--- trunk/src/math/ConvexHull.cpp 2009/10/20 20:36:56 1376 +++ branches/development/src/math/ConvexHull.cpp 2012/01/06 19:03:05 1668 @@ -1,23 +1,14 @@ -/* Copyright (c) 2008, 2009 The University of Notre Dame. All Rights Reserved. +/* Copyright (c) 2010 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. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 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. @@ -37,6 +28,15 @@ * 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * * * ConvexHull.cpp * @@ -44,7 +44,7 @@ * * Created by Charles F. Vardeman II on 11 Dec 2006. * @author Charles F. Vardeman II - * @version $Id: ConvexHull.cpp,v 1.17 2009-10-20 20:36:56 gezelter Exp $ + * @version $Id$ * */ @@ -62,12 +62,12 @@ #include #endif -using namespace oopse; +using namespace OpenMD; #ifdef HAVE_QHULL extern "C" { -#include +#include #include #include #include @@ -77,9 +77,6 @@ extern "C" #include } -/* Old options Qt Qu Qg QG0 FA */ -/* More old opts Qc Qi Pp*/ - ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { } @@ -93,9 +90,9 @@ void ConvexHull::computeHull(std::vector facetT *facet; setT *vertices; int curlong, totlong; + pointT *intPoint; - std::vector ptArray(numpoints*3); - std::vector isSurfaceID(numpoints); + std::vector ptArray(numpoints*dim_); // Copy the positon vector into a points vector for qhull. std::vector::iterator SD; @@ -108,12 +105,14 @@ void ConvexHull::computeHull(std::vector i++; } + /* Clean up memory from previous convex hull calculations */ boolT ismalloc = False; - /* Clean up memory from previous convex hull calculations*/ + /* compute the hull for our local points (or all the points for single + processor versions) */ if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, const_cast(options_.c_str()), NULL, stderr)) { - + sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); painCave.isFatal = 1; simError(); @@ -127,20 +126,24 @@ void ConvexHull::computeHull(std::vector int nproc = MPI::COMM_WORLD.Get_size(); int myrank = MPI::COMM_WORLD.Get_rank(); int localHullSites = 0; - int* hullSitesOnProc = new int[nproc]; - int* coordsOnProc = new int[nproc]; - int* displacements = new int[nproc]; - int* vectorDisplacements = new int[nproc]; + std::vector hullSitesOnProc(nproc, 0); + std::vector coordsOnProc(nproc, 0); + std::vector displacements(nproc, 0); + std::vector vectorDisplacements(nproc, 0); + std::vector coords; std::vector vels; - std::vector objectIDs; + std::vector indexMap; std::vector 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]); @@ -155,14 +158,11 @@ void ConvexHull::computeHull(std::vector 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++){ - std::cerr << "iproc = " << iproc << " sites = " << hullSitesOnProc[iproc] << "\n"; globalHullSites += hullSitesOnProc[iproc]; coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc]; } @@ -175,29 +175,34 @@ void ConvexHull::computeHull(std::vector vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; } - std::vector globalCoords(dim_*globalHullSites); - std::vector globalVels(dim_*globalHullSites); + std::vector globalCoords(dim_ * globalHullSites); + std::vector globalVels(dim_ * globalHullSites); std::vector globalMasses(globalHullSites); + int count = coordsOnProc[myrank]; - MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, - &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0], + 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::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); + &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 (curlong || totlong) { + sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" + "\tdid not free %d bytes of long memory (%d pieces)", + totlong, curlong); + painCave.isFatal = 1; + simError(); + } if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, const_cast(options_.c_str()), NULL, stderr)){ @@ -209,12 +214,13 @@ void ConvexHull::computeHull(std::vector } //qh_new_qhull #endif - + intPoint = qh interior_point; + RealType calcvol = 0.0; FORALLfacets { Triangle face; - + //Qhull sets the unit normal in facet->normal Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); - face.setNormal(V3dNormal); + face.setUnitNormal(V3dNormal); RealType faceArea = qh_facetarea(facet); face.setArea(faceArea); @@ -228,6 +234,7 @@ void ConvexHull::computeHull(std::vector Vector3d faceVel = V3Zero; Vector3d p[3]; RealType faceMass = 0.0; + int ver = 0; FOREACHvertex_(vertices){ @@ -235,7 +242,6 @@ void ConvexHull::computeHull(std::vector p[ver][0] = vertex->point[0]; p[ver][1] = vertex->point[1]; p[ver][2] = vertex->point[2]; - Vector3d vel; RealType mass; @@ -245,18 +251,22 @@ void ConvexHull::computeHull(std::vector globalVels[dim_ * id + 2]); mass = globalMasses[id]; - // localID will be between 0 and hullSitesOnProc[myrank] if we own this guy. + // localID will be between 0 and hullSitesOnProc[myrank] if we + // own this guy. + int localID = id - displacements[myrank]; - if (id >= 0 && id < hullSitesOnProc[myrank]) - face.addVertexSD(bodydoubles[localID]); - else + + + if (localID >= 0 && localID < hullSitesOnProc[myrank]){ + face.addVertexSD(bodydoubles[indexMap[localID]]); + }else{ face.addVertexSD(NULL); + } #else vel = bodydoubles[id]->getVel(); mass = bodydoubles[id]->getMass(); face.addVertexSD(bodydoubles[id]); -#endif - +#endif faceVel = faceVel + vel; faceMass = faceMass + mass; ver++; @@ -264,7 +274,16 @@ void ConvexHull::computeHull(std::vector face.addVertices(p[0], p[1], p[2]); face.setFacetMass(faceMass); - face.setFacetVelocity(faceVel/3.0); + face.setFacetVelocity(faceVel / RealType(3.0)); + /* + RealType comparea = face.computeArea(); + realT calcarea = qh_facetarea (facet); + Vector3d V3dCompNorm = -face.computeUnitNormal(); + RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]); + RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2]; + std::cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << std::endl; + calcvol += -dist*comparea/qh hull_dim; + */ Triangles_.push_back(face); qh_settempfree(&vertices); @@ -273,24 +292,23 @@ void ConvexHull::computeHull(std::vector qh_getarea(qh facet_list); volume_ = qh totvol; area_ = qh totarea; - -#ifdef IS_MPI - delete [] hullSitesOnProc; - delete [] coordsOnProc; - delete [] displacements; - delete [] vectorDisplacements; -#endif - + // std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; 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 (curlong || totlong) { + sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" + "\tdid not free %d bytes of long memory (%d pieces)", + totlong, curlong); + painCave.isFatal = 1; + simError(); + } } - - 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 @@ -300,5 +318,8 @@ void ConvexHull::printHull(const std::string& geomFile qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); fclose(newGeomFile); +#ifdef IS_MPI + } +#endif } #endif //QHULL