| 112 |
|
//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
| 113 |
|
//[rigidAtoms.begin(), rigidAtoms.end()). |
| 114 |
|
std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 115 |
< |
std::back_inserter(integrableObjects_)); |
| 115 |
> |
std::back_inserter(integrableObjects_.end())); |
| 116 |
|
|
| 117 |
|
if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 118 |
|
//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 196 |
|
++i; |
| 197 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 198 |
|
} |
| 199 |
– |
|
| 200 |
– |
void Molecule::calcForces() { |
| 201 |
– |
RigidBody* rb; |
| 202 |
– |
Bond* bond; |
| 203 |
– |
Bend* bend; |
| 204 |
– |
Torsion* torsion; |
| 205 |
– |
std::vector<RigidBody*>::iterator rbIter; |
| 206 |
– |
std::vector<Bond*>::iterator bondIter;; |
| 207 |
– |
std::vector<Bend*>::iterator bendIter; |
| 208 |
– |
std::vector<Torsion*>::iterator torsionIter; |
| 209 |
– |
|
| 210 |
– |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 211 |
– |
rb->updateAtoms(); |
| 212 |
– |
} |
| 213 |
– |
|
| 214 |
– |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 215 |
– |
bond->calc_forces(); |
| 216 |
– |
} |
| 217 |
– |
|
| 218 |
– |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 219 |
– |
bend->calc_forces(); |
| 220 |
– |
} |
| 221 |
– |
|
| 222 |
– |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 223 |
– |
torsion->calc_forces(); |
| 224 |
– |
} |
| 225 |
– |
|
| 226 |
– |
} |
| 227 |
– |
|
| 228 |
– |
double Molecule::getPotential() { |
| 229 |
– |
//RigidBody* rb; |
| 230 |
– |
Bond* bond; |
| 231 |
– |
Bend* bend; |
| 232 |
– |
Torsion* torsion; |
| 233 |
– |
//std::vector<RigidBody*> rbIter; |
| 234 |
– |
std::vector<Bond*>::iterator bondIter;; |
| 235 |
– |
std::vector<Bend*>::iterator bendIter; |
| 236 |
– |
std::vector<Torsion*>::iterator torsionIter; |
| 199 |
|
|
| 238 |
– |
double potential = 0; |
| 239 |
– |
|
| 240 |
– |
//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 241 |
– |
// rb->updateAtoms(); |
| 242 |
– |
//} |
| 200 |
|
|
| 244 |
– |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 245 |
– |
potential += bond->get_potential(); |
| 246 |
– |
} |
| 247 |
– |
|
| 248 |
– |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 249 |
– |
potential += bend->get_potential(); |
| 250 |
– |
} |
| 251 |
– |
|
| 252 |
– |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 253 |
– |
potential += torsion->get_potential(); |
| 254 |
– |
} |
| 255 |
– |
|
| 256 |
– |
return potential; |
| 257 |
– |
} |
| 258 |
– |
|
| 201 |
|
Vector3d Molecule::getCom() { |
| 202 |
|
StuntDouble* sd; |
| 203 |
|
std::vector<StuntDouble*>::iterator i; |
