| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 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 |
> |
|
| 57 |
> |
stuntdoubles_.resize(nObjects_[STUNTDOUBLE]); |
| 58 |
> |
bonds_.resize(nObjects_[BOND]); |
| 59 |
> |
bends_.resize(nObjects_[BEND]); |
| 60 |
> |
torsions_.resize(nObjects_[TORSION]); |
| 61 |
> |
inversions_.resize(nObjects_[INVERSION]); |
| 62 |
|
|
| 63 |
|
SimInfo::MoleculeIterator mi; |
| 64 |
+ |
Molecule::IntegrableObjectIterator ioi; |
| 65 |
+ |
Molecule::AtomIterator ai; |
| 66 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 67 |
+ |
Molecule::BondIterator bondIter; |
| 68 |
+ |
Molecule::BendIterator bendIter; |
| 69 |
+ |
Molecule::TorsionIterator torsionIter; |
| 70 |
+ |
Molecule::InversionIterator inversionIter; |
| 71 |
+ |
|
| 72 |
|
Molecule* mol; |
| 73 |
|
StuntDouble* sd; |
| 57 |
– |
Molecule::IntegrableObjectIterator ioi; |
| 58 |
– |
Molecule::AtomIterator ai; |
| 74 |
|
Atom* atom; |
| 60 |
– |
Molecule::RigidBodyIterator rbIter; |
| 75 |
|
RigidBody* rb; |
| 76 |
< |
|
| 76 |
> |
Bond* bond; |
| 77 |
> |
Bend* bend; |
| 78 |
> |
Torsion* torsion; |
| 79 |
> |
Inversion* inversion; |
| 80 |
> |
|
| 81 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 82 |
|
mol = info_->nextMolecule(mi)) { |
| 83 |
|
|
| 99 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 100 |
|
stuntdoubles_[rb->getGlobalIndex()] = rb; |
| 101 |
|
} |
| 102 |
< |
|
| 102 |
> |
|
| 103 |
> |
// These others are going to be inferred from the objects on the hull: |
| 104 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 105 |
> |
bond = mol->nextBond(bondIter)) { |
| 106 |
> |
bonds_[bond->getGlobalIndex()] = bond; |
| 107 |
> |
} |
| 108 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 109 |
> |
bend = mol->nextBend(bendIter)) { |
| 110 |
> |
bends_[bend->getGlobalIndex()] = bend; |
| 111 |
> |
} |
| 112 |
> |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 113 |
> |
torsion = mol->nextTorsion(torsionIter)) { |
| 114 |
> |
torsions_[torsion->getGlobalIndex()] = torsion; |
| 115 |
> |
} |
| 116 |
> |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 117 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 118 |
> |
inversions_[inversion->getGlobalIndex()] = inversion; |
| 119 |
> |
} |
| 120 |
> |
|
| 121 |
|
} |
| 122 |
|
#ifdef HAVE_QHULL |
| 123 |
|
surfaceMesh_ = new ConvexHull(); |
| 124 |
|
#endif |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
OpenMDBitSet HullFinder::findHull() { |
| 128 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 129 |
< |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 127 |
> |
HullFinder::~HullFinder() { |
| 128 |
> |
delete surfaceMesh_; |
| 129 |
> |
} |
| 130 |
> |
|
| 131 |
> |
SelectionSet HullFinder::findHull() { |
| 132 |
> |
SelectionSet ssResult(nObjects_); |
| 133 |
|
#ifdef HAVE_QHULL |
| 134 |
|
surfaceMesh_->computeHull(localSites_); |
| 135 |
|
#else |
| 136 |
|
sprintf( painCave.errMsg, |
| 137 |
|
"HullFinder : Hull calculation is not possible without libqhull.\n" |
| 138 |
|
"\tPlease rebuild OpenMD with qhull enabled."); |
| 139 |
< |
painCave.severity = OPENMD_ERROR; |
| 140 |
< |
painCave.isFatal = 1; |
| 141 |
< |
simError(); |
| 139 |
> |
painCave.severity = OPENMD_ERROR; |
| 140 |
> |
painCave.isFatal = 1; |
| 141 |
> |
simError(); |
| 142 |
|
#endif |
| 143 |
|
|
| 144 |
|
std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
| 106 |
– |
int nTriangles = sMesh.size(); |
| 145 |
|
// Loop over the mesh faces |
| 146 |
|
std::vector<Triangle>::iterator face; |
| 147 |
|
std::vector<StuntDouble*>::iterator vertex; |
| 154 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 155 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) { |
| 156 |
|
if ((*vertex) != NULL) { |
| 157 |
< |
bsResult.setBitOn((*vertex)->getGlobalIndex()); |
| 157 |
> |
ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex()); |
| 158 |
|
} |
| 159 |
|
} |
| 160 |
|
} |
| 161 |
< |
return bsResult; |
| 161 |
> |
return ssResult; |
| 162 |
|
} |
| 163 |
|
|
| 164 |
< |
OpenMDBitSet HullFinder::findHull(int frame) { |
| 165 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame); |
| 128 |
< |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 164 |
> |
SelectionSet HullFinder::findHull(int frame) { |
| 165 |
> |
SelectionSet ssResult(nObjects_); |
| 166 |
|
#ifdef HAVE_QHULL |
| 167 |
|
surfaceMesh_->computeHull(localSites_); |
| 168 |
|
#else |
| 175 |
|
#endif |
| 176 |
|
|
| 177 |
|
std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
| 141 |
– |
int nTriangles = sMesh.size(); |
| 178 |
|
// Loop over the mesh faces |
| 179 |
|
std::vector<Triangle>::iterator face; |
| 180 |
|
std::vector<StuntDouble*>::iterator vertex; |
| 187 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 188 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) { |
| 189 |
|
if ((*vertex) != NULL) { |
| 190 |
< |
bsResult.setBitOn((*vertex)->getGlobalIndex()); |
| 190 |
> |
ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex()); |
| 191 |
|
} |
| 192 |
|
} |
| 193 |
|
} |
| 194 |
< |
return bsResult; |
| 194 |
> |
surfaceArea_ = surfaceMesh_->getArea(); |
| 195 |
> |
return ssResult; |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
} |
