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/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
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/* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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 |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* |
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* NanoVolume.cpp |
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* |
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* Purpose: To calculate convexhull, hull volume and radius |
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* using the CGAL library. |
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* |
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* Created by Charles F. Vardeman II on 14 Dec 2006. |
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* @author Charles F. Vardeman II |
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* @version $Id: NanoVolume.cpp,v 1.3 2007-12-06 19:52:11 chuckv Exp $ |
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* @version $Id$ |
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* |
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*/ |
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#include "applications/staticProps/NanoVolume.hpp" |
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#if defined(HAVE_QHULL) |
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#include "math/ConvexHull.hpp" |
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#include "math/AlphaHull.hpp" |
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#endif |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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using namespace oopse; |
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using namespace OpenMD; |
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NanoVolume::NanoVolume(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) { |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
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seleMan_(info) { |
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setOutputName(getPrefix(filename) + ".avol"); |
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osq.open(getOutputFileName().c_str()); |
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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frameCounter_ = 0; |
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totalVolume_ = 0.0; |
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} |
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void NanoVolume::process() { |
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#if defined(HAVE_QHULL) |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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Vector3d vec; |
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int i,j; |
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int i; |
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ConvexHull* hull = new ConvexHull(); |
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AlphaHull* thishull = new AlphaHull(2.0); |
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//ConvexHull* thishull = new ConvexHull(); |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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pos_.reserve(info_->getNGlobalAtoms()); |
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theAtoms_.reserve(info_->getNGlobalAtoms()); |
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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RealType time = currentSnapshot_->getTime(); |
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// Clear pos vector between each frame. |
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pos_.clear(); |
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theAtoms_.clear(); |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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// update the positions of atoms which belong to the rigidbodies |
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// update the positions of atoms which belong to the rigid bodies |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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// outer loop is over the selected StuntDoubles: |
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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pos_.push_back(sd->getPos()); |
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myIndex = sd->getGlobalIndex(); |
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sd = seleMan_.nextSelected(i)) { |
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theAtoms_.push_back(sd); |
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} |
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/* variant below for signle atoms, not StuntDoubles: |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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theAtoms_.push_back(atom); |
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} |
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} |
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*/ |
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// Generate convex hull for this frame. |
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hull->genHull(pos_); |
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totalVolume_ += hull->getVolume(); |
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} |
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RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
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//std::cout.precision(7); |
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//std::cout << avgVolume << std::endl; |
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thishull->computeHull(theAtoms_); |
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RealType volume = thishull->getVolume(); |
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std::ofstream osq(getOutputFileName().c_str()); |
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osq.precision(7); |
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if (osq.is_open()){ |
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osq << avgVolume << std::endl; |
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osq.precision(7); |
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if (osq.is_open()){ |
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osq << time << "\t" << volume << std::endl; |
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} |
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} |
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osq.close(); |
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#else |
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sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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#endif |
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} |
