| 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 |
| 5 |
* redistribute this software in source and binary code form, provided |
| 6 |
* that the following conditions are met: |
| 7 |
* |
| 8 |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
* notice, this list of conditions and the following disclaimer. |
| 10 |
* |
| 11 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 12 |
* notice, this list of conditions and the following disclaimer in the |
| 13 |
* documentation and/or other materials provided with the |
| 14 |
* distribution. |
| 15 |
* |
| 16 |
* This software is provided "AS IS," without a warranty of any |
| 17 |
* kind. All express or implied conditions, representations and |
| 18 |
* warranties, including any implied warranty of merchantability, |
| 19 |
* fitness for a particular purpose or non-infringement, are hereby |
| 20 |
* excluded. The University of Notre Dame and its licensors shall not |
| 21 |
* be liable for any damages suffered by licensee as a result of |
| 22 |
* using, modifying or distributing the software or its |
| 23 |
* derivatives. In no event will the University of Notre Dame or its |
| 24 |
* licensors be liable for any lost revenue, profit or data, or for |
| 25 |
* direct, indirect, special, consequential, incidental or punitive |
| 26 |
* damages, however caused and regardless of the theory of liability, |
| 27 |
* arising out of the use of or inability to use software, even if the |
| 28 |
* University of Notre Dame has been advised of the possibility of |
| 29 |
* such damages. |
| 30 |
* |
| 31 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 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, 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 |
* |
| 41 |
* ConvexHull.cpp |
| 42 |
* |
| 43 |
* Purpose: To calculate a convex hull. |
| 44 |
*/ |
| 45 |
|
| 46 |
/* Standard includes independent of library */ |
| 47 |
|
| 48 |
#include <iostream> |
| 49 |
#include <fstream> |
| 50 |
#include <list> |
| 51 |
#include <algorithm> |
| 52 |
#include <iterator> |
| 53 |
#include "math/ConvexHull.hpp" |
| 54 |
#include "utils/simError.h" |
| 55 |
|
| 56 |
#ifdef IS_MPI |
| 57 |
#include <mpi.h> |
| 58 |
#endif |
| 59 |
|
| 60 |
#include "math/qhull.hpp" |
| 61 |
|
| 62 |
#ifdef HAVE_QHULL |
| 63 |
using namespace OpenMD; |
| 64 |
using namespace std; |
| 65 |
|
| 66 |
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") { |
| 67 |
} |
| 68 |
|
| 69 |
void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { |
| 70 |
|
| 71 |
int numpoints = bodydoubles.size(); |
| 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 |
vector<double> ptArray(numpoints*dim_); |
| 84 |
|
| 85 |
// Copy the positon vector into a points vector for qhull. |
| 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(); |
| 92 |
ptArray[dim_ * i + 1] = pos.y(); |
| 93 |
ptArray[dim_ * i + 2] = pos.z(); |
| 94 |
i++; |
| 95 |
} |
| 96 |
|
| 97 |
/* Clean up memory from previous convex hull calculations */ |
| 98 |
boolT ismalloc = False; |
| 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 |
|
| 105 |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 106 |
painCave.isFatal = 1; |
| 107 |
simError(); |
| 108 |
|
| 109 |
} //qh_new_qhull |
| 110 |
|
| 111 |
|
| 112 |
#ifdef IS_MPI |
| 113 |
//If we are doing the mpi version, set up some vectors for data communication |
| 114 |
|
| 115 |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 116 |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 117 |
