| 32 |
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* research, please cite the appropriate papers when you publish your |
| 33 |
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* work. Good starting points are: |
| 34 |
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* |
| 35 |
< |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
< |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 35 |
> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 38 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
< |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 39 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 40 |
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* |
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* ConvexHull.cpp |
| 42 |
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* |
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< |
* Purpose: To calculate convexhull, hull volume libqhull. |
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< |
* |
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< |
* Created by Charles F. Vardeman II on 11 Dec 2006. |
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< |
* @author Charles F. Vardeman II |
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< |
* @version $Id$ |
| 48 |
< |
* |
| 43 |
> |
* Purpose: To calculate a convex hull. |
| 44 |
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*/ |
| 45 |
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|
| 46 |
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/* Standard includes independent of library */ |
| 61 |
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|
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#ifdef HAVE_QHULL |
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using namespace OpenMD; |
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+ |
using namespace std; |
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|
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ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
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} |
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|
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< |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
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< |
|
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> |
void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { |
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> |
|
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int numpoints = bodydoubles.size(); |
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< |
|
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> |
|
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Triangles_.clear(); |
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vertexT *vertex, **vertexp; |
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facetT *facet; |
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setT *vertices; |
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int curlong, totlong; |
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pointT *intPoint; |
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> |
|
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Vector3d boxMax; |
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> |
Vector3d boxMin; |
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std::vector<double> ptArray(numpoints*dim_); |
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> |
vector<double> ptArray(numpoints*dim_); |
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// Copy the positon vector into a points vector for qhull. |
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std::vector<StuntDouble*>::iterator SD; |
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vector<StuntDouble*>::iterator SD; |
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int i = 0; |
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|
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for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
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Vector3d pos = (*SD)->getPos(); |
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ptArray[dim_ * i] = pos.x(); |
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int myrank = MPI::COMM_WORLD.Get_rank(); |
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int localHullSites = 0; |
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std::vector<int> hullSitesOnProc(nproc, 0); |
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std::vector<int> coordsOnProc(nproc, 0); |
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std::vector<int> displacements(nproc, 0); |
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< |
std::vector<int> vectorDisplacements(nproc, 0); |
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> |
vector<int> hullSitesOnProc(nproc, 0); |
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> |
vector<int> coordsOnProc(nproc, 0); |
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> |
