| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include <cmath> |
| 43 |
|
#include "constraints/ZconstraintForceManager.hpp" |
| 44 |
|
#include "integrators/Integrator.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
< |
#include "utils/OOPSEConstant.hpp" |
| 46 |
> |
#include "utils/PhysicalConstants.hpp" |
| 47 |
|
#include "utils/StringUtils.hpp" |
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) { |
| 50 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 51 |
|
Globals* simParam = info_->getSimParams(); |
| 77 |
|
zconsTol_ = 0.01; |
| 78 |
|
sprintf(painCave.errMsg, |
| 79 |
|
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
| 80 |
< |
"\tOOPSE will use a default value of %f.\n" |
| 80 |
> |
"\tOpenMD will use a default value of %f.\n" |
| 81 |
|
"\tTo set the tolerance, use the zconsTol variable.\n", |
| 82 |
|
zconsTol_); |
| 83 |
|
painCave.isFatal = 0; |
| 111 |
|
|
| 112 |
|
//estimate the force constant of harmonical potential |
| 113 |
|
Mat3x3d hmat = currSnapshot_->getHmat(); |
| 114 |
< |
double halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2; |
| 115 |
< |
double targetTemp; |
| 114 |
> |
RealType halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2; |
| 115 |
> |
RealType targetTemp; |
| 116 |
|
if (simParam->haveTargetTemp()) { |
| 117 |
|
targetTemp = simParam->getTargetTemp(); |
| 118 |
|
} else { |
| 119 |
|
targetTemp = 298.0; |
| 120 |
|
} |
| 121 |
< |
double zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
| 121 |
> |
RealType zforceConstant = PhysicalConstants::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
| 122 |
|
|
| 123 |
< |
int nZconstraints = simParam->getNZconstraints(); |
| 124 |
< |
ZconStamp** stamp = simParam->getZconStamp(); |
| 123 |
> |
int nZconstraints = simParam->getNZconsStamps(); |
| 124 |
> |
std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
| 125 |
|
// |
| 126 |
|
for (int i = 0; i < nZconstraints; i++){ |
| 127 |
|
|
| 148 |
|
update(); |
| 149 |
|
|
| 150 |
|
//calculate masss of unconstraint molecules in the whole system (never change during the simulation) |
| 151 |
< |
double totMassUnconsMols_local = 0.0; |
| 151 |
> |
RealType totMassUnconsMols_local = 0.0; |
| 152 |
|
std::vector<Molecule*>::iterator j; |
| 153 |
|
for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
| 154 |
|
totMassUnconsMols_local += (*j)->getMass(); |
| 156 |
|
#ifndef IS_MPI |
| 157 |
|
totMassUnconsMols_ = totMassUnconsMols_local; |
| 158 |
|
#else |
| 159 |
< |
MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_DOUBLE, |
| 159 |
> |
MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_REALTYPE, |
| 160 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 161 |
|
#endif |
| 162 |
|
|
| 194 |
|
zmol.param = i->second; |
| 195 |
|
zmol.cantPos = zmol.param.zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/ |
| 196 |
|
Vector3d com = zmol.mol->getCom(); |
| 197 |
< |
double diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
| 197 |
> |
RealType diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
| 198 |
|
if (diff < zconsTol_) { |
| 199 |
|
fixedZMols_.push_back(zmol); |
| 200 |
|
} else { |
| 240 |
|
currZconsTime_ = currSnapshot_->getTime(); |
| 241 |
|
} |
| 242 |
|
|
| 243 |
< |
void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){ |
| 244 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 243 |
> |
void ZconstraintForceManager::calcForces(){ |
| 244 |
> |
ForceManager::calcForces(); |
| 245 |
|
|
| 246 |
|
if (usingZconsGap_){ |
| 247 |
|
updateZPos(); |
| 299 |
|
|
| 300 |
|
// calculate the vz of center of mass of moving molecules(include unconstrained molecules |
| 301 |
|
// and moving z-constrained molecules) |
| 302 |
< |
double pzMovingMols_local = 0.0; |
| 303 |
< |
double pzMovingMols; |
| 302 |
> |
RealType pzMovingMols_local = 0.0; |
| 303 |
> |
RealType pzMovingMols; |
| 304 |
|
|
| 305 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 306 |
|
mol = i->mol; |
| 318 |
|
#ifndef IS_MPI |
| 319 |
|
pzMovingMols = pzMovingMols_local; |
| 320 |
|
#else |
| 321 |
< |
MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_DOUBLE, |
| 321 |
> |
MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_REALTYPE, |
| 322 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 323 |
|
#endif |
| 324 |
|
|
| 325 |
< |
double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
| 325 |
> |
RealType vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
| 326 |
|
|
| 327 |
|
//modify the velocities of moving z-constrained molecuels |
| 328 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 352 |
|
|
| 353 |
|
|
| 354 |
|
void ZconstraintForceManager::doZconstraintForce(){ |
| 355 |
< |
double totalFZ; |
| 356 |
< |
double totalFZ_local; |
| 355 |
> |
RealType totalFZ; |
| 356 |
> |
RealType totalFZ_local; |
| 357 |
|
Vector3d com; |
| 358 |
|
Vector3d force(0.0); |
