| 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 |
< |
#include "perturbations/ElectricField.hpp" |
| 42 |
> |
|
| 43 |
> |
#include "perturbations/UniformField.hpp" |
| 44 |
|
#include "types/FixedChargeAdapter.hpp" |
| 45 |
|
#include "types/FluctuatingChargeAdapter.hpp" |
| 46 |
|
#include "types/MultipoleAdapter.hpp" |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 49 |
+ |
#include "utils/PhysicalConstants.hpp" |
| 50 |
|
|
| 51 |
|
namespace OpenMD { |
| 52 |
< |
|
| 53 |
< |
ElectricField::ElectricField(SimInfo* info) : info_(info), |
| 54 |
< |
doElectricField(false), |
| 55 |
< |
doParticlePot(false), |
| 56 |
< |
initialized(false) { |
| 52 |
> |
|
| 53 |
> |
UniformField::UniformField(SimInfo* info) : info_(info), |
| 54 |
> |
doUniformField(false), |
| 55 |
> |
doParticlePot(false), |
| 56 |
> |
initialized(false) { |
| 57 |
|
simParams = info_->getSimParams(); |
| 58 |
|
} |
| 59 |
+ |
|
| 60 |
+ |
void UniformField::initialize() { |
| 61 |
|
|
| 62 |
< |
void ElectricField::initialize() { |
| 62 |
> |
std::vector<RealType> ef; |
| 63 |
> |
|
| 64 |
|
if (simParams->haveElectricField()) { |
| 65 |
< |
doElectricField = true; |
| 66 |
< |
EF = simParams->getElectricField(); |
| 65 |
> |
doUniformField = true; |
| 66 |
> |
ef = simParams->getElectricField(); |
| 67 |
|
} |
| 68 |
+ |
if (simParams->haveUniformField()) { |
| 69 |
+ |
doUniformField = true; |
| 70 |
+ |
ef = simParams->getUniformField(); |
| 71 |
+ |
} |
| 72 |
+ |
if (ef.size() != 3) { |
| 73 |
+ |
sprintf(painCave.errMsg, |
| 74 |
+ |
"UniformField: Incorrect number of parameters specified.\n" |
| 75 |
+ |
"\tthere should be 3 parameters, but %lu were specified.\n", ef.size()); |
| 76 |
+ |
painCave.isFatal = 1; |
| 77 |
+ |
simError(); |
| 78 |
+ |
} |
| 79 |
+ |
EF.x() = ef[0]; |
| 80 |
+ |
EF.y() = ef[1]; |
| 81 |
+ |
EF.z() = ef[2]; |
| 82 |
+ |
|
| 83 |
|
int storageLayout_ = info_->getSnapshotManager()->getStorageLayout(); |
| 84 |
|
if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true; |
| 85 |
|
initialized = true; |
| 86 |
|
} |
| 87 |
+ |
|
| 88 |
+ |
void UniformField::applyPerturbation() { |
| 89 |
|
|
| 68 |
– |
void ElectricField::applyPerturbation() { |
| 90 |
|
if (!initialized) initialize(); |
| 91 |
|
|
| 92 |
|
SimInfo::MoleculeIterator i; |
| 93 |
|
Molecule::AtomIterator j; |
| 94 |
|
Molecule* mol; |
| 95 |
|
Atom* atom; |
| 96 |
+ |
AtomType* atype; |
| 97 |
|
potVec longRangePotential(0.0); |
| 98 |
< |
Vector3d dip; |
| 99 |
< |
Vector3d trq; |
| 100 |
< |
Vector3d EFfrc; |
| 101 |
< |
Vector3d pos; |
| 102 |
< |
RealType chrg; |
| 103 |
< |
RealType pot, fieldPot, moment; |
| 104 |
< |
RealType chrgToKcal = 23.0609; |
| 105 |
< |
RealType debyeToKcal = 4.8018969509; |
| 98 |
> |
|
| 99 |
> |
RealType C; |
| 100 |
> |
Vector3d D; |
| 101 |
> |
RealType U; |
| 102 |
> |
RealType fPot; |
| 103 |
> |
Vector3d t; |
| 104 |
> |
Vector3d f; |
| 105 |
> |
Vector3d r; |
| 106 |
> |
|
| 107 |
|
bool isCharge; |
| 108 |
|
|
| 109 |
< |
if (doElectricField) { |
| 87 |
< |
fieldPot = 0.0; |
| 109 |
> |
if (doUniformField) { |
| 110 |
|
|
| 111 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 111 |
> |
U = 0.0; |
| 112 |
> |
fPot = 0.0; |
| 113 |
> |
|
| 114 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 115 |
> |
mol = info_->nextMolecule(i)) { |
| 116 |
> |
|
| 117 |
|
for (atom = mol->beginAtom(j); atom != NULL; |
| 118 |
|
atom = mol->nextAtom(j)) { |
| 92 |
– |
isCharge = false; |
| 93 |
– |
chrg = 0.0; |
| 119 |
|
|
| 120 |
< |
FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType()); |
| 120 |
> |
isCharge = false; |
| 121 |
> |
C = 0.0; |
