/* Portions copyright (c) 2006-2016 Stanford University and Simbios. * Contributors: Pande Group * * 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. */ #ifndef __ReferenceStochasticDynamics_H__ #define __ReferenceStochasticDynamics_H__ #include "ReferenceDynamics.h" #include "openmm/internal/windowsExport.h" namespace OpenMM { class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { protected: std::vector xPrime; std::vector inverseMasses; double friction; public: /**--------------------------------------------------------------------------------------- Constructor @param numberOfAtoms number of atoms @param deltaT delta t for dynamics @param friction friction coefficient @param temperature temperature --------------------------------------------------------------------------------------- */ ReferenceStochasticDynamics(int numberOfAtoms, double deltaT, double friction, double temperature); /**--------------------------------------------------------------------------------------- Destructor --------------------------------------------------------------------------------------- */ ~ReferenceStochasticDynamics(); /**--------------------------------------------------------------------------------------- Get friction coefficient --------------------------------------------------------------------------------------- */ double getFriction() const; /**--------------------------------------------------------------------------------------- Update @param system the System to be integrated @param atomCoordinates atom coordinates @param velocities velocities @param forces forces @param masses atom masses @param tolerance the constraint tolerance --------------------------------------------------------------------------------------- */ void update(const OpenMM::System& system, std::vector& atomCoordinates, std::vector& velocities, std::vector& forces, std::vector& masses, double tolerance); /**--------------------------------------------------------------------------------------- First update; based on code in update.c do_update_sd() Gromacs 3.1.4 @param numberOfAtoms number of atoms @param atomCoordinates atom coordinates @param velocities velocities @param forces forces @param inverseMasses inverse atom masses @param xPrime xPrime --------------------------------------------------------------------------------------- */ virtual void updatePart1(int numberOfAtoms, std::vector& atomCoordinates, std::vector& velocities, std::vector& forces, std::vector& inverseMasses, std::vector& xPrime); /**--------------------------------------------------------------------------------------- Second update @param numberOfAtoms number of atoms @param atomCoordinates atom coordinates @param velocities velocities @param forces forces @param inverseMasses inverse atom masses --------------------------------------------------------------------------------------- */ virtual void updatePart2(int numberOfAtoms, std::vector& atomCoordinates, std::vector& velocities, std::vector& forces, std::vector& inverseMasses, std::vector& xPrime); /**--------------------------------------------------------------------------------------- Third update @param numberOfAtoms number of atoms @param atomCoordinates atom coordinates @param velocities velocities @param inverseMasses inverse atom masses --------------------------------------------------------------------------------------- */ virtual void updatePart3(int numberOfAtoms, std::vector& atomCoordinates, std::vector& velocities, std::vector& inverseMasses, std::vector& xPrime); }; } // namespace OpenMM #endif // __ReferenceStochasticDynamics_H__