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/* Copyright (c) 2006 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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* sphericalLattice.cpp |
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* |
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* Created by Charles F. Vardeman II on 17 Feb 2006. |
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* @author Charles F. Vardeman II |
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* @version $Id: shapedLattice.cpp,v 1.7 2008-09-10 19:51:43 cli2 Exp $ |
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* |
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*/ |
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|
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#include <cstdlib> |
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#include "lattice/shapedLattice.hpp" |
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#include "math/Vector3.hpp" |
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#include "brains/Register.hpp" |
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#include "lattice/LatticeFactory.hpp" |
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|
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namespace oopse{ |
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shapedLattice::shapedLattice(RealType latticeConstant, |
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std::string latticeType) { |
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latticeConstant_ = latticeConstant; |
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latticeType_ = latticeType; |
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registerLattice(); |
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simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); |
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if (simpleLattice_ == NULL){ |
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std::cerr << "shapedLattice:: Error creating lattice" << std::endl; |
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exit(1); |
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} |
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|
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//Set the lattice constant |
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std::vector<RealType> lc; |
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lc.push_back(latticeConstant_); |
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simpleLattice_->setLatticeConstant(lc); |
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sitesComputed_ = false; |
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} |
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|
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void shapedLattice::setGridDimension(Vector3d dimension){ |
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dimension_ = dimension; |
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// Find number of unit cells in each direction |
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beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; |
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beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; |
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beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; |
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endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_); |
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endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); |
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endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); |
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sitesComputed_ = false; |
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} |
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|
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void shapedLattice::setOrigin(Vector3d origin){ |
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origin_ = origin; |
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simpleLattice_->setOrigin(origin_); |
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sitesComputed_ = false; |
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} |
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|
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void shapedLattice::findSites(){ |
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|
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sites_.clear(); |
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orientations_.clear(); |
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|
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std::vector<Vector3d> latticePos; |
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std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt(); |
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int numMolPerCell = simpleLattice_->getNumSitesPerCell(); |
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|
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for(int i = beginNx_; i < endNx_; i++) { |
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for(int j = beginNy_; j < endNy_; j++) { |
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for(int k = beginNz_; k < endNz_; k++) { |
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//get the position of the cell sites |
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simpleLattice_->getLatticePointsPos(latticePos, i, j, k); |
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for(int l = 0; l < numMolPerCell; l++) { |
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if (isInterior(latticePos[l])){ |
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Vector3d myPoint = latticePos[l]; |
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Vector3d myOrt = pointsOrt[l]; |
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sites_.push_back(myPoint); |
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orientations_.push_back(myOrt); |
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} |
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} |
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} |
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} |
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} |
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sitesComputed_ = true; |
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} |
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|
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std::vector<Vector3d> shapedLattice::getSites() { |
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if (!sitesComputed_) { |
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findSites(); |
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} |
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return sites_; |
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} |
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|
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std::vector<Vector3d> shapedLattice::getOrientations() { |
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if (!sitesComputed_) { |
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findSites(); |
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} |
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return orientations_; |
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} |
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} |
