| 96 |
|
|
| 97 |
|
void Molecule::complete() { |
| 98 |
|
|
| 99 |
– |
std::set<Atom*> allAtoms; |
| 100 |
– |
allAtoms.insert(atoms_.begin(), atoms_.end()); |
| 101 |
– |
|
| 99 |
|
std::set<Atom*> rigidAtoms; |
| 100 |
|
RigidBody* rb; |
| 101 |
|
std::vector<RigidBody*>::iterator rbIter; |
| 105 |
|
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
| 106 |
|
} |
| 107 |
|
|
| 108 |
+ |
Atom* atom; |
| 109 |
+ |
AtomIterator ai; |
| 110 |
+ |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 111 |
+ |
if (rigidAtoms.find(*ai) != rigidAtoms.end()) { |
| 112 |
+ |
integrableObjects_.push_back(*ai); |
| 113 |
+ |
} |
| 114 |
+ |
} |
| 115 |
+ |
|
| 116 |
|
//find all free atoms (which do not belong to rigid bodies) |
| 117 |
|
//performs the "difference" operation from set theory, the output range contains a copy of every |
| 118 |
|
//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
| 119 |
|
//[rigidAtoms.begin(), rigidAtoms.end()). |
| 120 |
< |
std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 121 |
< |
std::back_inserter(integrableObjects_)); |
| 120 |
> |
//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 121 |
> |
// std::back_inserter(integrableObjects_)); |
| 122 |
|
|
| 123 |
< |
if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 124 |
< |
//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 125 |
< |
sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
| 123 |
> |
//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 124 |
> |
// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 125 |
> |
// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
| 126 |
> |
// |
| 127 |
> |
// painCave.isFatal = 1; |
| 128 |
> |
// simError(); |
| 129 |
> |
//} |
| 130 |
|
|
| 122 |
– |
painCave.isFatal = 1; |
| 123 |
– |
simError(); |
| 124 |
– |
} |
| 125 |
– |
|
| 131 |
|
integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
| 132 |
|
} |
| 133 |
|
|
| 202 |
|
++i; |
| 203 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 204 |
|
} |
| 205 |
+ |
|
| 206 |
+ |
double Molecule::getMass() { |
| 207 |
+ |
StuntDouble* sd; |
| 208 |
+ |
std::vector<StuntDouble*>::iterator i; |
| 209 |
+ |
double mass = 0.0; |
| 210 |
+ |
|
| 211 |
+ |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 212 |
+ |
mass += sd->getMass(); |
| 213 |
+ |
} |
| 214 |
|
|
| 215 |
+ |
return mass; |
| 216 |
|
|
| 217 |
+ |
} |
| 218 |
+ |
|
| 219 |
|
Vector3d Molecule::getCom() { |
| 220 |
|
StuntDouble* sd; |
| 221 |
|
std::vector<StuntDouble*>::iterator i; |
| 262 |
|
return velCom; |
| 263 |
|
} |
| 264 |
|
|
| 265 |
+ |
double Molecule::getPotential() { |
| 266 |
+ |
|
| 267 |
+ |
Bond* bond; |
| 268 |
+ |
Bend* bend; |
| 269 |
+ |
Torsion* torsion; |
| 270 |
+ |
Molecule::BondIterator bondIter;; |
| 271 |
+ |
Molecule::BendIterator bendIter; |
| 272 |
+ |
Molecule::TorsionIterator torsionIter; |
| 273 |
+ |
|
| 274 |
+ |
double potential = 0.0; |
| 275 |
+ |
|
| 276 |
+ |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 277 |
+ |
potential += bond->getPotential(); |
| 278 |
+ |
} |
| 279 |
+ |
|
| 280 |
+ |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 281 |
+ |
potential += bend->getPotential(); |
| 282 |
+ |
} |
| 283 |
+ |
|
| 284 |
+ |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 285 |
+ |
potential += torsion->getPotential(); |
| 286 |
+ |
} |
| 287 |
+ |
|
| 288 |
+ |
return potential; |
| 289 |
+ |
|
| 290 |
+ |
} |
| 291 |
+ |
|
| 292 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 293 |
|
o << std::endl; |
| 294 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
