| 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 |
|
/** |
| 201 |
|
// electrostaticSummationMethod keyword. |
| 202 |
|
|
| 203 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 204 |
< |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 204 |
> |
string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 205 |
|
toUpper(myMethod); |
| 206 |
|
|
| 207 |
|
if (myMethod == "SHIFTED_POTENTIAL") { |
| 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 |
|
} |
| 330 |
– |
sprintf(painCave.errMsg, |
| 331 |
– |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 332 |
– |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 333 |
– |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 334 |
– |
painCave.isFatal = 0; |
| 335 |
– |
painCave.severity = OPENMD_WARNING; |
| 336 |
– |
simError(); |
| 342 |
|
} |
| 338 |
– |
|
| 343 |
|
rSwitch_ = rCut_; |
| 344 |
|
} |
| 345 |
|
|
| 388 |
|
setupCutoffs(); |
| 389 |
|
|
| 390 |
|
info_->prepareTopology(); |
| 391 |
+ |
|
| 392 |
+ |
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 393 |
+ |
cerr << "dPP = " << doParticlePot_ << "\n"; |
| 394 |
+ |
|
| 395 |
|
} |
| 396 |
|
|
| 397 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 654 |
|
idat.sw = &sw; |
| 655 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 656 |
|
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 657 |
+ |
idat.doParticlePot = doParticlePot_; |
| 658 |
+ |
sdat.doParticlePot = doParticlePot_; |
| 659 |
|
|
| 660 |
|
loopEnd = PAIR_LOOP; |
| 661 |
|
if (info_->requiresPrepair() ) { |
| 860 |
|
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 861 |
|
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 862 |
|
#endif |
| 863 |
< |
curSnapshot->statData.setTau(tau); |
| 863 |
> |
curSnapshot->setTau(tau); |
| 864 |
|
} |
| 865 |
|
|
| 866 |
|
} //end namespace OpenMD |
