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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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|
* |
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< |
* 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 |
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< |
* 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 |
|
* |
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+ |
* |
| 41 |
|
* ConvexHull.cpp |
| 42 |
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* |
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* Purpose: To calculate convexhull, hull volume libqhull. |
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* |
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* Created by Charles F. Vardeman II on 11 Dec 2006. |
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* @author Charles F. Vardeman II |
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< |
* @version $Id: ConvexHull.cpp,v 1.18 2009-10-21 02:49:43 gezelter Exp $ |
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> |
* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $ |
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* |
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*/ |
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|
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#include <mpi.h> |
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#endif |
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|
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< |
using namespace oopse; |
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> |
using namespace OpenMD; |
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|
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#ifdef HAVE_QHULL |
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extern "C" |
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#include <qhull/stat.h> |
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} |
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|
|
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– |
/* Old options Qt Qu Qg QG0 FA */ |
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– |
/* More old opts Qc Qi Pp*/ |
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– |
|
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ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
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} |
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|
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setT *vertices; |
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int curlong, totlong; |
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|
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< |
std::vector<double> ptArray(numpoints*3); |
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std::vector<bool> isSurfaceID(numpoints); |
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> |
std::vector<double> ptArray(numpoints*dim_); |
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|
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// Copy the positon vector into a points vector for qhull. |
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std::vector<StuntDouble*>::iterator SD; |
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int nproc = MPI::COMM_WORLD.Get_size(); |
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int myrank = MPI::COMM_WORLD.Get_rank(); |
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int localHullSites = 0; |
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– |
int* hullSitesOnProc = new int[nproc]; |
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– |
int* coordsOnProc = new int[nproc]; |
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– |
int* displacements = new int[nproc]; |
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– |
int* vectorDisplacements = new int[nproc]; |
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|
|
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+ |
std::vector<int> hullSitesOnProc(nproc, 0); |
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+ |
std::vector<int> coordsOnProc(nproc, 0); |
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+ |
std::vector<int> displacements(nproc, 0); |
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+ |
std::vector<int> vectorDisplacements(nproc, 0); |
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+ |
|
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std::vector<double> coords; |
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std::vector<double> vels; |
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< |
std::vector<int> objectIDs; |
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> |
std::vector<int> indexMap; |
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std::vector<double> masses; |
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|
|
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FORALLvertices{ |
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localHullSites++; |
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|
|
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int idx = qh_pointid(vertex->point); |
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+ |
|
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+ |
indexMap.push_back(idx); |
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+ |
|
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|
coords.push_back(ptArray[dim_ * idx]); |
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|
coords.push_back(ptArray[dim_ * idx + 1]); |
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coords.push_back(ptArray[dim_ * idx + 2]); |
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|
masses.push_back(sd->getMass()); |
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} |
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|
|
| 158 |
– |
|
| 159 |
– |
|
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|
MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0], |
| 159 |
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1, MPI::INT); |
| 160 |
|
|
| 250 |
|
int localID = id - displacements[myrank]; |
| 251 |
|
|
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|
if (localID >= 0 && localID < hullSitesOnProc[myrank]) |
| 253 |
< |
face.addVertexSD(bodydoubles[localID]); |
| 253 |
> |
face.addVertexSD(bodydoubles[indexMap[localID]]); |
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|
|
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|
#else |
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|
vel = bodydoubles[id]->getVel(); |
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|
volume_ = qh totvol; |
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|
area_ = qh totarea; |
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|
|
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– |
#ifdef IS_MPI |
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– |
delete [] hullSitesOnProc; |
| 282 |
– |
delete [] coordsOnProc; |
| 283 |
– |
delete [] displacements; |
| 284 |
– |
delete [] vectorDisplacements; |
| 285 |
– |
#endif |
| 286 |
– |
|
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|
qh_freeqhull(!qh_ALL); |
| 279 |
|
qh_memfreeshort(&curlong, &totlong); |
| 280 |
|
if (curlong || totlong) |
| 283 |
|
} |
| 284 |
|
|
| 285 |
|
void ConvexHull::printHull(const std::string& geomFileName) { |
| 286 |
+ |
|
| 287 |
+ |
#ifdef IS_MPI |
| 288 |
+ |
if (worldRank == 0) { |
| 289 |
+ |
#endif |
| 290 |
|
FILE *newGeomFile; |
| 291 |
|
|
| 292 |
|
//create new .md file based on old .md file |
| 296 |
|
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 297 |
|
|
| 298 |
|
fclose(newGeomFile); |
| 299 |
+ |
#ifdef IS_MPI |
| 300 |
+ |
} |
| 301 |
+ |
#endif |
| 302 |
|
} |
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|
#endif //QHULL |
