| 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 <iostream> |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
Molecule::IntegrableObjectIterator ii; |
| 76 |
< |
StuntDouble* integrableObject; |
| 76 |
> |
StuntDouble* sd; |
| 77 |
|
int i; |
| 78 |
< |
for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
| 79 |
< |
integrableObject = mol->nextIntegrableObject(ii), ++i) { |
| 78 |
> |
for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; |
| 79 |
> |
sd = mol->nextIntegrableObject(ii), ++i) { |
| 80 |
|
|
| 81 |
|
newCoor = rotMat * refCoords[i]; |
| 82 |
|
newCoor += offset; |
| 83 |
|
|
| 84 |
< |
integrableObject->setPos(newCoor); |
| 85 |
< |
integrableObject->setVel(V3Zero); |
| 84 |
> |
sd->setPos(newCoor); |
| 85 |
> |
sd->setVel(V3Zero); |
| 86 |
|
|
| 87 |
< |
if(integrableObject->isDirectional()){ |
| 88 |
< |
integrableObject->setA(rotMat * integrableObject->getA()); |
| 89 |
< |
integrableObject->setJ(V3Zero); |
| 87 |
> |
if(sd->isDirectional()){ |
| 88 |
> |
sd->setA(rotMat * sd->getA()); |
| 89 |
> |
sd->setJ(V3Zero); |
| 90 |
|
} |
| 91 |
|
} |
| 92 |
|
} |
| 94 |
|
void MoLocator::calcRef( void ){ |
| 95 |
|
AtomStamp* currAtomStamp; |
| 96 |
|
RigidBodyStamp* rbStamp; |
| 97 |
< |
int nAtoms; |
| 97 |
> |
unsigned int nAtoms; |
| 98 |
|
int nRigidBodies; |
| 99 |
|
std::vector<RealType> mass; |
| 100 |
|
Vector3d coor; |
| 107 |
|
nAtoms= myStamp->getNAtoms(); |
| 108 |
|
nRigidBodies = myStamp->getNRigidBodies(); |
| 109 |
|
|
| 110 |
< |
for(size_t i=0; i<nAtoms; i++){ |
| 110 |
> |
for(unsigned int i = 0; i < nAtoms; i++){ |
| 111 |
|
|
| 112 |
|
currAtomStamp = myStamp->getAtomStamp(i); |
| 113 |
|
|
| 197 |
|
} |
| 198 |
|
|
| 199 |
|
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 200 |
< |
int nAtoms; |
| 200 |
> |
unsigned int nAtoms; |
| 201 |
|
RealType totMass = 0; |
| 202 |
|
nAtoms = molStamp->getNAtoms(); |
| 203 |
|
|
| 204 |
< |
for(size_t i = 0; i < nAtoms; i++) { |
| 204 |
> |
for(unsigned int i = 0; i < nAtoms; i++) { |
| 205 |
|
AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
| 206 |
|
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
| 207 |
|
} |
