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/* |
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* Copyright (c) 2005 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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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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, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "selection/HullFinder.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "math/ConvexHull.hpp" |
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|
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namespace OpenMD { |
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|
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HullFinder::HullFinder(SimInfo* info) : info_(info) { |
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|
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nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
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stuntdoubles_.resize(nStuntDoubles_); |
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|
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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StuntDouble* sd; |
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Molecule::IntegrableObjectIterator ioi; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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// Hull is constructed from all known integrable objects. |
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for (sd = mol->beginIntegrableObject(ioi); |
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sd != NULL; |
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sd = mol->nextIntegrableObject(ioi)) { |
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localSites_.push_back(sd); |
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} |
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|
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// selection can include atoms (which may be a subset of the IOs) |
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for(atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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stuntdoubles_[atom->getGlobalIndex()] = atom; |
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} |
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|
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// and rigid bodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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stuntdoubles_[rb->getGlobalIndex()] = rb; |
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} |
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|
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} |
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#ifdef HAVE_QHULL |
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surfaceMesh_ = new ConvexHull(); |
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#endif |
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} |
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|
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OpenMDBitSet HullFinder::findHull() { |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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OpenMDBitSet bsResult(nStuntDoubles_); |
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#ifdef HAVE_QHULL |
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surfaceMesh_->computeHull(localSites_); |
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#else |
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sprintf( painCave.errMsg, |
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"HullFinder : Hull calculation is not possible without libqhull.\n" |
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"\tPlease rebuild OpenMD with qhull enabled."); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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#endif |
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|
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std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
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int nTriangles = sMesh.size(); |
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// Loop over the mesh faces |
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std::vector<Triangle>::iterator face; |
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std::vector<StuntDouble*>::iterator vertex; |
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|
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// This will work in parallel because the triangles returned by the mesh |
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// have a NULL stuntDouble if this processor doesn't own the |
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|
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for (face = sMesh.begin(); face != sMesh.end(); ++face) { |
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Triangle thisTriangle = *face; |
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std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
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for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) { |
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if ((*vertex) != NULL) { |
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bsResult.setBitOn((*vertex)->getGlobalIndex()); |
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} |
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} |
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} |
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return bsResult; |
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} |
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|
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} |
