#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_ #define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_ /* -------------------------------------------------------------------------- * * AmoebaOpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2008-2009 Stanford University and the Authors. * * Authors: * * Contributors: * * * * Permission is hereby granted, free of charge, to any person obtaining a * * copy of this software and associated documentation files (the "Software"), * * to deal in the Software without restriction, including without limitation * * the rights to use, copy, modify, merge, publish, distribute, sublicense, * * and/or sell copies of the Software, and to permit persons to whom the * * Software is furnished to do so, subject to the following conditions: * * * * The above copyright notice and this permission notice shall be included in * * all copies or substantial portions of the Software. * * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * * USE OR OTHER DEALINGS IN THE SOFTWARE. * * -------------------------------------------------------------------------- */ #include "openmm/Force.h" #include "openmm/Vec3.h" #include #include #include "openmm/internal/windowsExport.h" //namespace AmoebaOpenMM { namespace OpenMM { /** * This class implements an interaction between pairs of particles that varies harmonically with the distance * between them. To use it, create a HarmonicBondForce object then call addBond() once for each bond. After * a bond has been added, you can modify its force field parameters by calling setBondParameters(). */ class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force { public: /** * Create a Amoeba HarmonicBondForce. */ AmoebaHarmonicBondForce(); /** * Get the number of harmonic bond stretch terms in the potential function */ int getNumBonds() const { return bonds.size(); } /** * Set the global cubic term * * @param cubicK the cubic harmonic force constant for the bond */ void setAmoebaGlobalHarmonicBondCubic( double cubicK ); /** * Get the global cubic term * * @return global cubicK term */ double getAmoebaGlobalHarmonicBondCubic( void ) const; /** * Set the global cubic term * * @param quarticK the quartic harmonic force constant for the bond */ void setAmoebaGlobalHarmonicBondQuartic( double quarticK ); /** * Get the global quartic term * * @return global quartic term */ double getAmoebaGlobalHarmonicBondQuartic( void ) const; /** * Add a bond term to the force field. * * @param particle1 the index of the first particle connected by the bond * @param particle2 the index of the second particle connected by the bond * @param length the equilibrium length of the bond, measured in nm * @param cubic k the cubic harmonic force constant for the bond * @param quartic k the quartic harmonic force constant for the bond * @param quadratic k the quadratic harmonic force constant for the bond * @return the index of the bond that was added */ int addBond(int particle1, int particle2, double length, double quadraticK, double cubicK = DEFAULT_GLOBAL_K, double quarticK = DEFAULT_GLOBAL_K ); /** * Get the force field parameters for a bond term. * * @param index the index of the bond for which to get parameters * @param particle1 the index of the first particle connected by the bond * @param particle2 the index of the second particle connected by the bond * @param length the equilibrium length of the bond, measured in nm * @param quadratic k the quadratic harmonic force constant for the bond * @param cubic k the cubic harmonic force constant for the bond * @param quartic k the quartic harmonic force constant for the bond */ void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK, double& cubicK, double& quarticK ) const; /** * Set the force field parameters for a bond term. * * @param index the index of the bond for which to set parameters * @param particle1 the index of the first particle connected by the bond * @param particle2 the index of the second particle connected by the bond * @param length the equilibrium length of the bond, measured in nm * @param cubic k the cubic harmonic force constant for the bond * @param quartic k the quartic harmonic force constant for the bond * @param quadratic k the quadratic harmonic force constant for the bond */ void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK, double cubicK = DEFAULT_GLOBAL_K, double quarticK = DEFAULT_GLOBAL_K); protected: double _globalQuarticK, _globalCubicK; ForceImpl* createImpl(); private: static const double DEFAULT_GLOBAL_K; class BondInfo; // Retarded visual studio compiler complains about being unable to // export private stl class members. // This stanza explains that it should temporarily shut up. #if defined(_MSC_VER) #pragma warning(push) #pragma warning(disable:4251) #endif std::vector bonds; #if defined(_MSC_VER) #pragma warning(pop) #endif }; class AmoebaHarmonicBondForce::BondInfo { public: int particle1, particle2; double length, quadraticK, cubicK, quarticK; BondInfo() { particle1 = particle2 = -1; length = quadraticK = 0.0; cubicK = quarticK = DEFAULT_GLOBAL_K; } BondInfo(int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK) : particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK), cubicK(cubicK), quarticK(quarticK) { } }; } // namespace AmoebaOpenMM #endif /*OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_*/