--- trunk/src/applications/staticProps/NanoVolume.cpp 2008/01/08 19:36:28 1207 +++ trunk/src/applications/staticProps/NanoVolume.cpp 2010/01/08 17:15:27 1402 @@ -1,23 +1,14 @@ -/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. +/* Copyright (c) 2006, 2009, 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. @@ -37,27 +28,33 @@ * 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). * + * * NanoVolume.cpp * - * Purpose: To calculate convexhull, hull volume and radius - * using the CGAL library. - * * Created by Charles F. Vardeman II on 14 Dec 2006. * @author Charles F. Vardeman II - * @version $Id: NanoVolume.cpp,v 1.6 2008-01-08 19:36:28 chuckv Exp $ + * @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $ * */ #include "applications/staticProps/NanoVolume.hpp" #include "math/ConvexHull.hpp" -#include "math/AlphaShape.hpp" +#include "math/AlphaHull.hpp" #include "utils/simError.h" #include "io/DumpReader.hpp" #include "primitives/Molecule.hpp" #include "utils/NumericConstant.hpp" -using namespace oopse; +using namespace OpenMD; NanoVolume::NanoVolume(SimInfo* info, const std::string& filename, @@ -74,7 +71,7 @@ void NanoVolume::process() { } void NanoVolume::process() { -#if defined(HAVE_CGAL) || defined(HAVE_QHULL) +#if defined(HAVE_QHULL) Molecule* mol; Atom* atom; RigidBody* rb; @@ -87,17 +84,15 @@ void NanoVolume::process() { int i,j; #ifdef HAVE_QHULL - ConvexHull* hull = new ConvexHull(); + // ConvexHull* thishull = new ConvexHull(); + AlphaHull* thishull = new AlphaHull(2.0); #endif -#ifdef HAVE_CGAL - AlphaShape* hull = new AlphaShape(); -#endif DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); frameCounter_ = 0; - pos_.reserve(info_->getNGlobalAtoms()); + theAtoms_.reserve(info_->getNGlobalAtoms()); for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); @@ -105,7 +100,7 @@ void NanoVolume::process() { currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); // Clear pos vector between each frame. - pos_.clear(); + theAtoms_.clear(); if (evaluator_.isDynamic()) { seleMan_.setSelectionSet(evaluator_.evaluate()); @@ -124,14 +119,24 @@ void NanoVolume::process() { // outer loop is over the selected StuntDoubles: for (sd = seleMan_.beginSelected(i); sd != NULL; - sd = seleMan_.nextSelected(i)) { + sd = seleMan_.nextSelected(i)) { - pos_.push_back(sd->getPos()); + theAtoms_.push_back(sd); myIndex = sd->getGlobalIndex(); } + + /* + for (mol = info_->beginMolecule(mi); mol != NULL; + mol = info_->nextMolecule(mi)) { + for (atom = mol->beginAtom(ai); atom != NULL; + atom = mol->nextAtom(ai)) { + theAtoms_.push_back(atom); + } + } + */ // Generate convex hull for this frame. - hull->genHull(pos_); + thishull->computeHull(theAtoms_); // totalVolume_ += hull->getVolume(); } //RealType avgVolume = totalVolume_/(RealType) frameCounter_; @@ -147,7 +152,7 @@ void NanoVolume::process() { osq.close(); */ #else - sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n"); + sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); painCave.isFatal = 1; simError();