| 1 |
< |
/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
| 1 |
> |
/* Copyright (c) 2008, 2009 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. Acknowledgement of the program authors must be made in any |
| 9 |
< |
* publication of scientific results based in part on use of the |
| 10 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 11 |
< |
* the article in which the program was described (Matthew |
| 12 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 13 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 14 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 15 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 16 |
< |
* |
| 17 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 8 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
|
* notice, this list of conditions and the following disclaimer. |
| 10 |
|
* |
| 11 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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, 24107 (2008). |
| 38 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
|
* |
| 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 1.3 2007-05-30 18:47:03 chuckv Exp $ |
| 47 |
> |
* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $ |
| 48 |
|
* |
| 49 |
|
*/ |
| 50 |
|
|
| 51 |
+ |
/* Standard includes independent of library */ |
| 52 |
+ |
|
| 53 |
|
#include <iostream> |
| 54 |
|
#include <fstream> |
| 55 |
+ |
#include <list> |
| 56 |
+ |
#include <algorithm> |
| 57 |
+ |
#include <iterator> |
| 58 |
|
#include "math/ConvexHull.hpp" |
| 59 |
+ |
#include "utils/simError.h" |
| 60 |
|
|
| 61 |
< |
using namespace oopse; |
| 61 |
> |
#ifdef IS_MPI |
| 62 |
> |
#include <mpi.h> |
| 63 |
> |
#endif |
| 64 |
|
|
| 65 |
< |
ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") { |
| 65 |
> |
using namespace OpenMD; |
| 66 |
> |
|
| 67 |
> |
#ifdef HAVE_QHULL |
| 68 |
> |
extern "C" |
| 69 |
> |
{ |
| 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 |
|
} |
| 79 |
|
|
| 80 |
< |
bool ConvexHull::genHull(std::vector<Vector3d> pos) { |
| 81 |
< |
FILE *outfile = stdout; |
| 82 |
< |
FILE *errfile = stderr; |
| 80 |
> |
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
| 81 |
> |
} |
| 82 |
> |
|
| 83 |
> |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 84 |
> |
|
| 85 |
> |
int numpoints = bodydoubles.size(); |
| 86 |
> |
|
| 87 |
> |
Triangles_.clear(); |
| 88 |
> |
|
| 89 |
> |
vertexT *vertex, **vertexp; |
| 90 |
|
facetT *facet; |
| 91 |
< |
int exitcode; |
| 92 |
< |
boolT ismalloc = False; |
| 66 |
< |
int curlong,totlong; |
| 91 |
> |
setT *vertices; |
| 92 |
> |
int curlong, totlong; |
| 93 |
|
|
| 94 |
< |
int numpoints = pos.size(); |
| 95 |
< |
|
| 96 |
< |
coordT points[numpoints][dim_]; |
| 97 |
< |
|
| 98 |
< |
for (int i=0; i<numpoints; i++) { |
| 99 |
< |
points[i][0] = pos[i][0]; |
| 100 |
< |
points[i][1] = pos[i][1]; |
| 101 |
< |
points[i][2] = pos[i][2]; |
| 94 |
> |
std::vector<double> ptArray(numpoints*dim_); |
| 95 |
> |
|
| 96 |
> |
// Copy the positon vector into a points vector for qhull. |
| 97 |
> |
std::vector<StuntDouble*>::iterator SD; |
| 98 |
> |
int i = 0; |
| 99 |
> |
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 100 |
> |
Vector3d pos = (*SD)->getPos(); |
| 101 |
> |
ptArray[dim_ * i] = pos.x(); |
| 102 |
> |
ptArray[dim_ * i + 1] = pos.y(); |
| 103 |
> |
ptArray[dim_ * i + 2] = pos.z(); |
| 104 |
> |
i++; |
| 105 |
|
} |
| 106 |
|
|
| 107 |
+ |
boolT ismalloc = False; |
| 108 |
+ |
/* Clean up memory from previous convex hull calculations*/ |
| 109 |
|
|
| 110 |
+ |
if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
| 111 |
+ |
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 112 |
+ |
|
| 113 |
+ |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 114 |
+ |
painCave.isFatal = 1; |
| 115 |
+ |
simError(); |
| 116 |
+ |
|
| 117 |
+ |
} //qh_new_qhull |
| 118 |
