| 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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 116 |
|
else |
| 117 |
|
mdFileVersion = 0; |
| 118 |
|
|
| 118 |
– |
|
| 119 |
|
if (simParams_->haveCutoffRadius()) { |
| 120 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 121 |
|
} else { |
| 173 |
|
cutoffMethod_ = i->second; |
| 174 |
|
} |
| 175 |
|
} else { |
| 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; |
| 176 |
> |
if (mdFileVersion > 1) { |
| 177 |
> |
sprintf(painCave.errMsg, |
| 178 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 179 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 180 |
> |
painCave.isFatal = 0; |
| 181 |
> |
painCave.severity = OPENMD_INFO; |
| 182 |
> |
simError(); |
| 183 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 184 |
> |
} else { |
| 185 |
> |
// handle the case where the old file version was in play |
| 186 |
> |
// (there should be no cutoffMethod, so we have to deduce it |
| 187 |
> |
// from other data). |
| 188 |
> |
|
| 189 |
> |
sprintf(painCave.errMsg, |
| 190 |
> |
"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n" |
| 191 |
> |
"\tOpenMD found a file which does not set a cutoffMethod.\n" |
| 192 |
> |
"\tOpenMD will attempt to deduce a cutoffMethod using the\n" |
| 193 |
> |
"\tbehavior of the older (version 1) code. To remove this\n" |
| 194 |
> |
"\twarning, add an explicit cutoffMethod and change the top\n" |
| 195 |
> |
"\tof the file so that it begins with <OpenMD version=2>\n"); |
| 196 |
> |
painCave.isFatal = 0; |
| 197 |
> |
painCave.severity = OPENMD_WARNING; |
| 198 |
> |
simError(); |
| 199 |
> |
|
| 200 |
> |
// The old file version tethered the shifting behavior to the |
| 201 |
> |
// electrostaticSummationMethod keyword. |
| 202 |
> |
|
| 203 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 204 |
> |
string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 205 |
> |
toUpper(myMethod); |
| 206 |
> |
|
| 207 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 208 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 209 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 210 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 211 |
> |
} |
| 212 |
> |
|
| 213 |
> |
if (simParams_->haveSwitchingRadius()) |
| 214 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 215 |
> |
|
| 216 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 217 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 218 |
> |
sprintf(painCave.errMsg, |
| 219 |
> |
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 220 |
> |
"\tA value was set for the switchingRadius\n" |
| 221 |
> |
"\teven though the electrostaticSummationMethod was\n" |
| 222 |
> |
"\tset to %s\n", myMethod.c_str()); |
| 223 |
> |
painCave.severity = OPENMD_WARNING; |
| 224 |
> |
painCave.isFatal = 1; |
| 225 |
> |
simError(); |
| 226 |
> |
} |
| 227 |
> |
} |
| 228 |
> |
if (abs(rCut_ - rSwitch_) < 0.0001) { |
| 229 |
> |
if (cutoffMethod_ == SHIFTED_FORCE) { |
| 230 |
> |
sprintf(painCave.errMsg, |
| 231 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 232 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 233 |
> |
"\tsame value. OpenMD will use shifted force\n" |
| 234 |
> |
"\tpotentials instead of switching functions.\n"); |
| 235 |
> |
painCave.isFatal = 0; |
| 236 |
> |
painCave.severity = OPENMD_WARNING; |
| 237 |
> |
simError(); |
| 238 |
> |
} else { |
| 239 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 240 |
> |
sprintf(painCave.errMsg, |
| 241 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 242 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 243 |
> |
"\tsame value. OpenMD will use shifted potentials\n" |
| 244 |
> |
"\tinstead of switching functions.\n"); |
| 245 |
> |
painCave.isFatal = 0; |
| 246 |
