| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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 |
+ |
#ifdef IS_MPI |
| 44 |
+ |
#include <mpi.h> |
| 45 |
+ |
#endif |
| 46 |
+ |
|
| 47 |
+ |
#include "config.h" |
| 48 |
|
#include <cmath> |
| 49 |
+ |
|
| 50 |
|
#include "restraints/RestraintForceManager.hpp" |
| 51 |
|
#include "restraints/MolecularRestraint.hpp" |
| 52 |
|
#include "restraints/ObjectRestraint.hpp" |
| 56 |
|
#include "utils/StringUtils.hpp" |
| 57 |
|
#include "selection/SelectionEvaluator.hpp" |
| 58 |
|
#include "selection/SelectionManager.hpp" |
| 52 |
– |
#ifdef IS_MPI |
| 53 |
– |
#include <mpi.h> |
| 54 |
– |
#endif |
| 59 |
|
|
| 56 |
– |
|
| 60 |
|
namespace OpenMD { |
| 61 |
|
|
| 62 |
|
RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) { |
| 101 |
|
if (myType.compare("MOLECULAR")==0){ |
| 102 |
|
|
| 103 |
|
int molIndex; |
| 101 |
– |
std::vector<Vector3d> ref; |
| 104 |
|
Vector3d refCom; |
| 105 |
|
|
| 106 |
|
if (!stamp[i]->haveMolIndex()) { |
| 136 |
|
// this proc doesn't have the molecule. Do a quick check to |
| 137 |
|
// make sure another processor is supposed to have it. |
| 138 |
|
|
| 139 |
< |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 139 |
> |
int myrank; |
| 140 |
> |
MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
| 141 |
> |
|
| 142 |
|
if (info_->getMolToProc(molIndex) == myrank) { |
| 143 |
|
|
| 144 |
|
// If we were supposed to have it but got a null, then freak out. |
| 160 |
|
#ifdef IS_MPI |
| 161 |
|
// only handle this molecular restraint if this processor owns the |
| 162 |
|
// molecule |
| 163 |
< |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 163 |
> |
int myrank; |
| 164 |
> |
MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
| 165 |
|
if (info_->getMolToProc(molIndex) == myrank) { |
| 166 |
|
|
| 167 |
|
#endif |
| 225 |
|
evaluator.loadScriptString(objectSelection); |
| 226 |
|
seleMan.setSelectionSet(evaluator.evaluate()); |
| 227 |
|
int selectionCount = seleMan.getSelectionCount(); |
| 228 |
< |
|
| 228 |
> |
|
| 229 |
> |
#ifdef IS_MPI |
| 230 |
> |
MPI_Allreduce(MPI_IN_PLACE, &selectionCount, 1, MPI_INT, MPI_SUM, |
| 231 |
> |
MPI_COMM_WORLD); |
| 232 |
> |
#endif |
| 233 |
> |
|
| 234 |
|
sprintf(painCave.errMsg, |
| 235 |
|
"Restraint Info: The specified restraint objectSelection,\n" |
| 236 |
|
"\t\t%s\n" |
| 237 |
|
"\twill result in %d integrable objects being\n" |
| 238 |
|
"\trestrained.\n", objectSelection.c_str(), selectionCount); |
| 239 |
+ |
painCave.severity = OPENMD_INFO; |
| 240 |
|
painCave.isFatal = 0; |
| 241 |
|
simError(); |
| 242 |
|
|
| 316 |
|
currRestTime_ = currSnapshot_->getTime(); |
| 317 |
|
} |
| 318 |
|
|
| 319 |
< |
void RestraintForceManager::calcForces(bool needPotential, bool needStress){ |
| 319 |
> |
void RestraintForceManager::calcForces(){ |
| 320 |
> |
|
| 321 |
> |
ForceManager::calcForces(); |
| 322 |
> |
RealType restPot(0.0); |
| 323 |
|
|
| 324 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 311 |
< |
RealType restPot_local, restPot; |
| 324 |
> |
restPot = doRestraints(1.0); |
| 325 |
|
|
| 313 |
– |
restPot_local = doRestraints(1.0); |
| 314 |
– |
|
| 326 |
|
#ifdef IS_MPI |
| 327 |
< |
MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, |
| 328 |
< |
MPI::REALTYPE, MPI::SUM); |
| 318 |
< |
#else |
| 319 |
< |
restPot = restPot_local; |
| 327 |
> |
MPI_Allreduce(MPI_IN_PLACE, &restPot, 1, MPI_REALTYPE, MPI_SUM, |
| 328 |
> |
MPI_COMM_WORLD); |
| 329 |
|
#endif |
| 330 |
+ |
|
| 331 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 332 |
< |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot; |
| 323 |
< |
currSnapshot_->statData[Stats::VHARM] = restPot; |
| 332 |
> |
currSnapshot_->setRestraintPotential(restPot); |
| 333 |
|
|
| 334 |
|
//write out forces and current positions of restrained molecules |
| 335 |
|
if (currSnapshot_->getTime() >= currRestTime_){ |
| 342 |
|
std::vector<Molecule*>::const_iterator rm; |
| 343 |
|
GenericData* data; |
| 344 |
|
Molecule::IntegrableObjectIterator ioi; |
| 345 |
< |
MolecularRestraint* mRest; |
| 345 |
> |
MolecularRestraint* mRest = NULL; |
| 346 |
|
StuntDouble* sd; |
| 338 |
– |
RealType pTot; |
| 347 |
|
|
| 348 |
|
std::vector<StuntDouble*>::const_iterator ro; |
| 349 |
< |
ObjectRestraint* oRest; |
| 349 |
> |
ObjectRestraint* oRest = NULL; |
| 350 |
|
|
| 351 |
|
std::map<int, Restraint::RealPair> restInfo; |
| 352 |
|
|
| 393 |
|
|
| 394 |
|
std::vector<Vector3d> struc; |
| 395 |
|
std::vector<Vector3d> forces; |
| 396 |
+ |
|
| 397 |
|
|
| 398 |
|
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 399 |
|
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 412 |
|
index++; |
| 413 |
|
} |
| 414 |
|
|
| 415 |
< |
unscaledPotential_ += mRest->getUnscaledPotential(); |
| 415 |
> |
unscaledPotential_ += mRest->getUnscaledPotential(); |
| 416 |
|
|
| 408 |
– |
restInfo = mRest->getRestraintInfo(); |
| 409 |
– |
|
| 417 |
|
// only collect data on restraints that we're going to print: |
| 418 |
|
if (mRest->getPrintRestraint()) |
| 419 |
+ |
restInfo = mRest->getRestraintInfo(); |
| 420 |
|
restInfo_.push_back(restInfo); |
| 421 |
|
} |
| 422 |
|
|
| 453 |
|
|
| 454 |
|
// phew. At this point, we should have the pointer to the |
| 455 |
|
// correct Object restraint in the variable oRest. |
| 448 |
– |
|
| 456 |
|
oRest->setScaleFactor(scalingFactor); |
| 457 |
|
|
| 458 |
|
Vector3d pos = (*ro)->getPos(); |
| 476 |
|
|
| 477 |
|
unscaledPotential_ += oRest->getUnscaledPotential(); |
| 478 |
|
|
| 472 |
– |
restInfo = oRest->getRestraintInfo(); |
| 473 |
– |
|
| 479 |
|
// only collect data on restraints that we're going to print: |
| 480 |
|
if (oRest->getPrintRestraint()) |
| 481 |
+ |
restInfo = oRest->getRestraintInfo(); |
| 482 |
|
restInfo_.push_back(restInfo); |
| 483 |
|
} |
| 484 |
|
|
