src/math/ConvexHull.cpp

/* Copyright (c) 2008, 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *
 *  ConvexHull.cpp
 *
 *  Purpose: To calculate convexhull, hull volume libqhull.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $
 *
 */

/* Standard includes independent of library */

#include <iostream>
#include <fstream>
#include <list>
#include <algorithm>
#include <iterator>
#include "math/ConvexHull.hpp"
#include "utils/simError.h"

#ifdef IS_MPI
#include <mpi.h>
#endif

using namespace OpenMD;

#ifdef HAVE_QHULL
extern "C"
{
#include <qhull/qhull.h>
#include <qhull/mem.h>
#include <qhull/qset.h>
#include <qhull/geom.h>
#include <qhull/merge.h>
#include <qhull/poly.h>
#include <qhull/io.h>
#include <qhull/stat.h>
}

ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
}

void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { 
 
  int numpoints = bodydoubles.size();

  Triangles_.clear();
  
  vertexT *vertex, **vertexp;
  facetT *facet;
  setT *vertices;
  int curlong, totlong;
  
  std::vector<double> ptArray(numpoints*dim_);

  // Copy the positon vector into a points vector for qhull.
  std::vector<StuntDouble*>::iterator SD;
  int i = 0;
  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
    Vector3d pos = (*SD)->getPos();      
    ptArray[dim_ * i] = pos.x();
    ptArray[dim_ * i + 1] = pos.y();
    ptArray[dim_ * i + 2] = pos.z();
    i++;
  }
  
  boolT ismalloc = False;
  /* Clean up memory from previous convex hull calculations*/
  
  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)) {

    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull


#ifdef IS_MPI
  //If we are doing the mpi version, set up some vectors for data communication
  
  int nproc = MPI::COMM_WORLD.Get_size();
  int myrank = MPI::COMM_WORLD.Get_rank();
  int localHullSites = 0;

  std::vector<int> hullSitesOnProc(nproc, 0);
  std::vector<int> coordsOnProc(nproc, 0);
  std::vector<int> displacements(nproc, 0);
  std::vector<int> vectorDisplacements(nproc, 0);

  std::vector<double> coords;
  std::vector<double> vels;
  std::vector<int> indexMap;
  std::vector<double> masses;

  FORALLvertices{
    localHullSites++;
    
    int idx = qh_pointid(vertex->point);

    indexMap.push_back(idx);

    coords.push_back(ptArray[dim_  * idx]);
    coords.push_back(ptArray[dim_  * idx + 1]);
    coords.push_back(ptArray[dim_  * idx + 2]);

    StuntDouble* sd = bodydoubles[idx];

    Vector3d vel = sd->getVel();
    vels.push_back(vel.x());
    vels.push_back(vel.y());
    vels.push_back(vel.z());

    masses.push_back(sd->getMass());
  }

  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
                            1, MPI::INT);

  int globalHullSites = 0;
  for (int iproc = 0; iproc < nproc; iproc++){
    globalHullSites += hullSitesOnProc[iproc];
    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
  }

  displacements[0] = 0;
  vectorDisplacements[0] = 0;
  
  for (int iproc = 1; iproc < nproc; iproc++){
    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; 
  }

  std::vector<double> globalCoords(dim_ * globalHullSites);
  std::vector<double> globalVels(dim_ * globalHullSites);
  std::vector<double> globalMasses(globalHullSites);

  int count = coordsOnProc[myrank];
  
  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
                             &coordsOnProc[0], &vectorDisplacements[0], 
                             MPI::DOUBLE);

  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], 
                             &coordsOnProc[0], &vectorDisplacements[0],
                             MPI::DOUBLE);

  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
                             &globalMasses[0], &hullSitesOnProc[0], 
                             &displacements[0], MPI::DOUBLE);

  // Free previous hull
  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong)
    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
              << totlong << curlong << std::endl;
  
  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)){
    
    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull

#endif

  FORALLfacets {  
    Triangle face;

    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
    face.setNormal(V3dNormal);
    
    RealType faceArea = qh_facetarea(facet);
    face.setArea(faceArea);
    
    vertices = qh_facet3vertex(facet);
      
    coordT *center = qh_getcenter(vertices);
    Vector3d V3dCentroid(center[0], center[1], center[2]);
    face.setCentroid(V3dCentroid);

    Vector3d faceVel = V3Zero;
    Vector3d p[3];
    RealType faceMass = 0.0;

    int ver = 0;

    FOREACHvertex_(vertices){
      int id = qh_pointid(vertex->point);
      p[ver][0] = vertex->point[0];
      p[ver][1] = vertex->point[1];
      p[ver][2] = vertex->point[2];
      
      Vector3d vel;
      RealType mass;

#ifdef IS_MPI
      vel = Vector3d(globalVels[dim_ * id],
                     globalVels[dim_ * id + 1], 
                     globalVels[dim_ * id + 2]);
      mass = globalMasses[id];

      // localID will be between 0 and hullSitesOnProc[myrank] if we
      // own this guy.

