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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. 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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* 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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* 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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|
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#include "applications/hydrodynamics/RoughShell.hpp" |
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|
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namespace oopse { |
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|
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RoughShell::RoughShell(StuntDouble* sd, const DynamicProperty& extraParams) : HydrodynamicsModel(sd, extraParams), sdShape_(sd){ |
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DynamicProperty::const_iterator iter = extraParams.find("Sigma"); |
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if (iter != extraParams.end()) { |
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boost::any param = iter->second; |
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sigma_ = boost::any_cast<double>(param); |
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}else { |
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std::cout << "RoughShell Model Error\n" ; |
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} |
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} |
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|
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struct BeadLattice { |
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Vector3d origin; |
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double radius; |
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bool interior; |
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}; |
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|
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struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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|
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bool operator() (const BeadLattice& bead) { |
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return !bead.interior; |
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} |
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|
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}; |
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|
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struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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|
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bool operator() (const BeadLattice& bead) { |
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return bead.interior; |
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} |
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|
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}; |
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bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
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std::pair<Vector3d, Vector3d> boxBoundary = sdShape_.getBox(); |
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double len = boxBoundary.second[0] - boxBoundary.first[0]; |
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int numLattices = static_cast<int>(len/sigma_) + 1; |
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Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices); |
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|
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//fill beads |
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for (int i = 0; i < numLattices; ++i) { |
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for (int j = 0; j < numLattices; ++j) { |
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for (int k = 0; k < numLattices; ++k) { |
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BeadLattice& currentBead = grid(i, j, k); |
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currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]); |
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currentBead.radius = sigma_; |
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currentBead.interior = sdShape_.isInterior(grid(i, j, k).origin); |
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} |
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} |
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} |
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|
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//remove embedded beads |
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for (int i = 0; i < numLattices; ++i) { |
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for (int j = 0; j < numLattices; ++j) { |
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for (int k = 0; k < numLattices; ++k) { |
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std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k); |
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//if one of its neighbor cells is exterior, current cell is on the surface |
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|
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std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor()); |
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std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor()); |
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|
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if (ei != neighborCells.end() && ii != neighborCells.end()) { |
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BeadParam surfaceBead; |
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surfaceBead.atomName = "Bead"; |
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surfaceBead.pos = grid(i, j, k).origin; |
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surfaceBead.radius = grid(i, j, k).radius; |
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beads.push_back(surfaceBead); |
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} |
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|
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} |
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} |
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} |
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|
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return true; |
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} |
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|
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} |