| 359 |
|
|
| 383 |
|
|
| 384 |
|
//calculate total z-constraint force |
| 385 |
|
#ifdef IS_MPI |
| 386 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 386 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 387 |
|
#else |
| 388 |
|
totalFZ = totalFZ_local; |
| 389 |
|
#endif |
| 427 |
|
|
| 428 |
|
|
| 429 |
|
void ZconstraintForceManager::doHarmonic(){ |
| 430 |
< |
double totalFZ; |
| 430 |
> |
RealType totalFZ; |
| 431 |
|
Vector3d force(0.0); |
| 432 |
|
Vector3d com; |
| 433 |
< |
double totalFZ_local = 0; |
| 433 |
> |
RealType totalFZ_local = 0; |
| 434 |
|
std::list<ZconstraintMol>::iterator i; |
| 435 |
|
StuntDouble* integrableObject; |
| 436 |
|
Molecule::IntegrableObjectIterator ii; |
| 438 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 439 |
|
mol = i->mol; |
| 440 |
|
com = mol->getCom(); |
| 441 |
< |
double resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
| 442 |
< |
double diff = com[whichDirection] - resPos; |
| 443 |
< |
double harmonicU = 0.5 * i->param.kz * diff * diff; |
| 441 |
> |
RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
| 442 |
> |
RealType diff = com[whichDirection] - resPos; |
| 443 |
> |
RealType harmonicU = 0.5 * i->param.kz * diff * diff; |
| 444 |
|
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
| 445 |
< |
double harmonicF = -i->param.kz * diff; |
| 445 |
> |
RealType harmonicF = -i->param.kz * diff; |
| 446 |
|
totalFZ_local += harmonicF; |
| 447 |
|
|
| 448 |
|
//adjust force |
| 457 |
|
#ifndef IS_MPI |
| 458 |
|
totalFZ = totalFZ_local; |
| 459 |
|
#else |
| 460 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 460 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 461 |
|
#endif |
| 462 |
|
|
| 463 |
|
//modify the forces of unconstrained molecules |
| 476 |
|
|
| 477 |
|
bool ZconstraintForceManager::checkZConsState(){ |
| 478 |
|
Vector3d com; |
| 479 |
< |
double diff; |
| 479 |
> |
RealType diff; |
| 480 |
|
int changed_local = 0; |
| 481 |
|
|
| 482 |
|
std::list<ZconstraintMol>::iterator i; |
| 566 |
|
|
| 567 |
|
void ZconstraintForceManager::calcTotalMassMovingZMols(){ |
| 568 |
|
|
| 569 |
< |
double totMassMovingZMols_local = 0.0; |
| 569 |
> |
RealType totMassMovingZMols_local = 0.0; |
| 570 |
|
std::list<ZconstraintMol>::iterator i; |
| 571 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 572 |
|
totMassMovingZMols_local += i->mol->getMass(); |
| 573 |
|
} |
| 574 |
|
|
| 575 |
|
#ifdef IS_MPI |
| 576 |
< |
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE, |
| 576 |
> |
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_REALTYPE, |
| 577 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 578 |
|
#else |
| 579 |
|
totMassMovingZMols_ = totMassMovingZMols_local; |
| 581 |
|
|
| 582 |
|
} |
| 583 |
|
|
| 584 |
< |
double ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce){ |
| 584 |
> |
RealType ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce){ |
| 585 |
|
return totalForce * sd->getMass() / mol->getMass(); |
| 586 |
|
} |
| 587 |
|
|
| 588 |
< |
double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){ |
| 588 |
> |
RealType ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, RealType totalForce){ |
| 589 |
|
return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_); |
| 590 |
|
} |
| 591 |
|
|
| 592 |
< |
double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){ |
| 592 |
> |
RealType ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, RealType totalForce){ |
| 593 |
|
return totalForce * sd->getMass() / mol->getMass(); |
| 594 |
|
} |
| 595 |
|
|
| 596 |
< |
double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){ |
| 596 |
> |
RealType ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, RealType totalForce){ |
| 597 |
|
return totalForce * mol->getMass() / totMassUnconsMols_; |
| 598 |
|
} |
| 599 |
|
|
| 600 |
|
void ZconstraintForceManager::updateZPos(){ |
| 601 |
< |
double curTime = currSnapshot_->getTime(); |
| 601 |
> |
RealType curTime = currSnapshot_->getTime(); |
| 602 |
|
std::list<ZconstraintMol>::iterator i; |
| 603 |
|
for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
| 604 |
|
i->param.zTargetPos += zconsGap_; |
| 612 |
|
} |
| 613 |
|
} |
| 614 |
|
|
| 615 |
< |
double ZconstraintForceManager::getZTargetPos(int index){ |
| 616 |
< |
double zTargetPos; |
| 615 |
> |
RealType ZconstraintForceManager::getZTargetPos(int index){ |
| 616 |
> |
RealType zTargetPos; |
| 617 |
|
#ifndef IS_MPI |
| 618 |
|
Molecule* mol = info_->getMoleculeByGlobalIndex(index); |
| 619 |
|
assert(mol); |
| 621 |
|
zTargetPos = com[whichDirection]; |
| 622 |
|
#else |
| 623 |
|
int whicProc = info_->getMolToProc(index); |
| 624 |
< |
MPI_Bcast(&zTargetPos, 1, MPI_DOUBLE, whicProc, MPI_COMM_WORLD); |
| 624 |
> |
MPI_Bcast(&zTargetPos, 1, MPI_REALTYPE, whicProc, MPI_COMM_WORLD); |
| 625 |
|
#endif |
| 626 |
|
return zTargetPos; |
| 627 |
|
} |
