1 /* 2 * This file is part of the GROMACS molecular simulation package. 3 * 4 * Copyright (c) 2018,2019, 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 * 37 * \brief Declares the functions for generating update groups 38 * 39 * \author Berk Hess <hess@kth.se> 40 * \ingroup module_mdlib 41 * \inlibraryapi 42 */ 43 #ifndef GMX_MDLIB_UPDATEGROUPS 44 #define GMX_MDLIB_UPDATEGROUPS 45 46 #include <vector> 47 48 #include "gromacs/utility/arrayref.h" 49 #include "gromacs/utility/real.h" 50 51 struct gmx_mtop_t; 52 struct t_inputrec; 53 54 namespace gmx 55 { 56 class RangePartitioning; 57 58 /*! \brief Returns a vector with update groups for each moleculetype in \p mtop 59 * or an empty vector when the criteria (see below) are not satisfied. 60 * 61 * An empty vector is returned when at least one moleculetype does not obey 62 * the restrictions of update groups, e.g. more than two constraints in a row. 63 * 64 * Currently valid update groups are: 65 * a single atom which is not a virtual site and does not have constraints; 66 * or a group of atoms where all virtual sites are constructed from atoms 67 * within the group and at least one non-vsite atom is constrained to 68 * all other non-vsite atoms. 69 * To have update groups, all virtual sites should be linear 2 or 3 atom 70 * constructions with coefficients >= 0 and sum of coefficients <= 1. 71 * 72 * \param[in] mtop The system topology 73 */ 74 std::vector<RangePartitioning> makeUpdateGroups(const gmx_mtop_t& mtop); 75 76 /*! \brief Returns the maximum update group radius 77 * 78 * \note When \p updateGroups is empty, 0 is returned. 79 * 80 * \param[in] mtop The system topology 81 * \param[in] updateGroups List of update group, size should match the number of moltypes in \p mtop or be 0 82 * \param[in] temperature The maximum reference temperature, pass -1 when unknown or not applicable 83 */ 84 real computeMaxUpdateGroupRadius(const gmx_mtop_t& mtop, 85 gmx::ArrayRef<const RangePartitioning> updateGroups, 86 real temperature); 87 88 } // namespace gmx 89 90 #endif // GMX_MDLIB_UPDATEGROUPS 91