src/gromacs/mdlib/updategroups.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  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