| 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] 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> |
| 44 |
|
#include "constraints/ZconstraintForceManager.hpp" |
| 45 |
|
#include "integrators/Integrator.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
< |
#include "utils/OOPSEConstant.hpp" |
| 47 |
> |
#include "utils/PhysicalConstants.hpp" |
| 48 |
|
#include "utils/StringUtils.hpp" |
| 49 |
< |
namespace oopse { |
| 49 |
> |
#ifdef IS_MPI |
| 50 |
> |
#include <mpi.h> |
| 51 |
> |
#endif |
| 52 |
> |
|
| 53 |
> |
namespace OpenMD { |
| 54 |
|
ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) { |
| 55 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 56 |
|
Globals* simParam = info_->getSimParams(); |
| 64 |
|
simError(); |
| 65 |
|
} |
| 66 |
|
|
| 67 |
< |
if (simParam->haveZconstraintTime()){ |
| 67 |
> |
if (simParam->haveZconsTime()){ |
| 68 |
|
zconsTime_ = simParam->getZconsTime(); |
| 69 |
|
} |
| 70 |
|
else{ |
| 82 |
|
zconsTol_ = 0.01; |
| 83 |
|
sprintf(painCave.errMsg, |
| 84 |
|
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
| 85 |
< |
"\tOOPSE will use a default value of %f.\n" |
| 85 |
> |
"\tOpenMD will use a default value of %f.\n" |
| 86 |
|
"\tTo set the tolerance, use the zconsTol variable.\n", |
| 87 |
|
zconsTol_); |
| 88 |
|
painCave.isFatal = 0; |
| 90 |
|
} |
| 91 |
|
|
| 92 |
|
//set zcons gap |
| 93 |
< |
if (simParam->haveZConsGap()){ |
| 93 |
> |
if (simParam->haveZconsGap()){ |
| 94 |
|
usingZconsGap_ = true; |
| 95 |
|
zconsGap_ = simParam->getZconsGap(); |
| 96 |
|
}else { |
| 99 |
|
} |
| 100 |
|
|
| 101 |
|
//set zcons fixtime |
| 102 |
< |
if (simParam->haveZConsFixTime()){ |
| 102 |
> |
if (simParam->haveZconsFixtime()){ |
| 103 |
|
zconsFixingTime_ = simParam->getZconsFixtime(); |
| 104 |
|
} else { |
| 105 |
|
zconsFixingTime_ = infiniteTime; |
| 106 |
|
} |
| 107 |
|
|
| 108 |
|
//set zconsUsingSMD |
| 109 |
< |
if (simParam->haveZConsUsingSMD()){ |
| 109 |
> |
if (simParam->haveZconsUsingSMD()){ |
| 110 |
|
usingSMD_ = simParam->getZconsUsingSMD(); |
| 111 |
|
}else { |
| 112 |
|
usingSMD_ =false; |
| 116 |
|
|
| 117 |
|
//estimate the force constant of harmonical potential |
| 118 |
|
Mat3x3d hmat = currSnapshot_->getHmat(); |
| 119 |
< |
double halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2; |
| 120 |
< |
double targetTemp; |
| 119 |
> |
RealType halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2; |
| 120 |
> |
RealType targetTemp; |
| 121 |
|
if (simParam->haveTargetTemp()) { |
| 122 |
|
targetTemp = simParam->getTargetTemp(); |
| 123 |
|
} else { |
| 124 |
|
targetTemp = 298.0; |
| 125 |
|
} |
| 126 |
< |
double zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
| 126 |
> |
RealType zforceConstant = PhysicalConstants::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
| 127 |
|
|
| 128 |
< |
int nZconstraints = simParam->getNzConstraints(); |
| 129 |
< |
ZconStamp** stamp = simParam->getZconStamp(); |
| 128 |
> |
int nZconstraints = simParam->getNZconsStamps(); |
| 129 |
> |
std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
| 130 |
|
// |
| 131 |
|
for (int i = 0; i < nZconstraints; i++){ |
| 132 |
|
|
| 153 |
|
update(); |
| 154 |
|
|
| 155 |
|
//calculate masss of unconstraint molecules in the whole system (never change during the simulation) |
| 156 |
< |
double totMassUnconsMols_local = 0.0; |
| 156 |
> |
RealType totMassUnconsMols_local = 0.0; |
| 157 |
|
std::vector<Molecule*>::iterator j; |
| 158 |
|
for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
| 159 |
|
totMassUnconsMols_local += (*j)->getMass(); |
| 161 |
|
#ifndef IS_MPI |
| 162 |
|
