| 37 |
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#include "utils/MemoryUtils.hpp" |
| 38 |
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|
| 39 |
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namespace oopse { |
| 40 |
+ |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
| 41 |
+ |
: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
| 42 |
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|
| 43 |
+ |
} |
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+ |
|
| 45 |
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Molecule::~Molecule() { |
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|
| 47 |
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MemoryUtils::deleteVectorOfPointer(atoms_); |
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//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
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//[rigidAtoms.begin(), rigidAtoms.end()). |
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std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 115 |
< |
std::back_inserter(integrableObjects_)); |
| 115 |
> |
std::back_inserter(integrableObjects_.end())); |
| 116 |
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|
| 117 |
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if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
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//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
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sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
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|
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painCave.isFatal = 1; |
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+ |
simError(); |
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} |
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|
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integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
| 196 |
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++i; |
| 197 |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
| 198 |
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} |
| 191 |
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|
| 192 |
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void Molecule::calcForces() { |
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RigidBody* rb; |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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std::vector<RigidBody*>::iterator rbIter; |
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– |
std::vector<Bond*>::iterator bondIter;; |
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std::vector<Bend*>::iterator bendIter; |
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std::vector<Torsion*>::iterator torsionIter; |
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|
| 202 |
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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– |
rb->updateAtoms(); |
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} |
| 205 |
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|
| 206 |
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for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
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– |
bond->calcForce(); |
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} |
| 209 |
– |
|
| 210 |
– |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
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– |
bend->calcForce(); |
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– |
} |
| 213 |
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|
| 214 |
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for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 215 |
– |
torsion->calcForce(); |
| 216 |
– |
} |
| 217 |
– |
|
| 218 |
– |
} |
| 199 |
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|
| 220 |
– |
double Molecule::getPotential() { |
| 221 |
– |
//RigidBody* rb; |
| 222 |
– |
Bond* bond; |
| 223 |
– |
Bend* bend; |
| 224 |
– |
Torsion* torsion; |
| 225 |
– |
//std::vector<RigidBody*> rbIter; |
| 226 |
– |
std::vector<Bond*>::iterator bondIter;; |
| 227 |
– |
std::vector<Bend*>::iterator bendIter; |
| 228 |
– |
std::vector<Torsion*>::iterator torsionIter; |
| 200 |
|
|
| 230 |
– |
double potential = 0; |
| 231 |
– |
|
| 232 |
– |
//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 233 |
– |
// rb->updateAtoms(); |
| 234 |
– |
//} |
| 235 |
– |
|
| 236 |
– |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 237 |
– |
potential += bond->getPotential(); |
| 238 |
– |
} |
| 239 |
– |
|
| 240 |
– |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 241 |
– |
potential += bend->getPotential(); |
| 242 |
– |
} |
| 243 |
– |
|
| 244 |
– |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 245 |
– |
potential += torsion->getPotential(); |
| 246 |
– |
} |
| 247 |
– |
|
| 248 |
– |
return potential; |
| 249 |
– |
} |
| 250 |
– |
|
| 201 |
|
Vector3d Molecule::getCom() { |
| 202 |
|
StuntDouble* sd; |
| 203 |
|
std::vector<StuntDouble*>::iterator i; |