> |
painCave.severity = OPENMD_WARNING; |
| 247 |
> |
simError(); |
| 248 |
> |
} |
| 249 |
> |
} |
| 250 |
> |
} |
| 251 |
> |
} |
| 252 |
|
} |
| 253 |
|
|
| 254 |
|
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 256 |
|
stringToCutoffPolicy["MAX"] = MAX; |
| 257 |
|
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 258 |
|
|
| 259 |
< |
std::string cutPolicy; |
| 259 |
> |
string cutPolicy; |
| 260 |
|
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 261 |
|
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 262 |
|
}else if (simParams_->haveCutoffPolicy()) { |
| 318 |
|
simError(); |
| 319 |
|
} |
| 320 |
|
} else { |
| 321 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 322 |
< |
map<string, CutoffMethod>::const_iterator it; |
| 323 |
< |
string theMeth; |
| 324 |
< |
for (it = stringToCutoffMethod.begin(); |
| 325 |
< |
it != stringToCutoffMethod.end(); ++it) { |
| 326 |
< |
if (it->second == cutoffMethod_) { |
| 327 |
< |
theMeth = it->first; |
| 328 |
< |
break; |
| 321 |
> |
if (mdFileVersion > 1) { |
| 322 |
> |
// throw an error if we define a switching radius and don't need one. |
| 323 |
> |
// older file versions should not do this. |
| 324 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 325 |
> |
map<string, CutoffMethod>::const_iterator it; |
| 326 |
> |
string theMeth; |
| 327 |
> |
for (it = stringToCutoffMethod.begin(); |
| 328 |
> |
it != stringToCutoffMethod.end(); ++it) { |
| 329 |
> |
if (it->second == cutoffMethod_) { |
| 330 |
> |
theMeth = it->first; |
| 331 |
> |
break; |
| 332 |
> |
} |
| 333 |
|
} |
| 334 |
+ |
sprintf(painCave.errMsg, |
| 335 |
+ |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 336 |
+ |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 337 |
+ |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 338 |
+ |
painCave.isFatal = 0; |
| 339 |
+ |
painCave.severity = OPENMD_WARNING; |
| 340 |
+ |
simError(); |
| 341 |
|
} |
| 262 |
– |
sprintf(painCave.errMsg, |
| 263 |
– |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 264 |
– |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 265 |
– |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 266 |
– |
painCave.isFatal = 0; |
| 267 |
– |
painCave.severity = OPENMD_WARNING; |
| 268 |
– |
simError(); |
| 342 |
|
} |
| 270 |
– |
|
| 343 |
|
rSwitch_ = rCut_; |
| 344 |
|
} |
| 345 |
|
|
| 370 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 371 |
|
interactionMan_->setSwitchingRadius(rSwitch_); |
| 372 |
|
} |
| 373 |
+ |
|
| 374 |
+ |
|
| 375 |
+ |
|
| 376 |
|
|
| 377 |
|
void ForceManager::initialize() { |
| 378 |
|
|
| 689 |
|
|
| 690 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 691 |
|
rgrp); |
| 692 |
< |
|
| 692 |
> |
|
| 693 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 694 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 620 |
– |
|
| 695 |
|
|
| 696 |
|
for (vector<int>::iterator ia = atomListRow.begin(); |
| 697 |
|
ia != atomListRow.end(); ++ia) { |
| 731 |
|
} else { |
| 732 |
|
interactionMan_->doPair(idat); |
| 733 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 660 |
– |
|
| 734 |
|
vij += vpair; |
| 735 |
|
fij += f1; |
| 736 |
|
tau -= outProduct( *(idat.d), f1); |
| 757 |
|
// presence in switching region |
| 758 |
|
fg = swderiv * d_grp * mf; |
| 759 |
|
fDecomp_->addForceToAtomRow(atom1, fg); |
| 687 |
– |
|
| 760 |
|
if (atomListRow.size() > 1) { |
| 761 |
|
if (info_->usesAtomicVirial()) { |
| 762 |
|
// find the distance between the atom |
| 854 |
|
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 855 |
|
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 856 |
|
#endif |
| 857 |
< |
curSnapshot->statData.setTau(tau); |
| 857 |
> |
curSnapshot->setTau(tau); |
| 858 |
|
} |
| 859 |
|
|
| 860 |
|
} //end namespace OpenMD |
