--- trunk/src/integrators/DLM.cpp 2008/01/23 21:22:50 1216 +++ trunk/src/integrators/DLM.cpp 2013/06/17 18:28:30 1880 @@ -6,19 +6,10 @@ * 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. @@ -37,11 +28,21 @@ * arising out of the use of or inability to use software, even if the * 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). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "DLM.hpp" -namespace oopse { +namespace OpenMD { void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) { RealType dt2 = 0.5 * dt; @@ -77,7 +78,6 @@ namespace oopse { // rotate about the z-axis angle = dt * ji[2] / I(2, 2); - sd->addZangle(angle); rotateStep( 0, 1, angle, ji, A); // rotate about the y-axis @@ -129,7 +129,6 @@ namespace oopse { // rotate the momentum acoording to: ji[] = rot[][] * ji[] ji = rot * ji; - // This code comes from converting an algorithm detailed in // J. Chem. Phys. 107 (15), pp. 5840-5851 by Dullweber, // Leimkuhler and McLachlan (DLM) for use in our code.