| 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 |
|
#include <cmath> |
| 90 |
|
int nRestraintStamps = simParam->getNRestraintStamps(); |
| 91 |
|
std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps(); |
| 92 |
|
|
| 93 |
+ |
std::vector<int> stuntDoubleIndex; |
| 94 |
+ |
|
| 95 |
|
for (int i = 0; i < nRestraintStamps; i++){ |
| 96 |
|
|
| 97 |
|
std::string myType = toUpperCopy(stamp[i]->getType()); |
| 137 |
|
|
| 138 |
|
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 139 |
|
if (info_->getMolToProc(molIndex) == myrank) { |
| 140 |
+ |
|
| 141 |
|
// If we were supposed to have it but got a null, then freak out. |
| 142 |
|
#endif |
| 143 |
|
|
| 159 |
|
// molecule |
| 160 |
|
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 161 |
|
if (info_->getMolToProc(molIndex) == myrank) { |
| 162 |
+ |
|
| 163 |
|
#endif |
| 164 |
|
|
| 165 |
|
MolecularRestraint* rest = new MolecularRestraint(); |
| 235 |
|
|
| 236 |
|
for (sd = seleMan.beginSelected(selei); sd != NULL; |
| 237 |
|
sd = seleMan.nextSelected(selei)) { |
| 238 |
< |
|
| 238 |
> |
stuntDoubleIndex.push_back(sd->getGlobalIntegrableObjectIndex()); |
| 239 |
> |
|
| 240 |
|
ObjectRestraint* rest = new ObjectRestraint(); |
| 241 |
|
|
| 242 |
|
if (stamp[i]->haveDisplacementSpringConstant()) { |
| 276 |
|
// are times when it won't use restraints at all, so only open the |
| 277 |
|
// restraint file if we are actually using restraints: |
| 278 |
|
|
| 279 |
< |
if (simParam->getUseRestraints()) { |
| 279 |
> |
if (simParam->getUseRestraints()) { |
| 280 |
|
std::string refFile = simParam->getRestraint_file(); |
| 281 |
< |
RestReader* rr = new RestReader(info, refFile); |
| 276 |
< |
|
| 281 |
> |
RestReader* rr = new RestReader(info, refFile, stuntDoubleIndex); |
| 282 |
|
rr->readReferenceStructure(); |
| 283 |
|
} |
| 284 |
|
|
| 285 |
|
restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest"; |
| 286 |
|
restOut = new RestWriter(info_, restOutput_.c_str(), restraints_); |
| 282 |
– |
|
| 287 |
|
if(!restOut){ |
| 288 |
|
sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n"); |
| 289 |
|
painCave.isFatal = 1; |
| 306 |
|
currRestTime_ = currSnapshot_->getTime(); |
| 307 |
|
} |
| 308 |
|
|
| 309 |
< |
void RestraintForceManager::calcForces(bool needPotential, bool needStress){ |
| 309 |
> |
void RestraintForceManager::calcForces(){ |
| 310 |
|
|
| 311 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 311 |
> |
ForceManager::calcForces(); |
| 312 |
|
RealType restPot_local, restPot; |
| 313 |
|
|
| 314 |
|
restPot_local = doRestraints(1.0); |
| 320 |
|
restPot = restPot_local; |
| 321 |
|
#endif |
| 322 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 323 |
< |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot; |
| 324 |
< |
currSnapshot_->statData[Stats::VHARM] = restPot; |
| 323 |
> |
RealType pot = currSnapshot_->getLongRangePotential(); |
| 324 |
> |
pot += restPot; |
| 325 |
> |
currSnapshot_->setLongRangePotential(pot); |
| 326 |
> |
currSnapshot_->setRestraintPotential(restPot); |
| 327 |
|
|
| 328 |
|
//write out forces and current positions of restrained molecules |
| 329 |
|
if (currSnapshot_->getTime() >= currRestTime_){ |
| 390 |
|
std::vector<Vector3d> forces; |
| 391 |
|
|
| 392 |
|
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 393 |
< |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 393 |
> |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 394 |
|
struc.push_back(sd->getPos()); |
| 395 |
|
} |
| 396 |
|
|
