--- trunk/src/lattice/shapedLattice.cpp 2006/03/29 19:17:20 923 +++ branches/development/src/lattice/shapedLattice.cpp 2013/02/20 15:39:39 1850 @@ -5,19 +5,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,81 +28,109 @@ * University of Notre Dame has been advised of the possibility of * such damages. * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [4] Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * * * sphericalLattice.cpp * * Created by Charles F. Vardeman II on 17 Feb 2006. + * Edited by Kelsey M. Stocker on 23 Feb 2012. * @author Charles F. Vardeman II - * @version $Id: shapedLattice.cpp,v 1.3 2006-03-29 19:17:20 chuckv Exp $ + * @version $Id$ * */ - +#include #include "lattice/shapedLattice.hpp" #include "math/Vector3.hpp" #include "brains/Register.hpp" #include "lattice/LatticeFactory.hpp" -namespace oopse{ - shapedLattice::shapedLattice(double latticeConstant, +namespace OpenMD{ + shapedLattice::shapedLattice(RealType latticeConstant, std::string latticeType) { - latticeConstant_ = latticeConstant; - latticeType_ = latticeType; - registerLattice(); - simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); - if (simpleLattice_ == NULL){ - std::cerr << "shapedLattice:: Error creating lattice" << std::endl; - exit(1); - } + latticeConstant_ = latticeConstant; + latticeType_ = latticeType; + registerLattice(); + simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); + if (simpleLattice_ == NULL){ + std::cerr << "shapedLattice:: Error creating lattice" << std::endl; + exit(1); + } - //Set the lattice constant - std::vector lc; + //Set the lattice constant + std::vector lc; lc.push_back(latticeConstant_); - simpleLattice_->setLatticeConstant(lc); - } - - - + simpleLattice_->setLatticeConstant(lc); + sitesComputed_ = false; + } + void shapedLattice::setGridDimension(Vector3d dimension){ dimension_ = dimension; - // Find number of unit cells in each direction - beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; - beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; - beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; + // Find number of unit cells in each direction + beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; + beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; + beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_); - endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); - endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); + endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); + endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); + std::cerr << "begin = " << beginNx_ << " " << beginNy_ << " " << beginNz_ << "\n"; + std::cerr << "end = " << endNx_ << " " << endNy_ << " " << endNz_ << "\n"; + sitesComputed_ = false; } + + void shapedLattice::setOrigin(Vector3d origin){ + origin_ = origin; + simpleLattice_->setOrigin(origin_); + sitesComputed_ = false; + } - - - std::vector shapedLattice::getPoints(){ - std::vector latticePos; - - - std::vector pointsOrt = simpleLattice_->getLatticePointsOrt(); - int numMolPerCell = simpleLattice_->getNumSitesPerCell(); - for(int i = beginNx_; i < endNx_; i++) { - for(int j = beginNy_; j < endNy_; j++) { - for(int k = beginNz_; k < endNz_; k++) { - //get the position of the cell sites - simpleLattice_->getLatticePointsPos(latticePos, i, j, k); - - for(int l = 0; l < numMolPerCell; l++) { - - - if (isInterior(latticePos[l])){ - Vector3d myPoint = latticePos[l]; - Vector3d myOrt = pointsOrt[l]; - coords_.push_back(myPoint); - coordsOrt_.push_back(myOrt); - } + void shapedLattice::findSites(){ + + sites_.clear(); + orientations_.clear(); + + std::vector latticePos; + std::vector pointsOrt = simpleLattice_->getLatticePointsOrt(); + int numMolPerCell = simpleLattice_->getNumSitesPerCell(); + + for(int i = beginNx_; i < endNx_; i++) { + for(int j = beginNy_; j < endNy_; j++) { + for(int k = beginNz_; k < endNz_; k++) { + //get the position of the cell sites + simpleLattice_->getLatticePointsPos(latticePos, i, j, k); + for(int l = 0; l < numMolPerCell; l++) { + if (isInterior(latticePos[l])){ + Vector3d myPoint = latticePos[l]; + Vector3d myOrt = pointsOrt[l]; + sites_.push_back(myPoint); + orientations_.push_back(myOrt); } } } } - - return coords_; - - } + } + sitesComputed_ = true; + } + + std::vector shapedLattice::getSites() { + if (!sitesComputed_) { + findSites(); + } + return sites_; + } + + std::vector shapedLattice::getOrientations() { + if (!sitesComputed_) { + findSites(); + } + return orientations_; + } }