vector<int> displacements(nproc, 0); |
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> |
vector<int> vectorDisplacements(nproc, 0); |
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|
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< |
std::vector<double> coords; |
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< |
std::vector<double> vels; |
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< |
std::vector<int> indexMap; |
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< |
std::vector<double> masses; |
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> |
vector<double> coords; |
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> |
vector<double> vels; |
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> |
vector<int> indexMap; |
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> |
vector<double> masses; |
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|
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FORALLvertices{ |
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localHullSites++; |
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|
vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
| 165 |
|
} |
| 166 |
|
|
| 167 |
< |
std::vector<double> globalCoords(dim_ * globalHullSites); |
| 168 |
< |
std::vector<double> globalVels(dim_ * globalHullSites); |
| 169 |
< |
std::vector<double> globalMasses(globalHullSites); |
| 167 |
> |
vector<double> globalCoords(dim_ * globalHullSites); |
| 168 |
> |
vector<double> globalVels(dim_ * globalHullSites); |
| 169 |
> |
vector<double> globalMasses(globalHullSites); |
| 170 |
|
|
| 171 |
|
int count = coordsOnProc[myrank]; |
| 172 |
|
|
| 196 |
|
if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, |
| 197 |
|
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 198 |
|
|
| 199 |
< |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 199 |
> |
sprintf(painCave.errMsg, |
| 200 |
> |
"ConvexHull: Qhull failed to compute global convex hull"); |
| 201 |
|
painCave.isFatal = 1; |
| 202 |
|
simError(); |
| 203 |
|
|
| 204 |
|
} //qh_new_qhull |
| 205 |
|
|
| 206 |
|
#endif |
| 207 |
< |
|
| 208 |
< |
intPoint = qh interior_point; |
| 209 |
< |
RealType calcvol = 0.0; |
| 207 |
> |
// commented out below, so comment out here also. |
| 208 |
> |
// intPoint = qh interior_point; |
| 209 |
> |
// RealType calcvol = 0.0; |
| 210 |
|
FORALLfacets { |
| 211 |
|
Triangle face; |
| 212 |
|
//Qhull sets the unit normal in facet->normal |
| 272 |
|
Vector3d V3dCompNorm = -face.computeUnitNormal(); |
| 273 |
|
RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]); |
| 274 |
|
RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2]; |
| 275 |
< |
std::cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << std::endl; |
| 275 |
> |
cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl; |
| 276 |
|
calcvol += -dist*comparea/qh hull_dim; |
| 277 |
|
*/ |
| 278 |
|
Triangles_.push_back(face); |
| 283 |
|
qh_getarea(qh facet_list); |
| 284 |
|
volume_ = qh totvol; |
| 285 |
|
area_ = qh totarea; |
| 286 |
< |
// std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; |
| 286 |
> |
|
| 287 |
> |
int index = 0; |
| 288 |
> |
FORALLvertices { |
| 289 |
> |
Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]); |
| 290 |
> |
if (index == 0) { |
| 291 |
> |
boxMax = point; |
| 292 |
> |
boxMin = point; |
| 293 |
> |
} else { |
| 294 |
> |
for (int i = 0; i < 3; i++) { |
| 295 |
> |
boxMax[i] = max(boxMax[i], point[i]); |
| 296 |
> |
boxMin[i] = min(boxMin[i], point[i]); |
| 297 |
> |
} |
| 298 |
> |
} |
| 299 |
> |
index++; |
| 300 |
> |
} |
| 301 |
> |
boundingBox_ = Mat3x3d(0.0); |
| 302 |
> |
boundingBox_(0,0) = boxMax[0] - boxMin[0]; |
| 303 |
> |
boundingBox_(1,1) = boxMax[1] - boxMin[1]; |
| 304 |
> |
boundingBox_(2,2) = boxMax[2] - boxMin[2]; |
| 305 |
> |
|
| 306 |
|
qh_freeqhull(!qh_ALL); |
| 307 |
|
qh_memfreeshort(&curlong, &totlong); |
| 308 |
|
if (curlong || totlong) { |
| 314 |
|
} |
| 315 |
|
} |
| 316 |
|
|
| 317 |
< |
void ConvexHull::printHull(const std::string& geomFileName) { |
| 318 |
< |
|
| 317 |
> |
void ConvexHull::printHull(const string& geomFileName) { |
| 318 |
> |
|
| 319 |
|
#ifdef IS_MPI |
| 320 |
|
if (worldRank == 0) { |
| 321 |
|
#endif |
| 322 |
< |
FILE *newGeomFile; |
| 323 |
< |
|
| 324 |
< |
//create new .md file based on old .md file |
| 325 |
< |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 326 |
< |
qh_findgood_all(qh facet_list); |
| 327 |
< |
for (int i = 0; i < qh_PRINTEND; i++) |
| 328 |
< |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 329 |
< |
|
| 330 |
< |
fclose(newGeomFile); |
| 322 |
> |
FILE *newGeomFile; |
| 323 |
> |
|
| 324 |
> |
//create new .md file based on old .md file |
| 325 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 326 |
> |
qh_findgood_all(qh facet_list); |
| 327 |
> |
for (int i = 0; i < qh_PRINTEND; i++) |
| 328 |
> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 329 |
> |
|
| 330 |
> |
fclose(newGeomFile); |
| 331 |
|
#ifdef IS_MPI |
| 332 |
|
} |
| 333 |
|
#endif |
