| 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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "selection/HullFinder.hpp" |
| 53 |
|
|
| 54 |
|
SimInfo::MoleculeIterator mi; |
| 55 |
|
Molecule* mol; |
| 56 |
< |
StuntDouble* integrableObject; |
| 56 |
> |
StuntDouble* sd; |
| 57 |
|
Molecule::IntegrableObjectIterator ioi; |
| 58 |
|
Molecule::AtomIterator ai; |
| 59 |
|
Atom* atom; |
| 64 |
|
mol = info_->nextMolecule(mi)) { |
| 65 |
|
|
| 66 |
|
// Hull is constructed from all known integrable objects. |
| 67 |
< |
for (integrableObject = mol->beginIntegrableObject(ioi); |
| 68 |
< |
integrableObject != NULL; |
| 69 |
< |
integrableObject = mol->nextIntegrableObject(ioi)) { |
| 70 |
< |
localSites_.push_back(integrableObject); |
| 67 |
> |
for (sd = mol->beginIntegrableObject(ioi); |
| 68 |
> |
sd != NULL; |
| 69 |
> |
sd = mol->nextIntegrableObject(ioi)) { |
| 70 |
> |
localSites_.push_back(sd); |
| 71 |
|
} |
| 72 |
|
|
| 73 |
|
// selection can include atoms (which may be a subset of the IOs) |
| 85 |
|
} |
| 86 |
|
#ifdef HAVE_QHULL |
| 87 |
|
surfaceMesh_ = new ConvexHull(); |
| 87 |
– |
#else |
| 88 |
– |
sprintf( painCave.errMsg, |
| 89 |
– |
"Hullfinder error: Hull calculation not possible without libqhull.\n", |
| 90 |
– |
"Please rebuild with Qhull"); |
| 91 |
– |
painCave.severity = OPENMD_ERROR; |
| 92 |
– |
painCave.isFatal = 1; |
| 93 |
– |
simError(); |
| 94 |
– |
|
| 88 |
|
#endif |
| 89 |
|
} |
| 90 |
|
|
| 91 |
|
OpenMDBitSet HullFinder::findHull() { |
| 99 |
– |
StuntDouble* sd; |
| 92 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 93 |
|
OpenMDBitSet bsResult(nStuntDoubles_); |
| 94 |
< |
|
| 94 |
> |
#ifdef HAVE_QHULL |
| 95 |
|
surfaceMesh_->computeHull(localSites_); |
| 96 |
+ |
#else |
| 97 |
+ |
sprintf( painCave.errMsg, |
| 98 |
+ |
"HullFinder : Hull calculation is not possible without libqhull.\n" |
| 99 |
+ |
"\tPlease rebuild OpenMD with qhull enabled."); |
| 100 |
+ |
painCave.severity = OPENMD_ERROR; |
| 101 |
+ |
painCave.isFatal = 1; |
| 102 |
+ |
simError(); |
| 103 |
+ |
#endif |
| 104 |
+ |
|
| 105 |
|
std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
| 106 |
|
int nTriangles = sMesh.size(); |
| 107 |
|
// Loop over the mesh faces |
| 108 |
|
std::vector<Triangle>::iterator face; |
| 109 |
|
std::vector<StuntDouble*>::iterator vertex; |
| 110 |
|
|
| 111 |
+ |
// This will work in parallel because the triangles returned by the mesh |
| 112 |
+ |
// have a NULL stuntDouble if this processor doesn't own the |
| 113 |
+ |
|
| 114 |
|
for (face = sMesh.begin(); face != sMesh.end(); ++face) { |
| 115 |
|
Triangle thisTriangle = *face; |
| 116 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
