| 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). |
| 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 |
< |
#include "FluctuatingChargePropagator.hpp" |
| 44 |
< |
#include "primitives/Molecule.hpp" |
| 45 |
< |
#include "utils/simError.h" |
| 46 |
< |
#include "utils/PhysicalConstants.hpp" |
| 43 |
> |
#include "flucq/FluctuatingChargePropagator.hpp" |
| 44 |
> |
#include "flucq/FluctuatingChargeObjectiveFunction.hpp" |
| 45 |
> |
#include "optimization/Constraint.hpp" |
| 46 |
> |
#include "optimization/Problem.hpp" |
| 47 |
> |
#include "optimization/EndCriteria.hpp" |
| 48 |
> |
#include "optimization/StatusFunction.hpp" |
| 49 |
> |
#include "optimization/OptimizationFactory.hpp" |
| 50 |
> |
|
| 51 |
|
#ifdef IS_MPI |
| 52 |
|
#include <mpi.h> |
| 53 |
|
#endif |
| 54 |
|
|
| 55 |
+ |
using namespace QuantLib; |
| 56 |
|
namespace OpenMD { |
| 57 |
|
|
| 58 |
< |
void FluctuatingChargePropagator::applyConstraints() { |
| 59 |
< |
if (!hasFlucQ_) return; |
| 55 |
< |
|
| 56 |
< |
SimInfo::MoleculeIterator i; |
| 57 |
< |
Molecule::FluctuatingChargeIterator j; |
| 58 |
< |
Molecule* mol; |
| 59 |
< |
Atom* atom; |
| 58 |
> |
FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) : |
| 59 |
> |
info_(info), hasFlucQ_(false), forceMan_(NULL), initialized_(false) { |
| 60 |
|
|
| 61 |
< |
RealType totalFrc, totalMolFrc, constrainedFrc; |
| 61 |
> |
Globals* simParams = info_->getSimParams(); |
| 62 |
> |
fqParams_ = simParams->getFluctuatingChargeParameters(); |
| 63 |
> |
} |
| 64 |
|
|
| 65 |
< |
// accumulate the total system fluctuating charge forces |
| 66 |
< |
totalFrc = 0.0; |
| 65 |
> |
FluctuatingChargePropagator::~FluctuatingChargePropagator() { |
| 66 |
> |
} |
| 67 |
|
|
| 68 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 69 |
< |
mol = info_->nextMolecule(i)) { |
| 68 |
> |
void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) { |
| 69 |
> |
forceMan_ = forceMan; |
| 70 |
> |
} |
| 71 |
|
|
| 72 |
< |
for (atom = mol->beginFluctuatingCharge(j); atom != NULL; |
| 73 |
< |
atom = mol->nextFluctuatingCharge(j)) { |
| 74 |
< |
totalFrc += atom->getFlucQFrc(); |
| 72 |
> |
void FluctuatingChargePropagator::initialize() { |
| 73 |
> |
if (info_->usesFluctuatingCharges()) { |
| 74 |
> |
if (info_->getNFluctuatingCharges() > 0) { |
| 75 |
> |
hasFlucQ_ = true; |
| 76 |
> |
fqConstraints_ = new FluctuatingChargeConstraints(info_); |
| 77 |
> |
fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions()); |
| 78 |
|
} |
| 73 |
– |
|
| 79 |
|
} |
| 80 |
+ |
|
| 81 |
+ |
if (!hasFlucQ_) { |
| 82 |
+ |
initialized_ = true; |
| 83 |
+ |
return; |
| 84 |
+ |
} |
| 85 |
|
|
| 86 |
< |
#ifdef IS_MPI |
| 87 |
< |
// in parallel, we need to add up the contributions from all |
| 88 |
< |
// processors: |
| 89 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE, |
| 90 |
< |
MPI::SUM); |
| 91 |
< |
#endif |
| 92 |
< |
|
| 93 |
< |
// divide by the total number of fluctuating charges: |
| 94 |
< |
totalFrc /= info_->getNFluctuatingCharges(); |
| 86 |
> |
// SimInfo::MoleculeIterator i; |
| 87 |
> |
// Molecule::FluctuatingChargeIterator j; |
| 88 |
> |
// Molecule* mol; |
| 89 |
> |
// Atom* atom; |
| 90 |
> |
// |
| 91 |
> |
// For single-minima flucq, this ensures a net neutral system, but |
| 92 |
> |
// for multiple minima, this is no longer the right thing to do: |
| 93 |
> |
// |
| 94 |
> |
// for (mol = info_->beginMolecule(i); mol != NULL; |
| 95 |
> |
// mol = info_->nextMolecule(i)) { |
| 96 |
> |
// for (atom = mol->beginFluctuatingCharge(j); atom != NULL; |
| 97 |
> |
// atom = mol->nextFluctuatingCharge(j)) { |
| 98 |
> |
// atom->setFlucQPos(0.0); |
| 99 |
> |
// atom->setFlucQVel(0.0); |
| 100 |
> |
// } |
| 101 |
> |
// } |
| 102 |
> |
|
| 103 |
> |
FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, |
| 104 |
> |
fqConstraints_); |
| 105 |
|
|
| 106 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 107 |
< |
mol = info_->nextMolecule(i)) { |
| 108 |
< |
|
| 89 |
< |
totalMolFrc = 0.0; |
| 106 |
> |
DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords(); |
| 107 |
> |
Problem problem(flucQobjf, *(new NoConstraint()), *(new NoStatus()), |
| 108 |
> |
initCoords); |
| 109 |
|
|
| 110 |
< |
// molecular constraints can be done with a second loop. |
| 92 |
< |
if (mol->constrainTotalCharge()) { |
| 93 |
< |
for (atom = mol->beginFluctuatingCharge(j); atom != NULL; |
| 94 |
< |
atom = mol->nextFluctuatingCharge(j)) { |
| 95 |
< |
totalMolFrc += atom->getFlucQFrc(); |
| 96 |
< |
} |
| 97 |
< |
totalMolFrc /= mol->getNFluctuatingCharges(); |
| 98 |
< |
} |
| 110 |
> |
EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5); |
| 111 |
|
|
| 112 |
< |
for (atom = mol->beginFluctuatingCharge(j); atom != NULL; |
| 113 |
< |
atom = mol->nextFluctuatingCharge(j)) { |
| 114 |
< |
constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc; |
| 115 |
< |
atom->setFlucQFrc(constrainedFrc); |
| 116 |
< |
} |
| 117 |
< |
} |
| 112 |
> |
OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_); |
| 113 |
> |
|
| 114 |
> |
DumpStatusFunction dsf(info_); // we want a dump file written |
| 115 |
> |
// every iteration |
| 116 |
> |
minim->minimize(problem, endCriteria); |
| 117 |
> |
cerr << "back from minim\n"; |
| 118 |
> |
initialized_ = true; |
| 119 |
|
} |
| 120 |
+ |
|
| 121 |
+ |
void FluctuatingChargePropagator::applyConstraints() { |
| 122 |
+ |
if (!initialized_) initialize(); |
| 123 |
+ |
if (!hasFlucQ_) return; |
| 124 |
+ |
fqConstraints_->applyConstraints(); |
| 125 |
+ |
} |
| 126 |
|
} |
