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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 "applications/hydrodynamics/RoughShell.hpp" |
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#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "brains/SimInfo.hpp" |
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|
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namespace OpenMD { |
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|
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RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){ |
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shape_=ShapeBuilder::createShape(sd); |
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Globals* simParams = info->getSimParams(); |
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if (simParams->haveBeadSize()) { |
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sigma_ = simParams->getBeadSize(); |
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}else { |
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|
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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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RealType 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 = shape_->getBoundingBox(); |
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RealType firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]); |
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RealType secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]); |
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RealType len = secondMax - firstMin; |
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int numLattices = static_cast<int>(len/sigma_) + 2; |
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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-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]); |
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currentBead.radius = sigma_ / 2.0; |
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currentBead.interior = shape_->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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if (grid(i, j, k).interior){ |
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|
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bool allNeighBorIsInterior = true; |
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for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) { |
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if (!l->interior) { |
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allNeighBorIsInterior = false; |
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break; |
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} |
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} |
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|
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if (allNeighBorIsInterior) |
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continue; |
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|
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BeadParam surfaceBead; |
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surfaceBead.atomName = "H"; |
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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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} |
