| 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 |
|
*/ |
| 77 |
|
Vector3d trq; |
| 78 |
|
Vector3d EFfrc; |
| 79 |
|
Vector3d pos; |
| 80 |
– |
RealType chrg; |
| 81 |
– |
RealType pot, fieldPot, moment; |
| 82 |
– |
RealType chrgToKcal = 23.0609; |
| 83 |
– |
RealType debyeToKcal = 4.8018969509; |
| 84 |
– |
bool isCharge; |
| 80 |
|
|
| 81 |
|
if (doElectricField) { |
| 82 |
< |
fieldPot = 0.0; |
| 82 |
> |
const RealType chrgToKcal = 23.0609; |
| 83 |
> |
const RealType debyeToKcal = 4.8018969509; |
| 84 |
> |
RealType pot; |
| 85 |
> |
RealType fieldPot = 0.0; |
| 86 |
|
|
| 87 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 87 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 88 |
> |
mol = info_->nextMolecule(i)) { |
| 89 |
> |
|
| 90 |
|
for (atom = mol->beginAtom(j); atom != NULL; |
| 91 |
|
atom = mol->nextAtom(j)) { |
| 92 |
– |
isCharge = false; |
| 93 |
– |
chrg = 0.0; |
| 92 |
|
|
| 93 |
< |
FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType()); |
| 93 |
> |
bool isCharge = false; |
| 94 |
> |
RealType chrg = 0.0; |
| 95 |
> |
|
| 96 |
> |
AtomType* atype = atom->getAtomType(); |
| 97 |
> |
|
| 98 |
> |
if (atype->isElectrostatic()) { |
| 99 |
> |
atom->addElectricField(EF * chrgToKcal); |
| 100 |
> |
} |
| 101 |
> |
|
| 102 |
> |
FixedChargeAdapter fca = FixedChargeAdapter(atype); |
| 103 |
|
if ( fca.isFixedCharge() ) { |
| 104 |
|
isCharge = true; |
| 105 |
|
chrg = fca.getCharge(); |
| 106 |
|
} |
| 107 |
|
|
| 108 |
< |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType()); |
| 108 |
> |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype); |
| 109 |
|
if ( fqa.isFluctuatingCharge() ) { |
| 110 |
|
isCharge = true; |
| 111 |
|
chrg += atom->getFlucQPos(); |
| 115 |
|
EFfrc = EF*chrg; |
| 116 |
|
EFfrc *= chrgToKcal; |
| 117 |
|
atom->addFrc(EFfrc); |
| 118 |
< |
// totally ad-hoc choice of the origin for potential calculation |
| 118 |
> |
// ad-hoc choice of the origin for potential calculation |
| 119 |
|
pos = atom->getPos(); |
| 120 |
|
pot = -dot(pos, EFfrc); |
| 121 |
|
if (doParticlePot) { |
| 124 |
|
fieldPot += pot; |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
| 127 |
> |
MultipoleAdapter ma = MultipoleAdapter(atype); |
| 128 |
|
if (ma.isDipole() ) { |
| 129 |
< |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 130 |
< |
moment = ma.getDipoleMoment(); |
| 131 |
< |
moment *= debyeToKcal; |
| 132 |
< |
dip = u_i * moment; |
| 126 |
< |
trq = cross(dip, EF); |
| 127 |
< |
//cerr << "dip = " << dip << "\n"; |
| 128 |
< |
// cerr << "trq = " << trq << "\n"; |
| 129 |
> |
Vector3d dipole = atom->getDipole(); |
| 130 |
> |
dipole *= debyeToKcal; |
| 131 |
> |
|
| 132 |
> |
trq = cross(dipole, EF); |
| 133 |
|
atom->addTrq(trq); |
| 134 |
< |
pot = -dot(dip, EF); |
| 135 |
< |
//cerr << "pot = " << pot << "\n"; |
| 134 |
> |
|
| 135 |
> |
pot = -dot(dipole, EF); |
| 136 |
|
if (doParticlePot) { |
| 137 |
|
atom->addParticlePot(pot); |
| 138 |
|
} |
| 146 |
|
#endif |
| 147 |
|
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 148 |
|
longRangePotential = snap->getLongRangePotentials(); |
| 145 |
– |
// << "longRangePotential = " << longRangePotential << "\n"; |
| 149 |
|
longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot; |
| 147 |
– |
//cerr << "longRangePotential[ELECTROSTATIC_FAMILY] = " << longRangePotential[ELECTROSTATIC_FAMILY] << "\n"; |
| 150 |
|
snap->setLongRangePotential(longRangePotential); |
| 151 |
|
} |
| 152 |
|
} |
| 151 |
– |
|
| 153 |
|
} |
