src/gromacs/mdlib/vsite.h

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  37 #ifndef GMX_MDLIB_VSITE_H
  38 #define GMX_MDLIB_VSITE_H
  39
  40 #include <memory>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/pbcutil/ishift.h"
  44 #include "gromacs/topology/idef.h"
  45 #include "gromacs/utility/arrayref.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48
  49 struct gmx_localtop_t;
  50 struct gmx_mtop_t;
  51 struct t_commrec;
  52 struct t_graph;
  53 struct t_ilist;
  54 struct t_mdatoms;
  55 struct t_nrnb;
  56 struct gmx_wallcycle;
  57 struct VsiteThread;
  58
  59 namespace gmx
  60 {
  61 class RangePartitioning;
  62 }
  63
  64 /* The start and end values of for the vsite indices in the ftype enum.
  65  * The validity of these values is checked in init_vsite.
  66  * This is used to avoid loops over all ftypes just to get the vsite entries.
  67  * (We should replace the fixed ilist array by only the used entries.)
  68  */
  69 static constexpr int c_ftypeVsiteStart = F_VSITE2;
  70 static constexpr int c_ftypeVsiteEnd   = F_VSITEN + 1;
  71
  72 /* Type for storing PBC atom information for all vsite types in the system */
  73 typedef std::array<std::vector<int>, c_ftypeVsiteEnd - c_ftypeVsiteStart> VsitePbc;
  74
  75 /* Data for handling vsites, needed with OpenMP threading or with charge-groups and PBC */
  76 struct gmx_vsite_t
  77 {
  78     gmx_vsite_t();
  79
  80     ~gmx_vsite_t();
  81
  82     /* The number of vsites that cross update groups, when =0 no PBC treatment is needed */
  83     int                       numInterUpdategroupVsites;
  84     int                       nthreads;                  /* Number of threads used for vsites       */
  85     std::vector < std::unique_ptr < VsiteThread>> tData; /* Thread local vsites and work structs    */
  86     std::vector<int>          taskIndex;                 /* Work array                              */
  87     bool                      useDomdec;                 /* Tells whether we use domain decomposition with more than 1 DD rank */
  88 };
  89
  90 /*! \brief Create positions of vsite atoms based for the local system
  91  *
  92  * \param[in]     vsite    The vsite struct, when nullptr is passed, no MPI and no multi-threading is used
  93  * \param[in,out] x        The coordinates
  94  * \param[in]     dt       The time step
  95  * \param[in,out] v        When != nullptr, velocities for vsites are set as displacement/dt
  96  * \param[in]     ip       Interaction parameters
  97  * \param[in]     ilist    The interaction list
  98  * \param[in]     ePBC     The type of periodic boundary conditions
  99  * \param[in]     bMolPBC  When true, molecules are broken over PBC
 100  * \param[in]     cr       The communication record
 101  * \param[in]     box      The box
 102  */
 103 void construct_vsites(const gmx_vsite_t *vsite,
 104                       rvec x[],
 105                       real dt, rvec v[],
 106                       const t_iparams ip[], const t_ilist ilist[],
 107                       int ePBC, gmx_bool bMolPBC,
 108                       const t_commrec *cr,
 109                       const matrix box);
 110
 111 /*! \brief Create positions of vsite atoms for the whole system assuming all molecules are wholex
 112  *
 113  * \param[in]     mtop  The global topology
 114  * \param[in,out] x     The global coordinates
 115  */
 116 void constructVsitesGlobal(const gmx_mtop_t         &mtop,
 117                            gmx::ArrayRef<gmx::RVec>  x);
 118
 119 void spread_vsite_f(const gmx_vsite_t *vsite,
 120                     const rvec x[],
 121                     rvec f[], rvec *fshift,
 122                     gmx_bool VirCorr, matrix vir,
 123                     t_nrnb *nrnb, const t_idef *idef,
 124                     int ePBC, gmx_bool bMolPBC, const t_graph *g, const matrix box,
 125                     const t_commrec *cr, gmx_wallcycle *wcycle);
 126 /* Spread the force operating on the vsite atoms on the surrounding atoms.
 127  * If fshift!=NULL also update the shift forces.
 128  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
 129  * to vir. This correction is required when the virial is not calculated
 130  * afterwards from the particle position and forces, but in a different way,
 131  * as for instance for the PME mesh contribution.
 132  */
 133
 134 /* Return the number of non-linear virtual site constructions in the system */
 135 int countNonlinearVsites(const gmx_mtop_t &mtop);
 136
 137 /* Return the number of virtual sites that cross update groups
 138  *
 139  * \param[in] mtop                           The global topology
 140  * \param[in] updateGroupingPerMoleculetype  Update grouping per molecule type, pass empty when not using update groups
 141  */
 142 int countInterUpdategroupVsites(const gmx_mtop_t                            &mtop,
 143                                 gmx::ArrayRef<const gmx::RangePartitioning>  updateGroupingPerMoleculetype);
 144
 145 /* Initialize the virtual site struct,
 146  *
 147  * \param[in] mtop  The global topology
 148  * \param[in] cr    The communication record
 149  * \returns A valid vsite struct or nullptr when there are no virtual sites
 150  */
 151 std::unique_ptr<gmx_vsite_t>
 152 initVsite(const gmx_mtop_t &mtop,
 153           const t_commrec  *cr);
 154
 155 void split_vsites_over_threads(const t_ilist   *ilist,
 156                                const t_iparams *ip,
 157                                const t_mdatoms *mdatoms,
 158                                gmx_vsite_t     *vsite);
 159 /* Divide the vsite work-load over the threads.
 160  * Should be called at the end of the domain decomposition.
 161  */
 162
 163 void set_vsite_top(gmx_vsite_t          *vsite,
 164                    const gmx_localtop_t *top,
 165                    const t_mdatoms      *md);
 166 /* Set some vsite data for runs without domain decomposition.
 167  * Should be called once after init_vsite, before calling other routines.
 168  */
 169
 170 #endif