and torsions |
| 396 |
< |
// in this case the topological distance between atoms is: |
| 394 |
> |
// Force fields can set options on how to scale van der Waals and |
| 395 |
> |
// electrostatic interactions for atoms connected via bonds, bends |
| 396 |
> |
// and torsions in this case the topological distance between |
| 397 |
> |
// atoms is: |
| 398 |
|
// 0 = topologically unconnected |
| 399 |
|
// 1 = bonded together |
| 400 |
|
// 2 = connected via a bend |
| 446 |
|
|
| 447 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 448 |
|
mol = info_->nextMolecule(mi)) { |
| 449 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 449 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 450 |
> |
atom = mol->nextAtom(ai)) { |
| 451 |
|
atom->zeroForcesAndTorques(); |
| 452 |
|
} |
| 453 |
< |
|
| 453 |
> |
|
| 454 |
|
//change the positions of atoms which belong to the rigidbodies |
| 455 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 456 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 457 |
|
rb->zeroForcesAndTorques(); |
| 458 |
|
} |
| 459 |
< |
|
| 459 |
> |
|
| 460 |
|
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 461 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 462 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 465 |
|
} |
| 466 |
|
} |
| 467 |
|
} |
| 468 |
< |
|
| 468 |
> |
|
| 469 |
|
// Zero out the stress tensor |
| 470 |
|
tau *= 0.0; |
| 471 |
|
|
| 519 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 520 |
|
dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
| 521 |
|
dataSet.deltaV = 0.0; |
| 522 |
< |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
| 522 |
> |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, |
| 523 |
> |
dataSet)); |
| 524 |
|
}else { |
| 525 |
|
i->second.prev.angle = i->second.curr.angle; |
| 526 |
|
i->second.prev.potential = i->second.curr.potential; |
| 663 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 664 |
|
if (update_nlist) |
| 665 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 666 |
< |
} |
| 667 |
< |
|
| 666 |
> |
} |
| 667 |
> |
|
| 668 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 669 |
|
it != neighborList.end(); ++it) { |
| 670 |
|
|
| 674 |
|
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 675 |
|
|
| 676 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 677 |
+ |
|
| 678 |
|
curSnapshot->wrapVector(d_grp); |
| 679 |
|
rgrpsq = d_grp.lengthSquare(); |
| 569 |
– |
|
| 680 |
|
rCutSq = cuts.second; |
| 681 |
|
|
| 682 |
|
if (rgrpsq < rCutSq) { |
| 683 |
|
idat.rcut = &cuts.first; |
| 684 |
|
if (iLoop == PAIR_LOOP) { |
| 685 |
< |
vij *= 0.0; |
| 685 |
> |
vij = 0.0; |
| 686 |
|
fij = V3Zero; |
| 687 |
|
} |
| 688 |
|
|
| 689 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 690 |
|
rgrp); |
| 691 |
< |
|
| 691 |
> |
|
| 692 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 693 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 694 |
|
|
| 699 |
|
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 700 |
|
jb != atomListColumn.end(); ++jb) { |
| 701 |
|
atom2 = (*jb); |
| 702 |
< |
|
| 702 |
> |
|
| 703 |
|
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 704 |
|
vpair = 0.0; |
| 705 |
|
workPot = 0.0; |
| 721 |
|
idat.d = &d; |
| 722 |
|
idat.r2 = &r2; |
| 723 |
|
} |
| 724 |
< |
|
| 724 |
> |
|
| 725 |
|
r = sqrt( *(idat.r2) ); |
| 726 |
|
idat.rij = &r; |
| 727 |
|
|
| 742 |
|
if (in_switching_region) { |
| 743 |
|
swderiv = vij * dswdr / rgrp; |
| 744 |
|
fg = swderiv * d_grp; |
| 635 |
– |
|
| 745 |
|
fij += fg; |
| 746 |
|
|
| 747 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 756 |
|
// presence in switching region |
| 757 |
|
fg = swderiv * d_grp * mf; |
| 758 |
|
fDecomp_->addForceToAtomRow(atom1, fg); |
| 650 |
– |
|
| 759 |
|
if (atomListRow.size() > 1) { |
| 760 |
|
if (info_->usesAtomicVirial()) { |
| 761 |
|
// find the distance between the atom |
| 784 |
|
} |
| 785 |
|
} |
| 786 |
|
} |
| 787 |
< |
//if (!SIM_uses_AtomicVirial) { |
| 787 |
> |
//if (!info_->usesAtomicVirial()) { |
| 788 |
|
// tau -= outProduct(d_grp, fij); |
| 789 |
|
//} |
| 790 |
|
} |
| 792 |
|
} |
| 793 |
|
|
| 794 |
|
if (iLoop == PREPAIR_LOOP) { |
| 795 |
< |
if (info_->requiresPrepair()) { |
| 795 |
> |
if (info_->requiresPrepair()) { |
| 796 |
> |
|
| 797 |
|
fDecomp_->collectIntermediateData(); |
| 798 |
|
|
| 799 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 800 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 801 |
|
interactionMan_->doPreForce(sdat); |
| 802 |
|
} |
| 694 |
– |
|
| 695 |
– |
|
| 696 |
– |
fDecomp_->distributeIntermediateData(); |
| 697 |
– |
} |
| 698 |
– |
} |
| 803 |
|
|
| 804 |
< |
} |
| 701 |
< |
|
| 702 |
< |
fDecomp_->collectData(); |
| 703 |
< |
|
| 704 |
< |
if ( info_->requiresSkipCorrection() ) { |
| 705 |
< |
|
| 706 |
< |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 804 |
> |
fDecomp_->distributeIntermediateData(); |
| 805 |
|
|
| 708 |
– |
vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 ); |
| 709 |
– |
|
| 710 |
– |
for (vector<int>::iterator jb = skipList.begin(); |
| 711 |
– |
jb != skipList.end(); ++jb) { |
| 712 |
– |
|
| 713 |
– |
atom2 = (*jb); |
| 714 |
– |
fDecomp_->fillSkipData(idat, atom1, atom2); |
| 715 |
– |
interactionMan_->doSkipCorrection(idat); |
| 716 |
– |
fDecomp_->unpackSkipData(idat, atom1, atom2); |
| 717 |
– |
|
| 806 |
|
} |
| 807 |
|
} |
| 808 |
|
} |
| 809 |
|
|
| 810 |
+ |
fDecomp_->collectData(); |
| 811 |
+ |
|
| 812 |
|
if (info_->requiresSelfCorrection()) { |
| 813 |
|
|
| 814 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
