--- trunk/src/lattice/shapedLattice.cpp 2006/10/14 20:21:26 1070 +++ trunk/src/lattice/shapedLattice.cpp 2009/11/25 20:02:06 1390 @@ -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. @@ -37,22 +28,31 @@ * 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, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). * + * * sphericalLattice.cpp * * Created by Charles F. Vardeman II on 17 Feb 2006. * @author Charles F. Vardeman II - * @version $Id: shapedLattice.cpp,v 1.5 2006-10-14 20:21:26 gezelter Exp $ + * @version $Id: shapedLattice.cpp,v 1.8 2009-11-25 20:02:01 gezelter Exp $ * */ - +#include #include "lattice/shapedLattice.hpp" #include "math/Vector3.hpp" #include "brains/Register.hpp" #include "lattice/LatticeFactory.hpp" -namespace oopse{ +namespace OpenMD{ shapedLattice::shapedLattice(RealType latticeConstant, std::string latticeType) { latticeConstant_ = latticeConstant; @@ -82,6 +82,12 @@ namespace oopse{ endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); sitesComputed_ = false; } + + void shapedLattice::setOrigin(Vector3d origin){ + origin_ = origin; + simpleLattice_->setOrigin(origin_); + sitesComputed_ = false; + } void shapedLattice::findSites(){