| 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). |
| 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 |
< |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 39 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 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 $Id$ |
| 48 |
< |
* |
| 43 |
> |
* Purpose: To calculate a convex hull. |
| 44 |
|
*/ |
| 45 |
|
|
| 46 |
+ |
#ifdef IS_MPI |
| 47 |
+ |
#include <mpi.h> |
| 48 |
+ |
#endif |
| 49 |
+ |
|
| 50 |
|
/* Standard includes independent of library */ |
| 51 |
|
|
| 52 |
|
#include <iostream> |
| 57 |
|
#include "math/ConvexHull.hpp" |
| 58 |
|
#include "utils/simError.h" |
| 59 |
|
|
| 61 |
– |
#ifdef IS_MPI |
| 62 |
– |
#include <mpi.h> |
| 63 |
– |
#endif |
| 64 |
– |
|
| 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") { |
| 66 |
> |
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") { |
| 67 |
|
} |
| 68 |
|
|
| 69 |
< |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 70 |
< |
|
| 69 |
> |
void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { |
| 70 |
> |
|
| 71 |
|
int numpoints = bodydoubles.size(); |
| 72 |
< |
|
| 72 |
> |
|
| 73 |
|
Triangles_.clear(); |
| 74 |
|
|
| 75 |
|
vertexT *vertex, **vertexp; |
| 76 |
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facetT *facet; |
| 77 |
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setT *vertices; |
| 78 |
|
int curlong, totlong; |
| 83 |
– |
pointT *intPoint; |
| 84 |
– |
|
| 85 |
– |
std::vector<double> ptArray(numpoints*dim_); |
| 79 |
|
|
| 80 |
+ |
vector<double> ptArray(numpoints*dim_); |
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+ |
|
| 82 |
|
// Copy the positon vector into a points vector for qhull. |
| 83 |
< |
std::vector<StuntDouble*>::iterator SD; |
| 83 |
> |
vector<StuntDouble*>::iterator SD; |
| 84 |
|
int i = 0; |
| 85 |
+ |
|
| 86 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 87 |
|
Vector3d pos = (*SD)->getPos(); |
| 88 |
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ptArray[dim_ * i] = pos.x(); |
| 109 |
|
#ifdef IS_MPI |
| 110 |
|
//If we are doing the mpi version, set up some vectors for data communication |
| 111 |
|
|
| 112 |
< |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 113 |
< |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 112 |
> |
int nproc; |
| 113 |
> |
int myrank; |
| 114 |
> |
|
| 115 |
> |
MPI_Comm_size( MPI_COMM_WORLD, &nproc); |
| 116 |
> |
MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
| 117 |
> |
|
| 118 |
|
int localHullSites = 0; |
| 119 |
|
|
| 120 |
< |
std::vector<int> hullSitesOnProc(nproc, 0); |
| 121 |
< |
std::vector<int> coordsOnProc(nproc, 0); |
| 122 |
< |
std::vector<int> displacements(nproc, 0); |
| 123 |
< |
std::vector<int> vectorDisplacements(nproc, 0); |
| 120 |
> |
vector<int> hullSitesOnProc(nproc, 0); |
| 121 |
> |
vector<int> coordsOnProc(nproc, 0); |
| 122 |
> |
vector<int> displacements(nproc, 0); |
| 123 |
> |
vector<int> vectorDisplacements(nproc, 0); |
| 124 |
|
|
| 125 |
< |
std::vector<double> coords; |
| 126 |
< |
std::vector<double> vels; |
| 127 |
< |
std::vector<int> indexMap; |
| 128 |
< |
std::vector<double> masses; |
| 125 |
> |
vector<double> coords; |
| 126 |
> |
vector<double> vels; |
| 127 |
> |
vector<int> indexMap; |
| 128 |
> |
vector<double> masses; |
| 129 |
|
|
| 130 |
|
FORALLvertices{ |
| 131 |
|
localHullSites++; |
| 148 |
|
masses.push_back(sd->getMass()); |
| 149 |
|
} |
| 150 |
|
|
| 151 |
< |
MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0], |
| 152 |
< |
1, MPI::INT); |
| 151 |
> |
MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0], |
| 152 |
> |
1, MPI_INT, MPI_COMM_WORLD); |
| 153 |
|
|
| 154 |
|
int globalHullSites = 0; |
| 155 |
|
for (int iproc = 0; iproc < nproc; iproc++){ |
| 165 |
|
vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
| 166 |
|
} |
| 167 |
|
|
| 168 |
< |
std::vector<double> globalCoords(dim_ * globalHullSites); |
| 169 |
< |
std::vector<double> globalVels(dim_ * globalHullSites); |
| 170 |
< |
std::vector<double> globalMasses(globalHullSites); |
| 168 |
> |
vector<double> globalCoords(dim_ * globalHullSites); |
| 169 |
> |