int localHullSites = 0; |
| 118 |
|
| 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 |
vector<double> coords; |
| 125 |
vector<double> vels; |
| 126 |
vector<int> indexMap; |
| 127 |
vector<double> masses; |
| 128 |
|
| 129 |
FORALLvertices{ |
| 130 |
localHullSites++; |
| 131 |
|
| 132 |
int idx = qh_pointid(vertex->point); |
| 133 |
|
| 134 |
indexMap.push_back(idx); |
| 135 |
|
| 136 |
coords.push_back(ptArray[dim_ * idx]); |
| 137 |
coords.push_back(ptArray[dim_ * idx + 1]); |
| 138 |
coords.push_back(ptArray[dim_ * idx + 2]); |
| 139 |
|
| 140 |
StuntDouble* sd = bodydoubles[idx]; |
| 141 |
|
| 142 |
Vector3d vel = sd->getVel(); |
| 143 |
vels.push_back(vel.x()); |
| 144 |
vels.push_back(vel.y()); |
| 145 |
vels.push_back(vel.z()); |
| 146 |
|
| 147 |
masses.push_back(sd->getMass()); |
| 148 |
} |
| 149 |
|
| 150 |
MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0], |
| 151 |
1, MPI::INT); |
| 152 |
|
| 153 |
int globalHullSites = 0; |
| 154 |
for (int iproc = 0; iproc < nproc; iproc++){ |
| 155 |
globalHullSites += hullSitesOnProc[iproc]; |
| 156 |
coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc]; |
| 157 |
} |
| 158 |
|
| 159 |
displacements[0] = 0; |
| 160 |
vectorDisplacements[0] = 0; |
| 161 |
|
| 162 |
for (int iproc = 1; iproc < nproc; iproc++){ |
| 163 |
displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1]; |
| 164 |
vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
| 165 |
} |
| 166 |
|
| 167 |
vector<double> globalCoords(dim_ * globalHullSites); |
| 168 |
vector<double> globalVels(dim_ * globalHullSites); |
| 169 |
vector<double> globalMasses(globalHullSites); |
| 170 |
|
| 171 |
int count = coordsOnProc[myrank]; |
| 172 |
|
| 173 |
MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0], |
| 174 |
&coordsOnProc[0], &vectorDisplacements[0], |
| 175 |
MPI::DOUBLE); |
| 176 |
|
| 177 |
MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], |
| 178 |
&coordsOnProc[0], &vectorDisplacements[0], |
| 179 |
MPI::DOUBLE); |
| 180 |
|
| 181 |
MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE, |
| 182 |
&globalMasses[0], &hullSitesOnProc[0], |
| 183 |
&displacements[0], MPI::DOUBLE); |
| 184 |
|
| 185 |
// Free previous hull |
| 186 |
qh_freeqhull(!qh_ALL); |
| 187 |
qh_memfreeshort(&curlong, &totlong); |
| 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, |
| 200 |
"ConvexHull: Qhull failed to compute global convex hull"); |
| 201 |
painCave.isFatal = 1; |
| 202 |
simError(); |
| 203 |
|
| 204 |
} //qh_new_qhull |
| 205 |
|
| 206 |
#endif |
| 207 |
// commented out below, so comment out here also. |
| 208 |
// intPoint = qh interior_point; |
| 209 |
// RealType calcvol = 0.0; |
| 210 |
|
| 211 |
qh_triangulate (); |
| 212 |
int num_facets = qh num_facets; |
| 213 |
int num_vertices = qh num_vertices; |
| 214 |
|
| 215 |
FORALLfacets { |
| 216 |
Triangle face; |
| 217 |
//Qhull sets the unit normal in facet->normal |
| 218 |
Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 219 |
face.setUnitNormal(V3dNormal); |
| 220 |
|
| 221 |
RealType faceArea = qh_facetarea(facet); |
| 222 |
face.setArea(faceArea); |
| 223 |
|
| 224 |
vertices = qh_facet3vertex(facet); |
| 225 |
|
| 226 |
coordT *center = qh_getcenter(vertices); |
| 227 |
Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 228 |
face.setCentroid(V3dCentroid); |
| 229 |
|
| 230 |
Vector3d faceVel = V3Zero; |
| 231 |
Vector3d p[3]; |
| 232 |
RealType faceMass = 0.0; |
| 233 |
|
| 234 |
int ver = 0; |
