#ifndef OPENMM_OPENCLINTEGRATIONUTILITIES_H_ #define OPENMM_OPENCLINTEGRATIONUTILITIES_H_ /* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * 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) 2009-2018 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU Lesser General Public License as published * * by the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public License * * along with this program. If not, see . * * -------------------------------------------------------------------------- */ #include "openmm/System.h" #include "OpenCLContext.h" #include "windowsExportOpenCL.h" #include namespace OpenMM { /** * This class implements features that are used by many different integrators, including * common workspace arrays, random number generation, and enforcing constraints. */ class OPENMM_EXPORT_OPENCL OpenCLIntegrationUtilities { public: OpenCLIntegrationUtilities(OpenCLContext& context, const System& system); /** * Get the array which contains position deltas. */ OpenCLArray& getPosDelta() { return posDelta; } /** * Get the array which contains random values. Each element is a float4, whose components * are independent, normally distributed random numbers with mean 0 and variance 1. */ OpenCLArray& getRandom() { return random; } /** * Get the array which contains the current step size. */ OpenCLArray& getStepSize() { return stepSize; } /** * Set the size to use for the next step. */ void setNextStepSize(double size); /** * Get the size that was used for the last step. */ double getLastStepSize(); /** * Apply constraints to the atom positions. * * @param tol the constraint tolerance */ void applyConstraints(double tol); /** * Apply constraints to the atom velocities. * * @param tol the constraint tolerance */ void applyVelocityConstraints(double tol); /** * Initialize the random number generator. */ void initRandomNumberGenerator(unsigned int randomNumberSeed); /** * Ensure that sufficient random numbers are available in the array, and generate new ones if not. * * @param numValues the number of random float4's that will be required * @return the index in the array at which to start reading */ int prepareRandomNumbers(int numValues); /** * Compute the positions of virtual sites. */ void computeVirtualSites(); /** * Distribute forces from virtual sites to the atoms they are based on. */ void distributeForcesFromVirtualSites(); /** * Create a checkpoint recording the current state of the random number generator. * * @param stream an output stream the checkpoint data should be written to */ void createCheckpoint(std::ostream& stream); /** * Load a checkpoint that was written by createCheckpoint(). * * @param stream an input stream the checkpoint data should be read from */ void loadCheckpoint(std::istream& stream); /** * Compute the kinetic energy of the system, possibly shifting the velocities in time to account * for a leapfrog integrator. * * @param timeShift the amount by which to shift the velocities in time */ double computeKineticEnergy(double timeShift); private: void applyConstraints(bool constrainVelocities, double tol); OpenCLContext& context; cl::Kernel settlePosKernel, settleVelKernel; cl::Kernel shakePosKernel, shakeVelKernel; cl::Kernel ccmaDirectionsKernel; cl::Kernel ccmaPosForceKernel, ccmaVelForceKernel; cl::Kernel ccmaMultiplyKernel; cl::Kernel ccmaPosUpdateKernel, ccmaVelUpdateKernel; cl::Kernel vsitePositionKernel, vsiteForceKernel, vsiteAddForcesKernel; cl::Kernel randomKernel, timeShiftKernel; OpenCLArray posDelta; OpenCLArray settleAtoms; OpenCLArray settleParams; OpenCLArray shakeAtoms; OpenCLArray shakeParams; OpenCLArray random; OpenCLArray randomSeed; OpenCLArray stepSize; OpenCLArray ccmaAtoms; OpenCLArray ccmaDistance; OpenCLArray ccmaReducedMass; OpenCLArray ccmaAtomConstraints; OpenCLArray ccmaNumAtomConstraints; OpenCLArray ccmaConstraintMatrixColumn; OpenCLArray ccmaConstraintMatrixValue; OpenCLArray ccmaDelta1; OpenCLArray ccmaDelta2; OpenCLArray ccmaConverged; OpenCLArray ccmaConvergedHostBuffer; OpenCLArray vsite2AvgAtoms; OpenCLArray vsite2AvgWeights; OpenCLArray vsite3AvgAtoms; OpenCLArray vsite3AvgWeights; OpenCLArray vsiteOutOfPlaneAtoms; OpenCLArray vsiteOutOfPlaneWeights; OpenCLArray vsiteLocalCoordsIndex; OpenCLArray vsiteLocalCoordsAtoms; OpenCLArray vsiteLocalCoordsWeights; OpenCLArray vsiteLocalCoordsPos; OpenCLArray vsiteLocalCoordsStartIndex; int randomPos; int lastSeed, numVsites; bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer, hasOverlappingVsites; mm_double2 lastStepSize; struct ShakeCluster; struct ConstraintOrderer; }; } // namespace OpenMM #endif /*OPENMM_OPENCLINTEGRATIONUTILITIES_H_*/