--- trunk/src/brains/Register.cpp 2005/04/12 21:58:09 484 +++ branches/development/src/brains/Register.cpp 2010/07/09 23:08:25 1465 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -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. @@ -37,6 +28,15 @@ * 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] Vardeman & Gezelter, in progress (2009). */ #include "brains/Register.hpp" @@ -49,6 +49,14 @@ #include "integrators/NPTi.hpp" #include "integrators/NPTf.hpp" #include "integrators/NPTxyz.hpp" +#include "integrators/NPAT.hpp" +#include "integrators/NPrT.hpp" +#include "integrators/NgammaT.hpp" +#include "integrators/LangevinDynamics.hpp" +#if defined(HAVE_QHULL) +#include "integrators/SMIPDynamics.hpp" +#endif + #include "minimizers/MinimizerFactory.hpp" #include "minimizers/MinimizerCreator.hpp" #include "minimizers/PRCG.hpp" @@ -57,14 +65,19 @@ #include "UseTheForce/EAM_FF.hpp" #include "UseTheForce/ForceFieldFactory.hpp" #include "UseTheForce/ForceFieldCreator.hpp" +#include "UseTheForce/SHAPES_FF.hpp" +#include "UseTheForce/SC_FF.hpp" +#include "UseTheForce/MnM_FF.hpp" +#include "UseTheForce/CLAYFF.hpp" +#include "UseTheForce/Amber_FF.hpp" #include "lattice/LatticeFactory.hpp" #include "lattice/LatticeCreator.hpp" -#include "lattice/Lattice.hpp" +#include "lattice/FCCLattice.hpp" -namespace oopse { +namespace OpenMD { -void registerForceFields() { + void registerForceFields() { /** @todo move to a seperate initialization module */ //DUFF, WATER and LJ are merged into one force field ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("DUFF")); @@ -72,30 +85,48 @@ void registerForceFields() { ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("LJ")); //in theory, EAM can also be merged ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("EAM")); -} - -void registerIntegrators() { + //heck, that worked... let's try merging SHAPES + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("SHAPES")); + //Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not). + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("SC")); + //Well if Sutton-Chen worked... then lets just mangle all of the forcefields together in MnM. + //That sounds like a good idea right...... + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("MnM")); + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("CLAY")); + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("Amber")); + } + + void registerIntegrators() { IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NVE")); IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NVT")); - IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTi")); - IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTf")); - IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTxyz")); -} + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTI")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTF")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPTXYZ")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPAT")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPRT")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NPGT")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NGT")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("NGAMMAT")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("LANGEVINDYNAMICS")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("LD")); +#if defined(HAVE_QHULL) + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("SMIPD")); +#endif + } -void registerMinimizers() { + void registerMinimizers() { MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder("SD")); MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder("CG")); -} + } -void registerLattice(){ - LatticeFactory::getInstance()->registerLattice(new LatticeBuilder("CUBIC")); + void registerLattice(){ LatticeFactory::getInstance()->registerLattice(new LatticeBuilder("FCC")); -} + } -void registerAll() { + void registerAll() { registerForceFields(); registerIntegrators(); registerMinimizers(); -} + } }