totMassUnconsMols_ = totMassUnconsMols_local; |
| 163 |
|
#else |
| 164 |
< |
MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_DOUBLE, |
| 164 |
> |
MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_REALTYPE, |
| 165 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 166 |
|
#endif |
| 167 |
|
|
| 199 |
|
zmol.param = i->second; |
| 200 |
|
zmol.cantPos = zmol.param.zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/ |
| 201 |
|
Vector3d com = zmol.mol->getCom(); |
| 202 |
< |
double diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
| 202 |
> |
RealType diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
| 203 |
|
if (diff < zconsTol_) { |
| 204 |
|
fixedZMols_.push_back(zmol); |
| 205 |
|
} else { |
| 245 |
|
currZconsTime_ = currSnapshot_->getTime(); |
| 246 |
|
} |
| 247 |
|
|
| 248 |
< |
void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){ |
| 249 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 248 |
> |
void ZconstraintForceManager::calcForces(){ |
| 249 |
> |
ForceManager::calcForces(); |
| 250 |
|
|
| 251 |
|
if (usingZconsGap_){ |
| 252 |
|
updateZPos(); |
| 304 |
|
|
| 305 |
|
// calculate the vz of center of mass of moving molecules(include unconstrained molecules |
| 306 |
|
// and moving z-constrained molecules) |
| 307 |
< |
double pzMovingMols_local = 0.0; |
| 308 |
< |
double pzMovingMols; |
| 307 |
> |
RealType pzMovingMols_local = 0.0; |
| 308 |
> |
RealType pzMovingMols; |
| 309 |
|
|
| 310 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 311 |
|
mol = i->mol; |
| 323 |
|
#ifndef IS_MPI |
| 324 |
|
pzMovingMols = pzMovingMols_local; |
| 325 |
|
#else |
| 326 |
< |
MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_DOUBLE, |
| 326 |
> |
MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_REALTYPE, |
| 327 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 328 |
|
#endif |
| 329 |
|
|
| 330 |
< |
double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
| 330 |
> |
RealType vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
| 331 |
|
|
| 332 |
|
//modify the velocities of moving z-constrained molecuels |
| 333 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 357 |
|
|
| 358 |
|
|
| 359 |
|
void ZconstraintForceManager::doZconstraintForce(){ |
| 360 |
< |
double totalFZ; |
| 361 |
< |
double totalFZ_local; |
| 360 |
> |
RealType totalFZ; |
| 361 |
> |
RealType totalFZ_local; |
| 362 |
|
Vector3d com; |
| 363 |
|
Vector3d force(0.0); |
| 364 |
|
|
| 388 |
|
|
| 389 |
|
//calculate total z-constraint force |
| 390 |
|
#ifdef IS_MPI |
| 391 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 391 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 392 |
|
#else |
| 393 |
|
totalFZ = totalFZ_local; |
| 394 |
|
#endif |
| 432 |
|
|
| 433 |
|
|
| 434 |
|
void ZconstraintForceManager::doHarmonic(){ |
| 435 |
< |
double totalFZ; |
| 435 |
> |
RealType totalFZ; |
| 436 |
|
Vector3d force(0.0); |
| 437 |
|
Vector3d com; |
| 438 |
< |
double totalFZ_local = 0; |
| 438 |
> |
RealType totalFZ_local = 0; |
| 439 |
|
std::list<ZconstraintMol>::iterator i; |
| 440 |
|
StuntDouble* integrableObject; |
| 441 |
|
Molecule::IntegrableObjectIterator ii; |
| 443 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 444 |
|
mol = i->mol; |
| 445 |
|
com = mol->getCom(); |
| 446 |
< |
double resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
| 447 |
< |
double diff = com[whichDirection] - resPos; |
| 448 |
< |
double harmonicU = 0.5 * i->param.kz * diff * diff; |
| 446 |
> |
RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
| 447 |
> |
RealType diff = com[whichDirection] - resPos; |
| 448 |
> |
RealType harmonicU = 0.5 * i->param.kz * diff * diff; |
