--- trunk/src/brains/Register.cpp 2005/12/05 22:23:57 788 +++ branches/development/src/brains/Register.cpp 2011/09/14 21:15:17 1629 @@ -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" @@ -49,8 +49,14 @@ #include "integrators/NPTi.hpp" #include "integrators/NPTf.hpp" #include "integrators/NPTxyz.hpp" +#include "integrators/NPTsz.hpp" #include "integrators/NPAT.hpp" #include "integrators/NPrT.hpp" +#include "integrators/NgammaT.hpp" +#include "integrators/LangevinDynamics.hpp" +#if defined(HAVE_QHULL) +#include "integrators/LangevinHullDynamics.hpp" +#endif #include "minimizers/MinimizerFactory.hpp" #include "minimizers/MinimizerCreator.hpp" @@ -58,29 +64,21 @@ #include "minimizers/SDMinimizer.hpp" #include "UseTheForce/DUFF.hpp" #include "UseTheForce/EAM_FF.hpp" +#include "UseTheForce/EADM_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/FCCLattice.hpp" -#include "openbabel/amberformat.hpp" -#include "openbabel/fingerprintformat.hpp" -#include "openbabel/gromos96format.hpp" -#include "openbabel/oopseformat.hpp" -#include "openbabel/pdbformat.hpp" -#include "openbabel/povrayformat.hpp" -#include "openbabel/smilesformat.hpp" -#include "openbabel/tinkerformat.hpp" -#include "openbabel/xyzformat.hpp" +namespace OpenMD { -namespace oopse { - - void registerForceFields() { /** @todo move to a seperate initialization module */ //DUFF, WATER and LJ are merged into one force field @@ -89,13 +87,18 @@ namespace oopse { ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("LJ")); //in theory, EAM can also be merged ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("EAM")); + ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder("EADM")); //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")); @@ -104,7 +107,16 @@ namespace oopse { 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("LHULL")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("LANGEVINHULL")); + IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder("SMIPD")); +#endif } void registerMinimizers() { @@ -116,17 +128,6 @@ namespace oopse { LatticeFactory::getInstance()->registerLattice(new LatticeBuilder("FCC")); } - void registerOBFormats(){ - static OpenBabel::AmberPrepFormat amberFormatInstance; - static OpenBabel::FingerprintFormat fingerprintFormatInstance; - static OpenBabel::OOPSEFormat oopseFormatInstance; - static OpenBabel::PDBFormat pdbFormatInstance; - static OpenBabel::PovrayFormat povaryFormatInstance; - static OpenBabel::SMIFormat smilesFormatInstance; - static OpenBabel::TinkerFormat tinkerFormatInstance; - static OpenBabel::XYZFormat xyzFormatInstance; - } - void registerAll() { registerForceFields(); registerIntegrators();