      int localID = id - displacements[myrank];

      if (localID >= 0 && localID < hullSitesOnProc[myrank])
        face.addVertexSD(bodydoubles[indexMap[localID]]);
      
#else
      vel = bodydoubles[id]->getVel();
      mass = bodydoubles[id]->getMass();
      face.addVertexSD(bodydoubles[id]);      
#endif
        
      faceVel = faceVel + vel;
      faceMass = faceMass + mass;
      ver++;      
    } //Foreachvertex

    face.addVertices(p[0], p[1], p[2]);
    face.setFacetMass(faceMass);
    face.setFacetVelocity(faceVel/3.0);
    Triangles_.push_back(face);
    qh_settempfree(&vertices);      

  } //FORALLfacets
  
  qh_getarea(qh facet_list);
  volume_ = qh totvol;
  area_ = qh totarea;

  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong)
    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
              << totlong << curlong << std::endl;    
}

void ConvexHull::printHull(const std::string& geomFileName) {

#ifdef IS_MPI
  if (worldRank == 0)  {
#endif
  FILE *newGeomFile;
  
  //create new .md file based on old .md file
  newGeomFile = fopen(geomFileName.c_str(), "w");
  qh_findgood_all(qh facet_list);
  for (int i = 0; i < qh_PRINTEND; i++)
    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
  
