| 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). |
| 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 <cstring> |
| 75 |
|
AtomInfo* atomInfo = new AtomInfo(); |
| 76 |
|
atomInfo->atomTypeName = name; |
| 77 |
|
atomInfo->pos = refPos; |
| 78 |
< |
atomInfo->dipole = refVec; |
| 78 |
> |
atomInfo->vec = refVec; |
| 79 |
|
atomInfo->hasVector = true; |
| 80 |
|
sites_->addAtomInfo(atomInfo); |
| 81 |
|
} |
| 83 |
|
void ReplacementVisitor::visit(DirectionalAtom *datom) { |
| 84 |
|
std::vector<AtomInfo*>atoms; |
| 85 |
|
|
| 86 |
< |
RotMat3x3d rotMatrix; |
| 87 |
< |
RotMat3x3d rotTrans; |
| 88 |
< |
AtomInfo * atomInfo; |
| 86 |
> |
RotMat3x3d A; |
| 87 |
> |
RotMat3x3d Atrans; |
| 88 |
> |
Mat3x3d I; |
| 89 |
|
Vector3d pos; |
| 90 |
+ |
Vector3d vel; |
| 91 |
+ |
Vector3d frc; |
| 92 |
+ |
Vector3d trq; |
| 93 |
+ |
Vector3d j; |
| 94 |
+ |
Mat3x3d skewMat; |
| 95 |
+ |
|
| 96 |
|
Vector3d newVec; |
| 97 |
< |
Quat4d q; |
| 97 |
> |
AtomInfo * atomInfo; |
| 98 |
|
AtomData * atomData; |
| 99 |
|
GenericData *data; |
| 100 |
|
bool haveAtomData; |
| 118 |
|
atomData = new AtomData; |
| 119 |
|
haveAtomData = false; |
| 120 |
|
} |
| 121 |
< |
|
| 115 |
< |
|
| 121 |
> |
|
| 122 |
|
pos = datom->getPos(); |
| 123 |
< |
q = datom->getQ(); |
| 124 |
< |
rotMatrix = datom->getA(); |
| 123 |
> |
vel = datom->getVel(); |
| 124 |
> |
|
| 125 |
> |
j = datom->getJ(); |
| 126 |
> |
I = datom->getI(); |
| 127 |
> |
A = datom->getA(); |
| 128 |
> |
|
| 129 |
> |
skewMat(0, 0) = 0; |
| 130 |
> |
skewMat(0, 1) = j[2] / I(2, 2); |
| 131 |
> |
skewMat(0, 2) = -j[1] / I(1, 1); |
| 132 |
> |
skewMat(1, 0) = -j[2] / I(2, 2); |
| 133 |
> |
skewMat(1, 1) = 0; |
| 134 |
> |
skewMat(1, 2) = j[0] / I(0, 0); |
| 135 |
> |
skewMat(2, 0) = j[1] / I(1, 1); |
| 136 |
> |
skewMat(2, 1) = -j[0] / I(0, 0); |
| 137 |
> |
skewMat(2, 2) = 0; |
| 138 |
> |
Mat3x3d mat = (A * skewMat).transpose(); |
| 139 |
|
|
| 140 |
|
// We need A^T to convert from body-fixed to space-fixed: |
| 141 |
< |
rotTrans = rotMatrix.transpose(); |
| 141 |
> |
Atrans = A.transpose(); |
| 142 |
|
|
| 143 |
|
AtomInfo* siteInfo; |
| 144 |
|
std::vector<AtomInfo*>::iterator iter; |
| 146 |
|
for( siteInfo = sites_->beginAtomInfo(iter); siteInfo; |
| 147 |
|
siteInfo = sites_->nextAtomInfo(iter) ) { |
| 148 |
|
|
| 149 |
< |
newVec = rotTrans * siteInfo->pos; |
| 149 |
> |
newVec = Atrans * siteInfo->pos; |
| 150 |
|
|
| 151 |
|
atomInfo = new AtomInfo; |
| 152 |
|
atomInfo->atomTypeName = siteInfo->atomTypeName; |
| 153 |
|
atomInfo->pos = pos + newVec; |
| 154 |
|
|
| 155 |
|
if (siteInfo->hasVector) { |
| 156 |
< |
newVec = rotTrans * siteInfo->dipole; |
| 157 |
< |
atomInfo->dipole = newVec; |
| 156 |
> |
newVec = Atrans * siteInfo->vec; |
| 157 |
> |
atomInfo->vec = newVec; |
| 158 |
|
} else { |
| 159 |
< |
atomInfo->dipole = V3Zero; |
| 159 |
> |
atomInfo->vec = V3Zero; |
| 160 |
|
} |
| 161 |
< |
|
| 161 |
> |
|
| 162 |
> |
atomInfo->vel = vel + mat * siteInfo->pos; |
| 163 |
> |
atomInfo->hasVelocity = true; |
| 164 |
> |
|
| 165 |
|
atomData->addAtomInfo(atomInfo); |
| 166 |
|
} |
| 167 |
|
if (!haveAtomData) { |
