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root/OpenMD/branches/development/src/math/ConvexHull.cpp
Revision: 1858
Committed: Wed Apr 3 21:32:13 2013 UTC (12 years ago) by gezelter
File size: 10511 byte(s)
Log Message:
Some bugfixes for cell-linked-list-style neighbor lists when the simulation
doesn't use periodic boundary conditions.   Cleaning up some of the Hull
stuff while we're in there.

File Contents

# Content
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 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 FORALLfacets {
211 Triangle face;
212 //Qhull sets the unit normal in facet->normal
213 Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214 face.setUnitNormal(V3dNormal);
215
216 RealType faceArea = qh_facetarea(facet);
217 face.setArea(faceArea);
218
219 vertices = qh_facet3vertex(facet);
220
221 coordT *center = qh_getcenter(vertices);
222 Vector3d V3dCentroid(center[0], center[1], center[2]);
223 face.setCentroid(V3dCentroid);
224
225 Vector3d faceVel = V3Zero;
226 Vector3d p[3];
227 RealType faceMass = 0.0;
228
229 int ver = 0;
230
231 FOREACHvertex_(vertices){
232 int id = qh_pointid(vertex->point);
233 p[ver][0] = vertex->point[0];
234 p[ver][1] = vertex->point[1];
235 p[ver][2] = vertex->point[2];
236 Vector3d vel;
237 RealType mass;
238
239 #ifdef IS_MPI
240 vel = Vector3d(globalVels[dim_ * id],
241 globalVels[dim_ * id + 1],
242 globalVels[dim_ * id + 2]);
243 mass = globalMasses[id];
244
245 // localID will be between 0 and hullSitesOnProc[myrank] if we
246 // own this guy.
247
248 int localID = id - displacements[myrank];
249
250
251 if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252 face.addVertexSD(bodydoubles[indexMap[localID]]);
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
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 / 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
281 } //FORALLfacets
282
283 qh_getarea(qh facet_list);
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 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 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);
331 #ifdef IS_MPI
332 }
333 #endif
334 }
335 #endif //QHULL

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