  fclose(newGeomFile);
#ifdef IS_MPI
  }
#endif
}
#endif //QHULL
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/math/ConvexHull.cpp*
File size:	9291 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	chuckv	1365	/* Copyright (c) 2008, 2009 The University of Notre Dame. All Rights Reserved.
2	chuckv	1097	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	1097	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	1097	* 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	gezelter	1390	* 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	chuckv	1097	*
40	gezelter	1390	*
41	chuckv	1097	* ConvexHull.cpp
42			*
43	chuckv	1137	* Purpose: To calculate convexhull, hull volume libqhull.
44	chuckv	1097	*
45			* Created by Charles F. Vardeman II on 11 Dec 2006.
46			* @author Charles F. Vardeman II
47	gezelter	1390	* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $
48	chuckv	1097	*
49			*/
50
51	chuckv	1242	/* Standard includes independent of library */
52	chuckv	1374
53	chuckv	1097	#include <iostream>
54			#include <fstream>
55	chuckv	1188	#include <list>
56			#include <algorithm>
57			#include <iterator>
58	chuckv	1141	#include "math/ConvexHull.hpp"
59	chuckv	1188	#include "utils/simError.h"
60	chuckv	1293
61			#ifdef IS_MPI
62	chuckv	1374	#include <mpi.h>
63	chuckv	1293	#endif
64
65	gezelter	1390	using namespace OpenMD;
66	chuckv	1293
67	chuckv	1374	#ifdef HAVE_QHULL
68			extern "C"
69	chuckv	1242	{
70	chuckv	1374	#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	chuckv	1293	}
79
80	chuckv	1374	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81			}
82	chuckv	1293
83	chuckv	1374	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84	chuckv	1293
85	chuckv	1374	int numpoints = bodydoubles.size();
86	chuckv	1293
87	chuckv	1374	Triangles_.clear();
88	chuckv	1242
89	chuckv	1293	vertexT vertex, *vertexp;
90			facetT *facet;
91			setT *vertices;
92	chuckv	1374	int curlong, totlong;
93	chuckv	1242
94	gezelter	1378	std::vector<double> ptArray(numpoints*dim_);
95	chuckv	1293
96			// Copy the positon vector into a points vector for qhull.
97			std::vector<StuntDouble*>::iterator SD;
98			int i = 0;
99	chuckv	1374	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	chuckv	1242
107	chuckv	1293	boolT ismalloc = False;
108	chuckv	1302	/* Clean up memory from previous convex hull calculations*/
109	chuckv	1308
110	chuckv	1302	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111	chuckv	1374	const_cast<char *>(options_.c_str()), NULL, stderr)) {
112	chuckv	1188
113	chuckv	1374	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114			painCave.isFatal = 1;
115			simError();
116
117	chuckv	1293	} //qh_new_qhull
118
119
120			#ifdef IS_MPI
121	chuckv	1374	//If we are doing the mpi version, set up some vectors for data communication
122	chuckv	1242
123	chuckv	1374	int nproc = MPI::COMM_WORLD.Get_size();
124			int myrank = MPI::COMM_WORLD.Get_rank();
125			int localHullSites = 0;
126	chuckv	1293
127	gezelter	1384	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	chuckv	1374	std::vector<double> coords;
133			std::vector<double> vels;
134	gezelter	1378	std::vector<int> indexMap;
135	chuckv	1374	std::vector<double> masses;
136
137			FORALLvertices{
138			localHullSites++;
139	chuckv	1242
140	chuckv	1374	int idx = qh_pointid(vertex->point);
141	gezelter	1378
142			indexMap.push_back(idx);
143
144	chuckv	1374	coords.push_back(ptArray[dim_ * idx]);
145			coords.push_back(ptArray[dim_ * idx + 1]);
146			coords.push_back(ptArray[dim_ * idx + 2]);
147	chuckv	1293
148	chuckv	1374	StuntDouble* sd = bodydoubles[idx];
149	chuckv	1188
150	chuckv	1374	Vector3d vel = sd->getVel();
151			vels.push_back(vel.x());
152			vels.push_back(vel.y());
153			vels.push_back(vel.z());
154	chuckv	1188
155	chuckv	1374	masses.push_back(sd->getMass());
156			}
157	chuckv	1188
158	chuckv	1374	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159			1, MPI::INT);
160	chuckv	1307
161	chuckv	1374	int globalHullSites = 0;
162	gezelter	1376	for (int iproc = 0; iproc < nproc; iproc++){
163	chuckv	1374	globalHullSites += hullSitesOnProc[iproc];
164			coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165	chuckv	1302	}
166	chuckv	1293
167	chuckv	1374	displacements[0] = 0;
168			vectorDisplacements[0] = 0;
169	chuckv	1316
170	gezelter	1376	for (int iproc = 1; iproc < nproc; iproc++){
171	chuckv	1374	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
172			vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
173	chuckv	1293	}
174
175	gezelter	1377	std::vector<double> globalCoords(dim_ * globalHullSites);
176			std::vector<double> globalVels(dim_ * globalHullSites);
177	chuckv	1374	std::vector<double> globalMasses(globalHullSites);
178	gezelter	1377
179	chuckv	1374	int count = coordsOnProc[myrank];
180	chuckv	1365
181	gezelter	1377	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182			&coordsOnProc[0], &vectorDisplacements[0],
183	chuckv	1374	MPI::DOUBLE);
184	chuckv	1302
185	gezelter	1377	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186			&coordsOnProc[0], &vectorDisplacements[0],
187	chuckv	1374	MPI::DOUBLE);
188	chuckv	1302
189	chuckv	1374	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190	gezelter	1377	&globalMasses[0], &hullSitesOnProc[0],
191			&displacements[0], MPI::DOUBLE);
192	chuckv	1365
193	chuckv	1293	// Free previous hull
194	chuckv	1242	qh_freeqhull(!qh_ALL);
195			qh_memfreeshort(&curlong, &totlong);
196			if (curlong \|\| totlong)
197			std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
198			<< totlong << curlong << std::endl;
199	chuckv	1374
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	chuckv	1293	} //qh_new_qhull
208
209			#endif
210
211	chuckv	1374	FORALLfacets {
212			Triangle face;
213	chuckv	1293
214	chuckv	1374	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215			face.setNormal(V3dNormal);
216	chuckv	1371
217	chuckv	1374	RealType faceArea = qh_facetarea(facet);
218			face.setArea(faceArea);
219
220			vertices = qh_facet3vertex(facet);
221	chuckv	1293
222	chuckv	1374	coordT *center = qh_getcenter(vertices);
223			Vector3d V3dCentroid(center[0], center[1], center[2]);
224			face.setCentroid(V3dCentroid);
225	chuckv	1304
226	chuckv	1374	Vector3d faceVel = V3Zero;
227			Vector3d p[3];
228			RealType faceMass = 0.0;
229	gezelter	1377
230	chuckv	1374	int ver = 0;
231	chuckv	1293
232	chuckv	1374	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	chuckv	1293
241	chuckv	1302	#ifdef IS_MPI
242	chuckv	1374	vel = Vector3d(globalVels[dim_ * id],
243			globalVels[dim_ * id + 1],
244			globalVels[dim_ * id + 2]);
245			mass = globalMasses[id];
246
247	gezelter	1377	// localID will be between 0 and hullSitesOnProc[myrank] if we
248			// own this guy.
249
250	chuckv	1374	int localID = id - displacements[myrank];
251	gezelter	1377
252			if (localID >= 0 && localID < hullSitesOnProc[myrank])
253	gezelter	1378	face.addVertexSD(bodydoubles[indexMap[localID]]);
254	gezelter	1377
255	chuckv	1307	#else
256	chuckv	1374	vel = bodydoubles[id]->getVel();
257			mass = bodydoubles[id]->getMass();
258			face.addVertexSD(bodydoubles[id]);
259	chuckv	1302	#endif
260	chuckv	1374
261			faceVel = faceVel + vel;
262			faceMass = faceMass + mass;
263			ver++;
264			} //Foreachvertex
265	chuckv	1302
266	chuckv	1374	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	chuckv	1097	}
284
285	chuckv	1374	void ConvexHull::printHull(const std::string& geomFileName) {
286	gezelter	1384
287			#ifdef IS_MPI
288			if (worldRank == 0) {
289			#endif
290	chuckv	1242	FILE *newGeomFile;
291
292			//create new .md file based on old .md file
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			fclose(newGeomFile);
299	gezelter	1384	#ifdef IS_MPI
300			}
301			#endif
302	chuckv	1097	}
303	chuckv	1242	#endif //QHULL