| 48 |
|
|
| 49 |
|
HullFinder::HullFinder(SimInfo* info) : info_(info) { |
| 50 |
|
|
| 51 |
< |
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 52 |
< |
stuntdoubles_.resize(nStuntDoubles_); |
| 51 |
> |
nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies()); |
| 52 |
> |
nObjects_.push_back(info_->getNGlobalBonds()); |
| 53 |
> |
nObjects_.push_back(info_->getNGlobalBends()); |
| 54 |
> |
nObjects_.push_back(info_->getNGlobalTorsions()); |
| 55 |
> |
nObjects_.push_back(info_->getNGlobalInversions()); |
| 56 |
> |
nObjects_.push_back(info_->getNGlobalMolecules()); |
| 57 |
> |
|
| 58 |
> |
stuntdoubles_.resize(nObjects_[STUNTDOUBLE]); |
| 59 |
> |
bonds_.resize(nObjects_[BOND]); |
| 60 |
> |
bends_.resize(nObjects_[BEND]); |
| 61 |
> |
torsions_.resize(nObjects_[TORSION]); |
| 62 |
> |
inversions_.resize(nObjects_[INVERSION]); |
| 63 |
> |
molecules_.resize(nObjects_[MOLECULE]); |
| 64 |
|
|
| 65 |
|
SimInfo::MoleculeIterator mi; |
| 66 |
+ |
Molecule::IntegrableObjectIterator ioi; |
| 67 |
+ |
Molecule::AtomIterator ai; |
| 68 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 69 |
+ |
Molecule::BondIterator bondIter; |
| 70 |
+ |
Molecule::BendIterator bendIter; |
| 71 |
+ |
Molecule::TorsionIterator torsionIter; |
| 72 |
+ |
Molecule::InversionIterator inversionIter; |
| 73 |
+ |
|
| 74 |
|
Molecule* mol; |
| 75 |
|
StuntDouble* sd; |
| 57 |
– |
Molecule::IntegrableObjectIterator ioi; |
| 58 |
– |
Molecule::AtomIterator ai; |
| 76 |
|
Atom* atom; |
| 60 |
– |
Molecule::RigidBodyIterator rbIter; |
| 77 |
|
RigidBody* rb; |
| 78 |
< |
|
| 78 |
> |
Bond* bond; |
| 79 |
> |
Bend* bend; |
| 80 |
> |
Torsion* torsion; |
| 81 |
> |
Inversion* inversion; |
| 82 |
> |
|
| 83 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 84 |
|
mol = info_->nextMolecule(mi)) { |
| 85 |
< |
|
| 85 |
> |
|
| 86 |
> |
molecules_[mol->getGlobalIndex()] = mol; |
| 87 |
> |
|
| 88 |
|
// Hull is constructed from all known integrable objects. |
| 89 |
|
for (sd = mol->beginIntegrableObject(ioi); |
| 90 |
|
sd != NULL; |
| 103 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 104 |
|
stuntdoubles_[rb->getGlobalIndex()] = rb; |
| 105 |
|
} |
| 106 |
< |
|
| 106 |
> |
|
| 107 |
> |
// These others are going to be inferred from the objects on the hull: |
| 108 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 109 |
> |
bond = mol->nextBond(bondIter)) { |
| 110 |
> |
bonds_[bond->getGlobalIndex()] = bond; |
| 111 |
> |
} |
| 112 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 113 |
> |
bend = mol->nextBend(bendIter)) { |
| 114 |
> |
bends_[bend->getGlobalIndex()] = bend; |
| 115 |
> |
} |
| 116 |
> |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 117 |
> |
torsion = mol->nextTorsion(torsionIter)) { |
| 118 |
> |
torsions_[torsion->getGlobalIndex()] = torsion; |
| 119 |
> |
} |
| 120 |
> |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 121 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 122 |
> |
inversions_[inversion->getGlobalIndex()] = inversion; |
| 123 |
> |
} |
| 124 |
> |
|
| 125 |
|
} |
| 126 |
|
#ifdef HAVE_QHULL |
| 127 |
|
surfaceMesh_ = new ConvexHull(); |
| 132 |
|
delete surfaceMesh_; |
| 133 |
|
} |
| 134 |
|
|
| 135 |
< |
OpenMDBitSet HullFinder::findHull() { |
| 136 |
< |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 135 |
> |
SelectionSet HullFinder::findHull() { |
| 136 |
> |
SelectionSet ssResult(nObjects_); |
| 137 |
|
#ifdef HAVE_QHULL |
| 138 |
|
surfaceMesh_->computeHull(localSites_); |
| 139 |
|
#else |
| 158 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 159 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) { |
| 160 |
|
if ((*vertex) != NULL) { |
| 161 |
< |
bsResult.setBitOn((*vertex)->getGlobalIndex()); |
| 161 |
> |
ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex()); |
| 162 |
|
} |
| 163 |
|
} |
| 164 |
|
} |
| 165 |
< |
return bsResult; |
| 165 |
> |
surfaceArea_ = surfaceMesh_->getArea(); |
| 166 |
> |
return ssResult; |
| 167 |
|
} |
| 168 |
|
|
| 169 |
< |
OpenMDBitSet HullFinder::findHull(int frame) { |
| 170 |
< |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 169 |
> |
SelectionSet HullFinder::findHull(int frame) { |
| 170 |
> |
SelectionSet ssResult(nObjects_); |
| 171 |
|
#ifdef HAVE_QHULL |
| 172 |
|
surfaceMesh_->computeHull(localSites_); |
| 173 |
|
#else |
| 192 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 193 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) { |
| 194 |
|
if ((*vertex) != NULL) { |
| 195 |
< |
bsResult.setBitOn((*vertex)->getGlobalIndex()); |
| 195 |
> |
ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex()); |
| 196 |
|
} |
| 197 |
|
} |
| 198 |
|
} |
| 199 |
|
surfaceArea_ = surfaceMesh_->getArea(); |
| 200 |
< |
return bsResult; |
| 200 |
> |
return ssResult; |
| 201 |
|
} |
| 202 |
|
|
| 203 |
|
} |
