| 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). |
| 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 "primitives/DirectionalAtom.hpp" |
| 44 |
+ |
#include "types/DirectionalAdapter.hpp" |
| 45 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
|
namespace OpenMD { |
| 48 |
|
|
| 49 |
< |
DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
| 50 |
< |
: Atom(dAtomType){ |
| 49 |
> |
DirectionalAtom::DirectionalAtom(AtomType* dAtomType) |
| 50 |
> |
: Atom(dAtomType) { |
| 51 |
|
objType_= otDAtom; |
| 52 |
< |
if (dAtomType->isMultipole()) { |
| 53 |
< |
electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
| 52 |
> |
|
| 53 |
> |
DirectionalAdapter da = DirectionalAdapter(dAtomType); |
| 54 |
> |
I_ = da.getI(); |
| 55 |
> |
|
| 56 |
> |
MultipoleAdapter ma = MultipoleAdapter(dAtomType); |
| 57 |
> |
if (ma.isDipole()) { |
| 58 |
> |
dipole_ = ma.getDipole(); |
| 59 |
|
} |
| 60 |
< |
|
| 60 |
> |
if (ma.isQuadrupole()) { |
| 61 |
> |
quadrupole_ = ma.getQuadrupole(); |
| 62 |
> |
} |
| 63 |
> |
|
| 64 |
|
// Check if one of the diagonal inertia tensor of this directional |
| 65 |
|
// atom is zero: |
| 66 |
|
int nLinearAxis = 0; |
| 84 |
|
} |
| 85 |
|
|
| 86 |
|
Mat3x3d DirectionalAtom::getI() { |
| 87 |
< |
return static_cast<DirectionalAtomType*>(getAtomType())->getI(); |
| 87 |
> |
return I_; |
| 88 |
|
} |
| 89 |
|
|
| 90 |
|
void DirectionalAtom::setPrevA(const RotMat3x3d& a) { |
| 91 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 92 |
+ |
|
| 93 |
|
if (atomType_->isMultipole()) { |
| 94 |
< |
((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 94 |
> |
RotMat3x3d atrans = a.transpose(); |
| 95 |
> |
|
| 96 |
> |
if (atomType_->isDipole()) { |
| 97 |
> |
((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 98 |
> |
} |
| 99 |
> |
|
| 100 |
> |
if (atomType_->isQuadrupole()) { |
| 101 |
> |
((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 102 |
> |
} |
| 103 |
|
} |
| 104 |
|
} |
| 105 |
|
|
| 106 |
|
|
| 107 |
|
void DirectionalAtom::setA(const RotMat3x3d& a) { |
| 108 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
if (atomType_->isMultipole()) { |
| 111 |
< |
((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 111 |
> |
RotMat3x3d atrans = a.transpose(); |
| 112 |
> |
|
| 113 |
> |
if (atomType_->isDipole()) { |
| 114 |
> |
((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 115 |
> |
} |
| 116 |
> |
|
| 117 |
> |
if (atomType_->isQuadrupole()) { |
| 118 |
> |
((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 119 |
> |
} |
| 120 |
|
} |
| 121 |
+ |
|
| 122 |
|
} |
| 123 |
|
|
| 124 |
|
void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) { |
| 125 |
|
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
| 126 |
< |
|
| 126 |
> |
|
| 127 |
|
if (atomType_->isMultipole()) { |
| 128 |
< |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 128 |
> |
RotMat3x3d atrans = a.transpose(); |
| 129 |
> |
|
| 130 |
> |
if (atomType_->isDipole()) { |
| 131 |
> |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 132 |
> |
} |
| 133 |
> |
|
| 134 |
> |
if (atomType_->isQuadrupole()) { |
| 135 |
> |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 136 |
> |
} |
| 137 |
|
} |
| 138 |
+ |
|
| 139 |
|
} |
| 140 |
|
|
| 141 |
|
void DirectionalAtom::rotateBy(const RotMat3x3d& m) { |
| 147 |
|
Vector3d force; |
| 148 |
|
Vector3d torque; |
| 149 |
|
Vector3d myEuler; |
| 150 |
< |
RealType phi, theta, psi; |
| 150 |
> |
RealType phi, theta; |
| 151 |
> |
// RealType psi; |
| 152 |
|
RealType cphi, sphi, ctheta, stheta; |
| 153 |
|
Vector3d ephi; |
| 154 |
|
Vector3d etheta; |
| 160 |
|
|
| 161 |
|
phi = myEuler[0]; |
| 162 |
|
theta = myEuler[1]; |
| 163 |
< |
psi = myEuler[2]; |
| 163 |
> |
// psi = myEuler[2]; |
| 164 |
|
|
| 165 |
|
cphi = cos(phi); |
| 166 |
|
sphi = sin(phi); |
| 173 |
|
ephi[1] = 0.0; |
| 174 |
|
ephi[2] = 1.0; |
| 175 |
|
|
| 176 |
< |
etheta[0] = -sphi; |
| 177 |
< |
etheta[1] = cphi; |
| 178 |
< |
etheta[2] = 0.0; |
| 176 |
> |
//etheta[0] = -sphi; |
| 177 |
> |
//etheta[1] = cphi; |
| 178 |
> |
//etheta[2] = 0.0; |
| 179 |
|
|
| 180 |
+ |
etheta[0] = cphi; |
| 181 |
+ |
etheta[1] = sphi; |
| 182 |
+ |
etheta[2] = 0.0; |
| 183 |
+ |
|
| 184 |
|
epsi[0] = stheta * cphi; |
| 185 |
|
epsi[1] = stheta * sphi; |
| 186 |
|
epsi[2] = ctheta; |
