--- trunk/src/hydrodynamics/Sphere.cpp 2008/11/24 22:01:56 1322 +++ branches/development/src/hydrodynamics/Sphere.cpp 2011/11/22 20:38:56 1665 @@ -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. @@ -37,13 +28,23 @@ * 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, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "hydrodynamics/Sphere.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "math/LU.hpp" -namespace oopse { +namespace OpenMD { Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){ @@ -83,11 +84,11 @@ namespace oopse { Xi(4, 4) = Xirr; Xi(5, 5) = Xirr; - Xi *= OOPSEConstant::viscoConvert; + Xi *= PhysicalConstants::viscoConvert; XiCopy = Xi; invertMatrix(XiCopy, D); - RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1 + RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans) HydroProp* hprop = new HydroProp(V3Zero, Xi, D);