| 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 { |
| 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; |
| 366 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 367 |
|
interactionMan_->setSwitchingRadius(rSwitch_); |
| 368 |
|
} |
| 369 |
+ |
|
| 370 |
+ |
|
| 371 |
+ |
|
| 372 |
|
|
| 373 |
|
void ForceManager::initialize() { |
| 374 |
|
|
| 446 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 447 |
|
atom = mol->nextAtom(ai)) { |
| 448 |
|
atom->zeroForcesAndTorques(); |
| 371 |
– |
cerr << "apos = " << atom->getPos() << "\n"; |
| 449 |
|
} |
| 450 |
|
|
| 451 |
|
//change the positions of atoms which belong to the rigidbodies |
| 459 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 460 |
|
//calculate the center of mass of cutoff group |
| 461 |
|
cg->updateCOM(); |
| 385 |
– |
cerr << "cgpos = " << cg->getPos() << "\n"; |
| 462 |
|
} |
| 463 |
|
} |
| 464 |
|
} |
| 604 |
|
mol = info_->nextMolecule(mi)) { |
| 605 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 606 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 531 |
– |
cerr << "branch1\n"; |
| 532 |
– |
cerr << "globind = " << cg->getGlobalIndex() << "\n"; |
| 607 |
|
cg->updateCOM(); |
| 608 |
|
} |
| 609 |
|
} |
| 610 |
|
} else { |
| 611 |
|
// center of mass of the group is the same as position of the atom |
| 612 |
|
// if cutoff group does not exist |
| 539 |
– |
cerr << "branch2\n"; |
| 613 |
|
cgConfig->position = config->position; |
| 614 |
|
} |
| 615 |
|
|
| 660 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 661 |
|
if (update_nlist) |
| 662 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 663 |
< |
} |
| 664 |
< |
|
| 663 |
> |
} |
| 664 |
> |
|
| 665 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 666 |
|
it != neighborList.end(); ++it) { |
| 667 |
|
|
| 671 |
|
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 672 |
|
|
| 673 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 674 |
+ |
|
| 675 |
|
curSnapshot->wrapVector(d_grp); |
| 676 |
|
rgrpsq = d_grp.lengthSquare(); |
| 603 |
– |
|
| 677 |
|
rCutSq = cuts.second; |
| 678 |
|
|
| 679 |
|
if (rgrpsq < rCutSq) { |
| 685 |
|
|
| 686 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 687 |
|
rgrp); |
| 688 |
< |
|
| 688 |
> |
|
| 689 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 690 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 691 |
|
|
| 711 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 712 |
|
idat.d = &d_grp; |
| 713 |
|
idat.r2 = &rgrpsq; |
| 641 |
– |
cerr << "dgrp = " << d_grp << "\n"; |
| 714 |
|
} else { |
| 715 |
|
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 716 |
|
curSnapshot->wrapVector( d ); |
| 717 |
|
r2 = d.lengthSquare(); |
| 646 |
– |
cerr << "datm = " << d<< "\n"; |
| 718 |
|
idat.d = &d; |
| 719 |
|
idat.r2 = &r2; |
| 720 |
|
} |
| 721 |
< |
|
| 651 |
< |
cerr << "idat.d = " << *(idat.d) << "\n"; |
| 721 |
> |
|
| 722 |
|
r = sqrt( *(idat.r2) ); |
| 723 |
|
idat.rij = &r; |
| 724 |
|
|
| 727 |
|
} else { |
| 728 |
|
interactionMan_->doPair(idat); |
| 729 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 660 |
– |
|
| 661 |
– |
cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n"; |
| 730 |
|
vij += vpair; |
| 731 |
|
fij += f1; |
| 732 |
|
tau -= outProduct( *(idat.d), f1); |
| 753 |
|
// presence in switching region |
| 754 |
|
fg = swderiv * d_grp * mf; |
| 755 |
|
fDecomp_->addForceToAtomRow(atom1, fg); |
| 688 |
– |
|
| 756 |
|
if (atomListRow.size() > 1) { |
| 757 |
|
if (info_->usesAtomicVirial()) { |
| 758 |
|
// find the distance between the atom |
| 781 |
|
} |
| 782 |
|
} |
| 783 |
|
} |
| 784 |
< |
//if (!SIM_uses_AtomicVirial) { |
| 784 |
> |
//if (!info_->usesAtomicVirial()) { |
| 785 |
|
// tau -= outProduct(d_grp, fij); |
| 786 |
|
//} |
| 787 |
|
} |
| 802 |
|
|
| 803 |
|
} |
| 804 |
|
} |
| 738 |
– |
|
| 805 |
|
} |
| 806 |
|
|
| 807 |
|
fDecomp_->collectData(); |