| 122 |
> |
|
| 123 |
> |
atype = atom->getAtomType(); |
| 124 |
> |
|
| 125 |
> |
// ad-hoc choice of the origin for potential calculation and |
| 126 |
> |
// fluctuating charge force: |
| 127 |
> |
|
| 128 |
> |
r = atom->getPos(); |
| 129 |
> |
|
| 130 |
> |
if (atype->isElectrostatic()) { |
| 131 |
> |
atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert); |
| 132 |
> |
} |
| 133 |
> |
|
| 134 |
> |
FixedChargeAdapter fca = FixedChargeAdapter(atype); |
| 135 |
|
if ( fca.isFixedCharge() ) { |
| 136 |
|
isCharge = true; |
| 137 |
< |
chrg = fca.getCharge(); |
| 137 |
> |
C = fca.getCharge(); |
| 138 |
|
} |
| 139 |
|
|
| 140 |
< |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType()); |
| 140 |
> |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype); |
| 141 |
|
if ( fqa.isFluctuatingCharge() ) { |
| 142 |
|
isCharge = true; |
| 143 |
< |
chrg += atom->getFlucQPos(); |
| 143 |
> |
C += atom->getFlucQPos(); |
| 144 |
> |
atom->addFlucQFrc( dot(r, EF) |
| 145 |
> |
* PhysicalConstants::chargeFieldConvert ); |
| 146 |
|
} |
| 147 |
|
|
| 148 |
|
if (isCharge) { |
| 149 |
< |
EFfrc = EF*chrg; |
| 150 |
< |
EFfrc *= chrgToKcal; |
| 151 |
< |
atom->addFrc(EFfrc); |
| 152 |
< |
// totally ad-hoc choice of the origin for potential calculation |
| 112 |
< |
pos = atom->getPos(); |
| 113 |
< |
pot = -dot(pos, EFfrc); |
| 149 |
> |
f = EF * C * PhysicalConstants::chargeFieldConvert; |
| 150 |
> |
atom->addFrc(f); |
| 151 |
> |
U = -dot(r, f); |
| 152 |
> |
|
| 153 |
|
if (doParticlePot) { |
| 154 |
< |
atom->addParticlePot(pot); |
| 154 |
> |
atom->addParticlePot(U); |
| 155 |
|
} |
| 156 |
< |
fieldPot += pot; |
| 156 |
> |
fPot += U; |
| 157 |
|
} |
| 158 |
|
|
| 159 |
< |
MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
| 159 |
> |
MultipoleAdapter ma = MultipoleAdapter(atype); |
| 160 |
|
if (ma.isDipole() ) { |
| 161 |
< |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 162 |
< |
moment = ma.getDipoleMoment(); |
| 163 |
< |
moment *= debyeToKcal; |
| 164 |
< |
dip = u_i * moment; |
| 165 |
< |
trq = cross(dip, EF); |
| 166 |
< |
//cerr << "dip = " << dip << "\n"; |
| 167 |
< |
// cerr << "trq = " << trq << "\n"; |
| 168 |
< |
atom->addTrq(trq); |
| 130 |
< |
pot = -dot(dip, EF); |
| 131 |
< |
//cerr << "pot = " << pot << "\n"; |
| 161 |
> |
|
| 162 |
> |
D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert; |
| 163 |
> |
|
| 164 |
> |
t = cross(D, EF); |
| 165 |
> |
atom->addTrq(t); |
| 166 |
> |
|
| 167 |
> |
U = -dot(D, EF); |
| 168 |
> |
|
| 169 |
|
if (doParticlePot) { |
| 170 |
< |
atom->addParticlePot(pot); |
| 170 |
> |
atom->addParticlePot(U); |
| 171 |
|
} |
| 172 |
< |
fieldPot += pot; |
| 172 |
> |
fPot += U; |
| 173 |
|
} |
| 174 |
|
} |
| 175 |
|
} |
| 176 |
+ |
|
| 177 |
|
#ifdef IS_MPI |
| 178 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &fieldPot, 1, MPI::REALTYPE, |
| 179 |
< |
MPI::SUM); |
| 178 |
> |
MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE, |
| 179 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 180 |
|
#endif |
| 181 |
+ |
|
| 182 |
|
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 183 |
|
longRangePotential = snap->getLongRangePotentials(); |
| 184 |
< |
// << "longRangePotential = " << longRangePotential << "\n"; |
| 146 |
< |
longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot; |
| 147 |
< |
//cerr << "longRangePotential[ELECTROSTATIC_FAMILY] = " << longRangePotential[ELECTROSTATIC_FAMILY] << "\n"; |
| 184 |
> |
longRangePotential[ELECTROSTATIC_FAMILY] += fPot; |
| 185 |
|
snap->setLongRangePotential(longRangePotential); |
| 186 |
|
} |
| 187 |
|
} |
| 151 |
– |
|
| 188 |
|
} |
