| 1 |
< |
/* Copyright (c) 2008, 2009 The University of Notre Dame. All Rights Reserved. |
| 1 |
> |
/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved. |
| 2 |
|
* |
| 3 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 4 |
|
* non-exclusive, royalty free, license to use, modify and |
| 32 |
|
* research, please cite the appropriate papers when you publish your |
| 33 |
|
* work. Good starting points are: |
| 34 |
|
* |
| 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). |
| 38 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 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 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 40 |
|
* |
| 40 |
– |
* |
| 41 |
|
* ConvexHull.cpp |
| 42 |
|
* |
| 43 |
< |
* Purpose: To calculate convexhull, hull volume libqhull. |
| 44 |
< |
* |
| 45 |
< |
* Created by Charles F. Vardeman II on 11 Dec 2006. |
| 46 |
< |
* @author Charles F. Vardeman II |
| 47 |
< |
* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $ |
| 48 |
< |
* |
| 43 |
> |
* Purpose: To calculate a convex hull. |
| 44 |
|
*/ |
| 45 |
|
|
| 46 |
|
/* Standard includes independent of library */ |
| 57 |
|
#include <mpi.h> |
| 58 |
|
#endif |
| 59 |
|
|
| 60 |
< |
using namespace OpenMD; |
| 60 |
> |
#include "math/qhull.hpp" |
| 61 |
|
|
| 62 |
|
#ifdef HAVE_QHULL |
| 63 |
< |
extern "C" |
| 64 |
< |
{ |
| 70 |
< |
#include <qhull/qhull.h> |
| 71 |
< |
#include <qhull/mem.h> |
| 72 |
< |
#include <qhull/qset.h> |
| 73 |
< |
#include <qhull/geom.h> |
| 74 |
< |
#include <qhull/merge.h> |
| 75 |
< |
#include <qhull/poly.h> |
| 76 |
< |
#include <qhull/io.h> |
| 77 |
< |
#include <qhull/stat.h> |
| 78 |
< |
} |
| 63 |
> |
using namespace OpenMD; |
| 64 |
> |
using namespace std; |
| 65 |
|
|
| 66 |
|
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
| 67 |
|
} |
| 68 |
|
|
| 69 |
< |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 70 |
< |
|
| 69 |
> |
void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { |
| 70 |
> |
|
| 71 |
|
int numpoints = bodydoubles.size(); |
| 72 |
< |
|
| 72 |
> |
|
| 73 |
|
Triangles_.clear(); |
| 74 |
|
|
| 75 |
|
vertexT *vertex, **vertexp; |
| 76 |
|
facetT *facet; |
| 77 |
|
setT *vertices; |
| 78 |
|
int curlong, totlong; |
| 79 |
+ |
|
| 80 |
+ |
Vector3d boxMax; |
| 81 |
+ |
Vector3d boxMin; |
| 82 |
|
|
| 83 |
< |
std::vector<double> ptArray(numpoints*dim_); |
| 83 |
> |
vector<double> ptArray(numpoints*dim_); |
| 84 |
|
|
| 85 |
|
// Copy the positon vector into a points vector for qhull. |
| 86 |
< |
std::vector<StuntDouble*>::iterator SD; |
| 86 |
> |
vector<StuntDouble*>::iterator SD; |
| 87 |
|
int i = 0; |
| 88 |
+ |
|
| 89 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 90 |
|
Vector3d pos = (*SD)->getPos(); |
| 91 |
|
ptArray[dim_ * i] = pos.x(); |
| 94 |
|
i++; |
| 95 |
|
} |
| 96 |
|
|
| 97 |
+ |
/* Clean up memory from previous convex hull calculations */ |
| 98 |
|
boolT ismalloc = False; |
| 108 |
– |
/* Clean up memory from previous convex hull calculations*/ |
| 99 |
|
|
| 100 |
+ |
/* compute the hull for our local points (or all the points for single |
| 101 |
+ |
processor versions) */ |
| 102 |
|
if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
| 103 |
|
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 104 |
< |
|
| 104 |
> |
|
| 105 |
|
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 106 |
|
painCave.isFatal = 1; |
| 107 |
|
simError(); |
| 116 |
|
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 117 |
|
int localHullSites = 0; |
| 118 |
|
|
| 119 |
< |
std::vector<int> hullSitesOnProc(nproc, 0); |
| 120 |
< |
std::vector<int> coordsOnProc(nproc, 0); |
| 121 |
< |
std::vector<int> displacements(nproc, 0); |
| 122 |
< |
std::vector<int> vectorDisplacements(nproc, 0); |
