| 1 |
< |
/* Copyright (c) 2008, 2009, 2010 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 |
| 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). |
| 38 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
> |
* [4] , 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 $ |
| 47 |
> |
* @version $Id$ |
| 48 |
|
* |
| 49 |
|
*/ |
| 50 |
|
|
| 62 |
|
#include <mpi.h> |
| 63 |
|
#endif |
| 64 |
|
|
| 65 |
< |
using namespace OpenMD; |
| 65 |
> |
#include "math/qhull.hpp" |
| 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 |
< |
} |
| 68 |
> |
using namespace OpenMD; |
| 69 |
|
|
| 70 |
|
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
| 71 |
|
} |
| 95 |
|
i++; |
| 96 |
|
} |
| 97 |
|
|
| 98 |
+ |
/* Clean up memory from previous convex hull calculations */ |
| 99 |
|
boolT ismalloc = False; |
| 109 |
– |
/* Clean up memory from previous convex hull calculations*/ |
| 100 |
|
|
| 101 |
+ |
/* compute the hull for our local points (or all the points for single |
| 102 |
+ |
processor versions) */ |
| 103 |
|
if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
| 104 |
|
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 105 |
< |
|
| 105 |
> |
|
| 106 |
|
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 107 |
|
painCave.isFatal = 1; |
| 108 |
|
simError(); |
| 186 |
|
// Free previous hull |
| 187 |
|
qh_freeqhull(!qh_ALL); |
| 188 |
|
qh_memfreeshort(&curlong, &totlong); |
| 189 |
< |
if (curlong || totlong) |
| 190 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 191 |
< |
<< totlong << curlong << std::endl; |
| 189 |
> |
if (curlong || totlong) { |
| 190 |
> |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 191 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 192 |
> |
totlong, curlong); |
| 193 |
> |
painCave.isFatal = 1; |
| 194 |
> |
simError(); |
| 195 |
> |
} |
| 196 |
|
|
| 197 |
|
if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, |
| 198 |
|
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 256 |
|
vel = bodydoubles[id]->getVel(); |
| 257 |
|
mass = bodydoubles[id]->getMass(); |
| 258 |
|
face.addVertexSD(bodydoubles[id]); |
| 259 |
< |
|
| 264 |
< |
|
| 265 |
< |
#endif |
| 266 |
< |
|
| 259 |
> |
#endif |
| 260 |
|
faceVel = faceVel + vel; |
| 261 |
|
faceMass = faceMass + mass; |
| 262 |
|
ver++; |
| 264 |
|
|
| 265 |
|
face.addVertices(p[0], p[1], p[2]); |
| 266 |
|
face.setFacetMass(faceMass); |
| 267 |
< |
face.setFacetVelocity(faceVel/3.0); |
| 267 |
> |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 268 |
|
/* |
| 269 |
|
RealType comparea = face.computeArea(); |
| 270 |
|
realT calcarea = qh_facetarea (facet); |
| 285 |
|
// std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; |
| 286 |
|
qh_freeqhull(!qh_ALL); |
| 287 |
|
qh_memfreeshort(&curlong, &totlong); |
| 288 |
< |
if (curlong || totlong) |
| 289 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 290 |
< |
<< totlong << curlong << std::endl; |
| 288 |
> |
if (curlong || totlong) { |
| 289 |
> |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 290 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 291 |
> |
totlong, curlong); |
| 292 |
> |
painCave.isFatal = 1; |
| 293 |
> |
simError(); |
| 294 |
> |
} |
| 295 |
|
} |
| 296 |
|
|
| 297 |
|
void ConvexHull::printHull(const std::string& geomFileName) { |