vector<double> globalVels(dim_ * globalHullSites); |
| 170 |
> |
vector<double> globalMasses(globalHullSites); |
| 171 |
|
|
| 172 |
|
int count = coordsOnProc[myrank]; |
| 173 |
|
|
| 174 |
< |
MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0], |
| 175 |
< |
&coordsOnProc[0], &vectorDisplacements[0], |
| 176 |
< |
MPI::DOUBLE); |
| 177 |
< |
|
| 178 |
< |
MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], |
| 179 |
< |
&coordsOnProc[0], &vectorDisplacements[0], |
| 180 |
< |
MPI::DOUBLE); |
| 181 |
< |
|
| 182 |
< |
MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE, |
| 183 |
< |
&globalMasses[0], &hullSitesOnProc[0], |
| 184 |
< |
&displacements[0], MPI::DOUBLE); |
| 185 |
< |
|
| 174 |
> |
MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0], |
| 175 |
> |
&coordsOnProc[0], &vectorDisplacements[0], |
| 176 |
> |
MPI_DOUBLE, MPI_COMM_WORLD); |
| 177 |
> |
|
| 178 |
> |
MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0], |
| 179 |
> |
&coordsOnProc[0], &vectorDisplacements[0], |
| 180 |
> |
MPI_DOUBLE, MPI_COMM_WORLD); |
| 181 |
> |
|
| 182 |
> |
MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE, |
| 183 |
> |
&globalMasses[0], &hullSitesOnProc[0], |
| 184 |
> |
&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD); |
| 185 |
> |
|
| 186 |
|
// Free previous hull |
| 187 |
|
qh_freeqhull(!qh_ALL); |
| 188 |
|
qh_memfreeshort(&curlong, &totlong); |
| 197 |
|
if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, |
| 198 |
|
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 199 |
|
|
| 200 |
< |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 200 |
> |
sprintf(painCave.errMsg, |
| 201 |
> |
"ConvexHull: Qhull failed to compute global convex hull"); |
| 202 |
|
painCave.isFatal = 1; |
| 203 |
|
simError(); |
| 204 |
|
|
| 205 |
|
} //qh_new_qhull |
| 206 |
|
|
| 207 |
|
#endif |
| 208 |
+ |
// commented out below, so comment out here also. |
| 209 |
+ |
// intPoint = qh interior_point; |
| 210 |
+ |
// RealType calcvol = 0.0; |
| 211 |
+ |
|
| 212 |
+ |
qh_triangulate (); |
| 213 |
|
|
| 208 |
– |
intPoint = qh interior_point; |
| 209 |
– |
RealType calcvol = 0.0; |
| 214 |
|
FORALLfacets { |
| 215 |
|
Triangle face; |
| 216 |
|
//Qhull sets the unit normal in facet->normal |
| 276 |
|
Vector3d V3dCompNorm = -face.computeUnitNormal(); |
| 277 |
|
RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]); |
| 278 |
|
RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2]; |
| 279 |
< |
std::cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << std::endl; |
| 279 |
> |
cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl; |
| 280 |
|
calcvol += -dist*comparea/qh hull_dim; |
| 281 |
|
*/ |
| 282 |
|
Triangles_.push_back(face); |
| 287 |
|
qh_getarea(qh facet_list); |
| 288 |
|
volume_ = qh totvol; |
| 289 |
|
area_ = qh totarea; |
| 290 |
< |
// std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; |
| 290 |
> |
|
| 291 |
|
qh_freeqhull(!qh_ALL); |
| 292 |
|
qh_memfreeshort(&curlong, &totlong); |
| 293 |
|
if (curlong || totlong) { |
| 299 |
|
} |
| 300 |
|
} |
| 301 |
|
|
| 302 |
< |
void ConvexHull::printHull(const std::string& geomFileName) { |
| 303 |
< |
|
| 302 |
> |
void ConvexHull::printHull(const string& geomFileName) { |
| 303 |
> |
|
| 304 |
|
#ifdef IS_MPI |
| 305 |
|
if (worldRank == 0) { |
| 306 |
|
#endif |
| 307 |
< |
FILE *newGeomFile; |
| 308 |
< |
|
| 309 |
< |
//create new .md file based on old .md file |
| 310 |
< |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 311 |
< |
qh_findgood_all(qh facet_list); |
| 312 |
< |
for (int i = 0; i < qh_PRINTEND; i++) |
| 313 |
< |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 314 |
< |
|
| 315 |
< |
fclose(newGeomFile); |
| 307 |
> |
FILE *newGeomFile; |
| 308 |
> |
|
| 309 |
> |
//create new .md file based on old .md file |
| 310 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 311 |
> |
qh_findgood_all(qh facet_list); |
| 312 |
> |
for (int i = 0; i < qh_PRINTEND; i++) |
| 313 |
> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 314 |
> |
|
| 315 |
> |
fclose(newGeomFile); |
| 316 |
|
#ifdef IS_MPI |
| 317 |
|
} |
| 318 |
|
#endif |
