1 /* 2 * This file is part of the GROMACS molecular simulation package. 3 * 4 * Copyright (c) 2020,2021, by the GROMACS development team, led by 5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, 6 * and including many others, as listed in the AUTHORS file in the 7 * top-level source directory and at http://www.gromacs.org. 8 * 9 * GROMACS is free software; you can redistribute it and/or 10 * modify it under the terms of the GNU Lesser General Public License 11 * as published by the Free Software Foundation; either version 2.1 12 * of the License, or (at your option) any later version. 13 * 14 * GROMACS is distributed in the hope that it will be useful, 15 * but WITHOUT ANY WARRANTY; without even the implied warranty of 16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 17 * Lesser General Public License for more details. 18 * 19 * You should have received a copy of the GNU Lesser General Public 20 * License along with GROMACS; if not, see 21 * http://www.gnu.org/licenses, or write to the Free Software Foundation, 22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 23 * 24 * If you want to redistribute modifications to GROMACS, please 25 * consider that scientific software is very special. Version 26 * control is crucial - bugs must be traceable. We will be happy to 27 * consider code for inclusion in the official distribution, but 28 * derived work must not be called official GROMACS. Details are found 29 * in the README & COPYING files - if they are missing, get the 30 * official version at http://www.gromacs.org. 31 * 32 * To help us fund GROMACS development, we humbly ask that you cite 33 * the research papers on the package. Check out http://www.gromacs.org. 34 */ 35 /*! \libinternal \file 36 * \brief Translation layer to GROMACS data structures for force calculations. 37 * 38 * Implements the translation layer between the user scope and 39 * GROMACS data structures for force calculations. Sets up the 40 * non-bonded verlet. 41 * 42 * \author Victor Holanda <victor.holanda@cscs.ch> 43 * \author Joe Jordan <ejjordan@kth.se> 44 * \author Prashanth Kanduri <kanduri@cscs.ch> 45 * \author Sebastian Keller <keller@cscs.ch> 46 */ 47 48 #ifndef NBLIB_GMXSETUP_H 49 #define NBLIB_GMXSETUP_H 50 51 #include "nblib/gmxcalculator.h" 52 #include "nblib/simulationstate.h" 53 54 namespace Nbnxm 55 { 56 struct KernelSetup; 57 } 58 59 namespace nblib 60 { 61 62 /*! \brief Sets up the GROMACS data structures for the non-bonded force calculator 63 * 64 * This data structure initializes the GmxForceCalculator object which internally 65 * contains various objects needed to perform non-bonded force calculations using 66 * the internal representation for the problem as required for GROMACS. 67 * 68 * The public functions of this class basically translate the problem description 69 * specified by the user in NBLIB. This ultimately returns the GmxForceCalculator 70 * object which is used by the ForceCalculator object in the user-facing library. 71 * 72 */ 73 class NbvSetupUtil final 74 { 75 public: 76 NbvSetupUtil(); 77 78 //! Sets hardware params from the execution context 79 void setExecutionContext(const NBKernelOptions& options); 80 81 //! Sets non-bonded parameters to be used to build GMX data structures 82 void setNonBondedParameters(const std::vector<ParticleType>& particleTypes, 83 const NonBondedInteractionMap& nonBondedInteractionMap); 84 85 //! Marks particles to have Van der Waals interactions 86 void setParticleInfoAllVdv(size_t numParticles); 87 88 //! Returns the kernel setup 89 Nbnxm::KernelSetup getKernelSetup(const NBKernelOptions& options); 90 91 //! Set up StepWorkload data 92 void setupStepWorkload(const NBKernelOptions& options); 93 94 //! Return an interaction constants struct with members set appropriately 95 void setupInteractionConst(const NBKernelOptions& options); 96 97 //! Sets Particle Types and Charges and VdW params 98 void setAtomProperties(const std::vector<int>& particleTypeIdOfAllParticles, 99 const std::vector<real>& charges); 100 101 //! Sets up non-bonded verlet on the GmxForceCalculator 102 void setupNbnxmInstance(size_t numParticleTypes, const NBKernelOptions& options); 103 104 //! Puts particles on a grid based on bounds specified by the box 105 void setParticlesOnGrid(const std::vector<Vec3>& coordinates, const Box& box); 106 107 //! Constructs pair lists 108 void constructPairList(ExclusionLists<int> exclusionLists); 109 110 //! Sets up t_forcerec object on the GmxForceCalculator 111 void setupForceRec(const matrix& box); 112 113 //! Returns a unique pointer a GmxForceCalculator object getGmxForceCalculator()114 std::unique_ptr<GmxForceCalculator> getGmxForceCalculator() 115 { 116 return std::move(gmxForceCalculator_); 117 } 118 119 private: 120 //! Storage for parameters for short range interactions. 121 std::vector<real> nonbondedParameters_; 122 123 //! Particle info where all particles are marked to have Van der Waals interactions 124 std::vector<int> particleInfoAllVdw_; 125 126 //! GROMACS force calculator to compute forces 127 std::unique_ptr<GmxForceCalculator> gmxForceCalculator_; 128 }; 129 130 /*! \brief Calls the setup utilities needed to initialize a GmxForceCalculator object 131 * 132 * The GmxSetupDirector encapsulates the multi-stage setup of the GmxForceCalculator which 133 * is done using the public functions of the NbvSetupUtil. This separation ensures that the 134 * NbvSetupUtil object is temporary in scope. The function definition makes it easy for the 135 * developers to follow the sequence of calls and the dataflow involved in setting up 136 * the non-bonded force calculation backend. This is the only function needed to be called 137 * from the ForceCalculator during construction. 138 * 139 */ 140 class GmxSetupDirector 141 { 142 public: 143 //! Sets up and returns a GmxForceCalculator 144 static std::unique_ptr<GmxForceCalculator> setupGmxForceCalculator(const SimulationState& system, 145 const NBKernelOptions& options); 146 }; 147 148 } // namespace nblib 149 #endif // NBLIB_GMXSETUP_H 150