#ifndef OPENMM_AMOEBA_STRETCH_BEND_FORCE_H_ #define OPENMM_AMOEBA_STRETCH_BEND_FORCE_H_ /* -------------------------------------------------------------------------- * * OpenMMAmoeba * * -------------------------------------------------------------------------- * * 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) 2008-2016 Stanford University and the Authors. * * Authors: Mark Friedrichs, Peter Eastman * * 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 "internal/windowsExportAmoeba.h" #include namespace OpenMM { /** * This class implements the Amoeba stretch-bend interaction. * * To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend. After * a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters(). * This will have no effect on Contexts that already exist unless you call updateParametersInContext(). */ class OPENMM_EXPORT_AMOEBA AmoebaStretchBendForce : public Force { public: /** * Create an AmoebaStretchBendForce. */ AmoebaStretchBendForce(); /** * Get the number of stretch-bend terms in the potential function */ int getNumStretchBends() const { return stretchBends.size(); } /** * Add a stretch-bend term to the force field. * * @param particle1 the index of the first particle connected by the stretch-bend * @param particle2 the index of the second particle connected by the stretch-bend * @param particle3 the index of the third particle connected by the stretch-bend * @param lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm * @param lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm * @param angle the equilibrium angle in radians * @param k1 the force constant of the product of bond ab and angle a-b-c * @param k2 the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1) * @return the index of the stretch-bend that was added */ int addStretchBend(int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k1, double k2); /** * Get the force field parameters for a stretch-bend term. * * @param index the index of the stretch-bend for which to get parameters * @param[out] particle1 the index of the first particle connected by the stretch-bend * @param[out] particle2 the index of the second particle connected by the stretch-bend * @param[out] particle3 the index of the third particle connected by the stretch-bend * @param[out] lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm * @param[out] lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm * @param[out] angle the equilibrium angle in radians * @param[out] k1 the force constant of the product of bond ab and angle a-b-c * @param[out] k2 the force constant of the product of bond bc and angle a-b-c */ void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3, double& lengthAB, double& lengthCB, double& angle, double& k1, double& k2) const; /** * Set the force field parameters for a stretch-bend term. * * @param index the index of the stretch-bend for which to set parameters * @param particle1 the index of the first particle connected by the stretch-bend * @param particle2 the index of the second particle connected by the stretch-bend * @param particle3 the index of the third particle connected by the stretch-bend * @param lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm * @param lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm * @param angle the equilibrium angle in radians * @param k1 the force constant of the product of bond ab and angle a-b-c * @param k2 the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1) */ void setStretchBendParameters(int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k1, double k2); /** * Update the per-stretch-bend term parameters in a Context to match those stored in this Force object. This method provides * an efficient method to update certain parameters in an existing Context without needing to reinitialize it. * Simply call setStretchBendParameters() to modify this object's parameters, then call updateParametersInContext() * to copy them over to the Context. * * The only information this method updates is the values of per-stretch-bend term parameters. The set of particles involved * in a term cannot be changed, nor can new terms be added. */ void updateParametersInContext(Context& context); /** * Set whether this force should apply periodic boundary conditions when calculating displacements. * Usually this is not appropriate for bonded forces, but there are situations when it can be useful. */ void setUsesPeriodicBoundaryConditions(bool periodic); /** * Returns whether or not this force makes use of periodic boundary * conditions. * * @returns true if force uses PBC and false otherwise */ bool usesPeriodicBoundaryConditions() const; protected: ForceImpl* createImpl() const; private: class StretchBendInfo; std::vector stretchBends; bool usePeriodic; }; /** * This is an internal class used to record information about a stretch-bend. * @private */ class AmoebaStretchBendForce::StretchBendInfo { public: int particle1, particle2, particle3; double lengthAB, lengthCB, angle, k1, k2; StretchBendInfo() { particle1 = particle2 = particle3 = -1; lengthAB = lengthCB = angle = k1 = k2 = 0.0; } StretchBendInfo(int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k1, double k2) : particle1(particle1), particle2(particle2), particle3(particle3), lengthAB(lengthAB), lengthCB(lengthCB), angle(angle), k1(k1), k2(k2) { } }; } // namespace OpenMM #endif /*OPENMM_AMOEBA_STRETCH_BEND_FORCE_H_*/