--- trunk/src/applications/staticProps/NanoVolume.cpp 2008/09/14 01:32:26 1293 +++ trunk/src/applications/staticProps/NanoVolume.cpp 2009/11/25 20:02:06 1390 @@ -5,19 +5,10 @@ * 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 +28,32 @@ * 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 1.7 2008-09-14 01:32:23 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 "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 +70,7 @@ void NanoVolume::process() { } void NanoVolume::process() { -#if defined(HAVE_CGAL) || defined(HAVE_QHULL) +#if defined(HAVE_QHULL) Molecule* mol; Atom* atom; RigidBody* rb; @@ -89,10 +85,6 @@ void NanoVolume::process() { #ifdef HAVE_QHULL ConvexHull* thishull = new ConvexHull(); #endif -#ifdef HAVE_CGAL - // AlphaShape* hull = new AlphaShape(); - ConvexHull* thishull = new ConvexHull(); -#endif DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); @@ -123,15 +115,16 @@ void NanoVolume::process() { } // outer loop is over the selected StuntDoubles: - /* + for (sd = seleMan_.beginSelected(i); sd != NULL; 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; @@ -139,7 +132,7 @@ void NanoVolume::process() { theAtoms_.push_back(atom); } } - + */ // Generate convex hull for this frame. thishull->computeHull(theAtoms_); // totalVolume_ += hull->getVolume(); @@ -157,7 +150,7 @@ 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();