+ |
|
| 119 |
+ |
|
| 120 |
+ |
#ifdef IS_MPI |
| 121 |
+ |
//If we are doing the mpi version, set up some vectors for data communication |
| 122 |
|
|
| 123 |
< |
qh_initflags (const_cast<char *>(options_.c_str())); |
| 124 |
< |
qh_init_B (points[0], numpoints, dim_, ismalloc); |
| 125 |
< |
qh_qhull(); |
| 126 |
< |
qh_check_output(); |
| 123 |
> |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 124 |
> |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 125 |
> |
int localHullSites = 0; |
| 126 |
> |
|
| 127 |
> |
std::vector<int> hullSitesOnProc(nproc, 0); |
| 128 |
> |
std::vector<int> coordsOnProc(nproc, 0); |
| 129 |
> |
std::vector<int> displacements(nproc, 0); |
| 130 |
> |
std::vector<int> vectorDisplacements(nproc, 0); |
| 131 |
> |
|
| 132 |
> |
std::vector<double> coords; |
| 133 |
> |
std::vector<double> vels; |
| 134 |
> |
std::vector<int> indexMap; |
| 135 |
> |
std::vector<double> masses; |
| 136 |
> |
|
| 137 |
> |
FORALLvertices{ |
| 138 |
> |
localHullSites++; |
| 139 |
> |
|
| 140 |
> |
int idx = qh_pointid(vertex->point); |
| 141 |
> |
|
| 142 |
> |
indexMap.push_back(idx); |
| 143 |
> |
|
| 144 |
> |
coords.push_back(ptArray[dim_ * idx]); |
| 145 |
> |
coords.push_back(ptArray[dim_ * idx + 1]); |
| 146 |
> |
coords.push_back(ptArray[dim_ * idx + 2]); |
| 147 |
> |
|
| 148 |
> |
StuntDouble* sd = bodydoubles[idx]; |
| 149 |
> |
|
| 150 |
> |
Vector3d vel = sd->getVel(); |
| 151 |
> |
vels.push_back(vel.x()); |
| 152 |
> |
vels.push_back(vel.y()); |
| 153 |
> |
vels.push_back(vel.z()); |
| 154 |
> |
|
| 155 |
> |
masses.push_back(sd->getMass()); |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
> |
MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0], |
| 159 |
> |
1, MPI::INT); |
| 160 |
> |
|
| 161 |
> |
int globalHullSites = 0; |
| 162 |
> |
for (int iproc = 0; iproc < nproc; iproc++){ |
| 163 |
> |
globalHullSites += hullSitesOnProc[iproc]; |
| 164 |
> |
coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc]; |
| 165 |
> |
} |
| 166 |
> |
|
| 167 |
> |
displacements[0] = 0; |
| 168 |
> |
vectorDisplacements[0] = 0; |
| 169 |
|
|
| 170 |
+ |
for (int iproc = 1; iproc < nproc; iproc++){ |
| 171 |
+ |
displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1]; |
| 172 |
+ |
vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
| 173 |
+ |
} |
| 174 |
+ |
|
| 175 |
+ |
std::vector<double> globalCoords(dim_ * globalHullSites); |
| 176 |
+ |
std::vector<double> globalVels(dim_ * globalHullSites); |
| 177 |
+ |
std::vector<double> globalMasses(globalHullSites); |
| 178 |
+ |
|
| 179 |
+ |
int count = coordsOnProc[myrank]; |
| 180 |
|
|
| 181 |
< |
|
| 182 |
< |
qh_getarea(qh facet_list); |
| 183 |
< |
volume_ = qh totvol; |
| 184 |
< |
area_ = qh totarea; |
| 185 |
< |
|
| 186 |
< |
|
| 187 |
< |
|
| 181 |
> |
MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0], |
| 182 |
> |
&coordsOnProc[0], &vectorDisplacements[0], |
| 183 |
> |
MPI::DOUBLE); |
| 184 |
> |
|
| 185 |
> |
MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], |
| 186 |
> |
&coordsOnProc[0], &vectorDisplacements[0], |
| 187 |
> |
MPI::DOUBLE); |
| 188 |
> |
|
| 189 |
> |
MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE, |
| 190 |
> |
&globalMasses[0], &hullSitesOnProc[0], |
| 191 |
> |
&displacements[0], MPI::DOUBLE); |
| 192 |
> |
|
| 193 |
> |
// Free previous hull |
| 194 |
|
qh_freeqhull(!qh_ALL); |
| 195 |
< |
qh_memfreeshort (&curlong, &totlong); |
| 195 |
> |
qh_memfreeshort(&curlong, &totlong); |
| 196 |
|
if (curlong || totlong) |
| 197 |
< |
fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n", |
| 198 |
< |
totlong, curlong); |
| 197 |
> |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 198 |
> |
<< totlong << curlong << std::endl; |
| 199 |
|
|
| 200 |
< |
|
| 201 |
< |
return true; |
| 202 |
< |
} |
| 200 |
> |
if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, |