| 449 |
|
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
| 450 |
< |
double harmonicF = -i->param.kz * diff; |
| 450 |
> |
RealType harmonicF = -i->param.kz * diff; |
| 451 |
|
totalFZ_local += harmonicF; |
| 452 |
|
|
| 453 |
|
//adjust force |
| 462 |
|
#ifndef IS_MPI |
| 463 |
|
totalFZ = totalFZ_local; |
| 464 |
|
#else |
| 465 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 465 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 466 |
|
#endif |
| 467 |
|
|
| 468 |
|
//modify the forces of unconstrained molecules |
| 481 |
|
|
| 482 |
|
bool ZconstraintForceManager::checkZConsState(){ |
| 483 |
|
Vector3d com; |
| 484 |
< |
double diff; |
| 484 |
> |
RealType diff; |
| 485 |
|
int changed_local = 0; |
| 486 |
|
|
| 487 |
|
std::list<ZconstraintMol>::iterator i; |
| 571 |
|
|
| 572 |
|
void ZconstraintForceManager::calcTotalMassMovingZMols(){ |
| 573 |
|
|
| 574 |
< |
double totMassMovingZMols_local = 0.0; |
| 574 |
> |
RealType totMassMovingZMols_local = 0.0; |
| 575 |
|
std::list<ZconstraintMol>::iterator i; |
| 576 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 577 |
|
totMassMovingZMols_local += i->mol->getMass(); |
| 578 |
|
} |
| 579 |
|
|
| 580 |
|
#ifdef IS_MPI |
| 581 |
< |
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE, |
| 581 |
> |
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_REALTYPE, |
| 582 |
|
MPI_SUM, MPI_COMM_WORLD); |
| 583 |
|
#else |
| 584 |
|
totMassMovingZMols_ = totMassMovingZMols_local; |
| 586 |
|
|
| 587 |
|
} |
| 588 |
|
|
| 589 |
< |
double ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce){ |
| 589 |
> |
RealType ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce){ |
| 590 |
|
return totalForce * sd->getMass() / mol->getMass(); |
| 591 |
|
} |
| 592 |
|
|
| 593 |
< |
double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){ |
| 593 |
> |
RealType ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, RealType totalForce){ |
| 594 |
|
return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_); |
| 595 |
|
} |
| 596 |
|
|
| 597 |
< |
double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){ |
| 597 |
> |
RealType ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, RealType totalForce){ |
| 598 |
|
return totalForce * sd->getMass() / mol->getMass(); |
| 599 |
|
} |
| 600 |
|
|
| 601 |
< |
double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){ |
| 601 |
> |
RealType ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, RealType totalForce){ |
| 602 |
|
return totalForce * mol->getMass() / totMassUnconsMols_; |
| 603 |
|
} |
| 604 |
|
|
| 605 |
|
void ZconstraintForceManager::updateZPos(){ |
| 606 |
< |
double curTime = currSnapshot_->getTime(); |
| 606 |
> |
RealType curTime = currSnapshot_->getTime(); |
| 607 |
|
std::list<ZconstraintMol>::iterator i; |
| 608 |
|
for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
| 609 |
|
i->param.zTargetPos += zconsGap_; |
| 617 |
|
} |
| 618 |
|
} |
| 619 |
|
|
| 620 |
< |
double ZconstraintForceManager::getZTargetPos(int index){ |
| 621 |
< |
double zTargetPos; |
| 620 |
> |
RealType ZconstraintForceManager::getZTargetPos(int index){ |
| 621 |
> |
RealType zTargetPos; |
| 622 |
|
#ifndef IS_MPI |
| 623 |
|
Molecule* mol = info_->getMoleculeByGlobalIndex(index); |
| 624 |
|
assert(mol); |
| 626 |
|
zTargetPos = com[whichDirection]; |
| 627 |
|
#else |
| 628 |
|
int whicProc = info_->getMolToProc(index); |
| 629 |
< |
MPI_Bcast(&zTargetPos, 1, MPI_DOUBLE, whicProc, MPI_COMM_WORLD); |
| 629 |
> |
MPI_Bcast(&zTargetPos, 1, MPI_REALTYPE, whicProc, MPI_COMM_WORLD); |
| 630 |
|
#endif |
| 631 |
|
return zTargetPos; |
| 632 |
|
} |