| 235 |
|
| 236 |
FOREACHvertex_(vertices){ |
| 237 |
int id = qh_pointid(vertex->point); |
| 238 |
p[ver][0] = vertex->point[0]; |
| 239 |
p[ver][1] = vertex->point[1]; |
| 240 |
p[ver][2] = vertex->point[2]; |
| 241 |
Vector3d vel; |
| 242 |
RealType mass; |
| 243 |
|
| 244 |
#ifdef IS_MPI |
| 245 |
vel = Vector3d(globalVels[dim_ * id], |
| 246 |
globalVels[dim_ * id + 1], |
| 247 |
globalVels[dim_ * id + 2]); |
| 248 |
mass = globalMasses[id]; |
| 249 |
|
| 250 |
// localID will be between 0 and hullSitesOnProc[myrank] if we |
| 251 |
// own this guy. |
| 252 |
|
| 253 |
int localID = id - displacements[myrank]; |
| 254 |
|
| 255 |
|
| 256 |
if (localID >= 0 && localID < hullSitesOnProc[myrank]){ |
| 257 |
face.addVertexSD(bodydoubles[indexMap[localID]]); |
| 258 |
}else{ |
| 259 |
face.addVertexSD(NULL); |
| 260 |
} |
| 261 |
#else |
| 262 |
vel = bodydoubles[id]->getVel(); |
| 263 |
mass = bodydoubles[id]->getMass(); |
| 264 |
face.addVertexSD(bodydoubles[id]); |
| 265 |
#endif |
| 266 |
faceVel = faceVel + vel; |
| 267 |
faceMass = faceMass + mass; |
| 268 |
ver++; |
| 269 |
} //Foreachvertex |
| 270 |
|
| 271 |
face.addVertices(p[0], p[1], p[2]); |
| 272 |
face.setFacetMass(faceMass); |
| 273 |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 274 |
/* |
| 275 |
RealType comparea = face.computeArea(); |
| 276 |
realT calcarea = qh_facetarea (facet); |
| 277 |
Vector3d V3dCompNorm = -face.computeUnitNormal(); |
| 278 |
RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]); |
| 279 |
RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2]; |
| 280 |
cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl; |
| 281 |
calcvol += -dist*comparea/qh hull_dim; |
| 282 |
*/ |
| 283 |
Triangles_.push_back(face); |
| 284 |
qh_settempfree(&vertices); |
| 285 |
|
| 286 |
} //FORALLfacets |
| 287 |
|
| 288 |
qh_getarea(qh facet_list); |
| 289 |
volume_ = qh totvol; |
| 290 |
area_ = qh totarea; |
| 291 |
|
| 292 |
int index = 0; |
| 293 |
FORALLvertices { |
| 294 |
Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]); |
| 295 |
if (index == 0) { |
| 296 |
boxMax = point; |
| 297 |
boxMin = point; |
| 298 |
} else { |
| 299 |
for (int i = 0; i < 3; i++) { |
| 300 |
boxMax[i] = max(boxMax[i], point[i]); |
| 301 |
boxMin[i] = min(boxMin[i], point[i]); |
| 302 |
} |
| 303 |
} |
| 304 |
index++; |
| 305 |
} |
| 306 |
boundingBox_ = Mat3x3d(0.0); |
| 307 |
boundingBox_(0,0) = boxMax[0] - boxMin[0]; |
| 308 |
boundingBox_(1,1) = boxMax[1] - boxMin[1]; |
| 309 |
boundingBox_(2,2) = boxMax[2] - boxMin[2]; |
| 310 |
|
| 311 |
qh_freeqhull(!qh_ALL); |
| 312 |
qh_memfreeshort(&curlong, &totlong); |
| 313 |
if (curlong || totlong) { |
| 314 |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 315 |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 316 |
totlong, curlong); |
| 317 |
painCave.isFatal = 1; |
| 318 |
simError(); |
| 319 |
} |
| 320 |
} |
| 321 |
|
| 322 |
void ConvexHull::printHull(const string& geomFileName) { |
| 323 |
|
| 324 |
#ifdef IS_MPI |
| 325 |
if (worldRank == 0) { |
| 326 |
#endif |
| 327 |
FILE *newGeomFile; |
| 328 |
|
| 329 |
//create new .md file based on old .md file |
| 330 |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 331 |
qh_findgood_all(qh facet_list); |
| 332 |
for (int i = 0; i < qh_PRINTEND; i++) |
| 333 |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 334 |
|
| 335 |
fclose(newGeomFile); |
| 336 |
#ifdef IS_MPI |
| 337 |
} |
| 338 |
#endif |
| 339 |
} |
| 340 |
#endif //QHULL |