| 119 |
> |
vector<int> hullSitesOnProc(nproc, 0); |
| 120 |
> |
vector<int> coordsOnProc(nproc, 0); |
| 121 |
> |
vector<int> displacements(nproc, 0); |
| 122 |
> |
vector<int> vectorDisplacements(nproc, 0); |
| 123 |
|
|
| 124 |
< |
std::vector<double> coords; |
| 125 |
< |
std::vector<double> vels; |
| 126 |
< |
std::vector<int> indexMap; |
| 127 |
< |
std::vector<double> masses; |
| 124 |
> |
vector<double> coords; |
| 125 |
> |
vector<double> vels; |
| 126 |
> |
vector<int> indexMap; |
| 127 |
> |
vector<double> masses; |
| 128 |
|
|
| 129 |
|
FORALLvertices{ |
| 130 |
|
localHullSites++; |
| 164 |
|
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 |
|
|
| 185 |
|
// Free previous hull |
| 186 |
|
qh_freeqhull(!qh_ALL); |
| 187 |
|
qh_memfreeshort(&curlong, &totlong); |
| 188 |
< |
if (curlong || totlong) |
| 189 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 190 |
< |
<< totlong << curlong << std::endl; |
| 188 |
> |
if (curlong || totlong) { |
| 189 |
> |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 190 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 191 |
> |
totlong, curlong); |
| 192 |
> |
painCave.isFatal = 1; |
| 193 |
> |
simError(); |
| 194 |
> |
} |
| 195 |
|
|
| 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 |
< |
|
| 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 |
< |
|
| 212 |
> |
//Qhull sets the unit normal in facet->normal |
| 213 |
|
Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 214 |
< |
face.setNormal(V3dNormal); |
| 214 |
> |
face.setUnitNormal(V3dNormal); |
| 215 |
|
|
| 216 |
|
RealType faceArea = qh_facetarea(facet); |
| 217 |
|
face.setArea(faceArea); |
| 233 |
|
p[ver][0] = vertex->point[0]; |
| 234 |
|
p[ver][1] = vertex->point[1]; |
| 235 |
|
p[ver][2] = vertex->point[2]; |
| 237 |
– |
|
| 236 |
|
Vector3d vel; |
| 237 |
|
RealType mass; |
| 238 |
|
|
| 247 |
|
|
| 248 |
|
int localID = id - displacements[myrank]; |
| 249 |
|
|
| 250 |
< |
if (localID >= 0 && localID < hullSitesOnProc[myrank]) |
| 250 |
> |
|
| 251 |
> |
if (localID >= 0 && localID < hullSitesOnProc[myrank]){ |
| 252 |
|
face.addVertexSD(bodydoubles[indexMap[localID]]); |
| 253 |
< |
|
| 253 |
> |
}else{ |
| 254 |
> |
face.addVertexSD(NULL); |
| 255 |
> |
} |
| 256 |
|
#else |
| 257 |
|
vel = bodydoubles[id]->getVel(); |
| 258 |
|
mass = bodydoubles[id]->getMass(); |
| 259 |
|
face.addVertexSD(bodydoubles[id]); |
| 260 |
< |
#endif |
| 260 |
< |
|
| 260 |
> |
#endif |
| 261 |
|
faceVel = faceVel + vel; |
| 262 |
|
faceMass = faceMass + mass; |
| 263 |
|
ver++; |
| 265 |
|
|
| 266 |
|
face.addVertices(p[0], p[1], p[2]); |
| 267 |
|
face.setFacetMass(faceMass); |
| 268 |
< |
face.setFacetVelocity(faceVel/3.0); |
| 268 |
> |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 269 |
> |
/* |
| 270 |
> |
RealType comparea = face.computeArea(); |
| 271 |
> |
realT calcarea = qh_facetarea (facet); |
| 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 |
> |
cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl; |
| 276 |
> |
calcvol += -dist*comparea/qh hull_dim; |
| 277 |
> |
*/ |
| 278 |
|
Triangles_.push_back(face); |
| 279 |
|
qh_settempfree(&vertices); |
| 280 |
|
|
| 284 |
|
volume_ = qh totvol; |
| 285 |
|
area_ = qh totarea; |
| 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) |
| 309 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 310 |
< |
<< totlong << curlong << std::endl; |
| 308 |
> |
if (curlong || totlong) { |
| 309 |
> |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 310 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 311 |
> |
totlong, curlong); |
| 312 |
> |
painCave.isFatal = 1; |
| 313 |
> |
simError(); |
| 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 |