| 201 |
> |
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 202 |
> |
|
| 203 |
> |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 204 |
> |
painCave.isFatal = 1; |
| 205 |
> |
simError(); |
| 206 |
> |
|
| 207 |
> |
} //qh_new_qhull |
| 208 |
|
|
| 209 |
+ |
#endif |
| 210 |
|
|
| 211 |
< |
RealType ConvexHull::getVolume() { |
| 212 |
< |
return volume_; |
| 211 |
> |
FORALLfacets { |
| 212 |
> |
Triangle face; |
| 213 |
> |
|
| 214 |
> |
Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 215 |
> |
face.setNormal(V3dNormal); |
| 216 |
> |
|
| 217 |
> |
RealType faceArea = qh_facetarea(facet); |
| 218 |
> |
face.setArea(faceArea); |
| 219 |
> |
|
| 220 |
> |
vertices = qh_facet3vertex(facet); |
| 221 |
> |
|
| 222 |
> |
coordT *center = qh_getcenter(vertices); |
| 223 |
> |
Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 224 |
> |
face.setCentroid(V3dCentroid); |
| 225 |
> |
|
| 226 |
> |
Vector3d faceVel = V3Zero; |
| 227 |
> |
Vector3d p[3]; |
| 228 |
> |
RealType faceMass = 0.0; |
| 229 |
> |
|
| 230 |
> |
int ver = 0; |
| 231 |
> |
|
| 232 |
> |
FOREACHvertex_(vertices){ |
| 233 |
> |
int id = qh_pointid(vertex->point); |
| 234 |
> |
p[ver][0] = vertex->point[0]; |
| 235 |
> |
p[ver][1] = vertex->point[1]; |
| 236 |
> |
p[ver][2] = vertex->point[2]; |
| 237 |
> |
|
| 238 |
> |
Vector3d vel; |
| 239 |
> |
RealType mass; |
| 240 |
> |
|
| 241 |
> |
#ifdef IS_MPI |
| 242 |
> |
vel = Vector3d(globalVels[dim_ * id], |
| 243 |
> |
globalVels[dim_ * id + 1], |
| 244 |
> |
globalVels[dim_ * id + 2]); |
| 245 |
> |
mass = globalMasses[id]; |
| 246 |
> |
|
| 247 |
> |
// localID will be between 0 and hullSitesOnProc[myrank] if we |
| 248 |
> |
// own this guy. |
| 249 |
> |
|
| 250 |
> |
int localID = id - displacements[myrank]; |
| 251 |
> |
|
| 252 |
> |
if (localID >= 0 && localID < hullSitesOnProc[myrank]) |
| 253 |
> |
face.addVertexSD(bodydoubles[indexMap[localID]]); |
| 254 |
> |
|
| 255 |
> |
#else |
| 256 |
> |
vel = bodydoubles[id]->getVel(); |
| 257 |
> |
mass = bodydoubles[id]->getMass(); |
| 258 |
> |
face.addVertexSD(bodydoubles[id]); |
| 259 |
> |
#endif |
| 260 |
> |
|
| 261 |
> |
faceVel = faceVel + vel; |
| 262 |
> |
faceMass = faceMass + mass; |
| 263 |
> |
ver++; |
| 264 |
> |
} //Foreachvertex |
| 265 |
> |
|
| 266 |
> |
face.addVertices(p[0], p[1], p[2]); |
| 267 |
> |
face.setFacetMass(faceMass); |
| 268 |
> |
face.setFacetVelocity(faceVel/3.0); |
| 269 |
> |
Triangles_.push_back(face); |
| 270 |
> |
qh_settempfree(&vertices); |
| 271 |
> |
|
| 272 |
> |
} //FORALLfacets |
| 273 |
> |
|
| 274 |
> |
qh_getarea(qh facet_list); |
| 275 |
> |
volume_ = qh totvol; |
| 276 |
> |
area_ = qh totarea; |
| 277 |
> |
|
| 278 |
> |
qh_freeqhull(!qh_ALL); |
| 279 |
> |
qh_memfreeshort(&curlong, &totlong); |
| 280 |
> |
if (curlong || totlong) |
| 281 |
> |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 282 |
> |
<< totlong << curlong << std::endl; |
| 283 |
|
} |
| 284 |
|
|
| 285 |
< |
void ConvexHull::geomviewHull(const std::string& geomFileName) { |
| 285 |
> |
void ConvexHull::printHull(const std::string& geomFileName) { |
| 286 |
> |
|
| 287 |
> |
#ifdef IS_MPI |
| 288 |
> |
if (worldRank == 0) { |
| 289 |
> |
#endif |
| 290 |
> |
FILE *newGeomFile; |
| 291 |
|
|
| 110 |
– |
std::ofstream newGeomFile; |
| 111 |
– |
|
| 292 |
|
//create new .md file based on old .md file |
| 293 |
< |
newGeomFile.open(geomFileName.c_str()); |
| 293 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 294 |
> |
qh_findgood_all(qh facet_list); |
| 295 |
> |
for (int i = 0; i < qh_PRINTEND; i++) |
| 296 |
> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 297 |
|
|
| 298 |
< |
|
| 299 |
< |
newGeomFile.close(); |
| 298 |
> |
fclose(newGeomFile); |
| 299 |
> |
#ifdef IS_MPI |
| 300 |
> |
} |
| 301 |
> |
#endif |
| 302 |
|
} |
| 303 |
+ |
#endif //QHULL |
