src/gromacs/domdec/domdec_struct.h

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  37 /*! \libinternal \file
  38  * \brief Declares structures related to domain decomposition.
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  42  * \inlibraryapi
  43  * \ingroup module_domdec
  44  */
  45 #ifndef GMX_DOMDEC_DOMDEC_STRUCT_H
  46 #define GMX_DOMDEC_DOMDEC_STRUCT_H
  47
  48 #include <cstddef>
  49
  50 #include <array>
  51 #include <memory>
  52 #include <vector>
  53
  54 #include "gromacs/math/vectypes.h"
  55 #include "gromacs/topology/block.h"
  56 #include "gromacs/utility/basedefinitions.h"
  57 #include "gromacs/utility/gmxmpi.h"
  58 #include "gromacs/utility/range.h"
  59 #include "gromacs/utility/real.h"
  60
  61 //! Max number of zones in domain decomposition
  62 #define DD_MAXZONE  8
  63 //! Max number of izones in domain decomposition
  64 #define DD_MAXIZONE 4
  65
  66 struct AtomDistribution;
  67 struct gmx_domdec_comm_t;
  68 struct gmx_domdec_constraints_t;
  69 struct gmx_domdec_specat_comm_t;
  70 class gmx_ga2la_t;
  71 struct gmx_pme_comm_n_box_t;
  72 struct gmx_reverse_top_t;
  73 struct t_inputrec;
  74
  75 namespace gmx
  76 {
  77 template <typename T> class HashedMap;
  78 class LocalAtomSetManager;
  79 class GpuHaloExchange;
  80 }
  81
  82 /*! \internal
  83  * \brief Pair interaction zone and atom range for an i-zone
  84  */
  85 struct DDPairInteractionRanges
  86 {
  87     //! The index of this i-zone in the i-zone list
  88     int             iZoneIndex = -1;
  89     //! The range of j-zones
  90     gmx::Range<int> jZoneRange;
  91     //! The i-atom range
  92     gmx::Range<int> iAtomRange;
  93     //! The j-atom range
  94     gmx::Range<int> jAtomRange;
  95     //! Minimum shifts to consider
  96     ivec            shift0 = { };
  97     //! Maximum shifts to consider
  98     ivec            shift1 = { };
  99 };
 100
 101 typedef struct {
 102     /* Zone lower corner in triclinic coordinates         */
 103     rvec x0 = { };
 104     /* Zone upper corner in triclinic coordinates         */
 105     rvec x1 = { };
 106     /* Zone bounding box lower corner in Cartesian coords */
 107     rvec bb_x0 = { };
 108     /* Zone bounding box upper corner in Cartesian coords */
 109     rvec bb_x1 = { };
 110 } gmx_domdec_zone_size_t;
 111
 112 struct gmx_domdec_zones_t {
 113     /* The number of zones including the home zone */
 114     int                                  n = 0;
 115     /* The shift of the zones with respect to the home zone */
 116     ivec                                 shift[DD_MAXZONE] = { };
 117     /* The charge group boundaries for the zones */
 118     int                                  cg_range[DD_MAXZONE+1] = { };
 119     /* The pair interaction zone and atom ranges per each i-zone */
 120     std::vector<DDPairInteractionRanges> iZones;
 121     /* Boundaries of the zones */
 122     gmx_domdec_zone_size_t               size[DD_MAXZONE];
 123     /* The cg density of the home zone */
 124     real                                 dens_zone0 = 0;
 125 };
 126
 127 struct gmx_ddbox_t {
 128     int  npbcdim;
 129     int  nboundeddim;
 130     rvec box0;
 131     rvec box_size;
 132     /* Tells if the box is skewed for each of the three cartesian directions */
 133     ivec tric_dir;
 134     rvec skew_fac;
 135     /* Orthogonal vectors for triclinic cells, Cartesian index */
 136     rvec v[DIM][DIM];
 137     /* Normal vectors for the cells walls */
 138     rvec normal[DIM];
 139 };
 140
 141 /*! \internal \brief Provides information about properties of the unit cell */
 142 struct UnitCellInfo
 143 {
 144     //! Constructor
 145     UnitCellInfo(const t_inputrec &ir);
 146
 147     //! We have PBC from dim 0 (X) up to npbcdim
 148     int  npbcdim;
 149     //! The system is bounded from 0 (X) to numBoundedDimensions
 150     int  numBoundedDimensions;
 151     //! Tells whether the box bounding the atoms is dynamic
 152     bool ddBoxIsDynamic;
 153     //! Screw PBC?
 154     bool haveScrewPBC;
 155 };
 156
 157 struct gmx_domdec_t { //NOLINT(clang-analyzer-optin.performance.Padding)
 158     //! Constructor, only partial for now
 159     gmx_domdec_t(const t_inputrec &ir);
 160
 161     /* The DD particle-particle nodes only */
 162     /* The communication setup within the communicator all
 163      * defined in dd->comm in domdec.c
 164      */
 165     int                    nnodes       = 0;
 166     MPI_Comm               mpi_comm_all = MPI_COMM_NULL;
 167     /* The local DD cell index and rank */
 168     ivec                   ci         = { 0, 0, 0 };
 169     int                    rank       = 0;
 170     ivec                   master_ci  = { 0, 0, 0 };
 171     int                    masterrank = 0;
 172     /* Communication with the PME only nodes */
 173     int                    pme_nodeid           = 0;
 174     gmx_bool               pme_receive_vir_ener = false;
 175     gmx_pme_comm_n_box_t  *cnb                  = nullptr;
 176     int                    nreq_pme             = 0;
 177     MPI_Request            req_pme[8];
 178
 179     /* Properties of the unit cell */
 180     UnitCellInfo unitCellInfo;
 181
 182     /* The communication setup, identical for each cell, cartesian index */
 183     ivec     nc   = { 0, 0, 0 };
 184     int      ndim = 0;
 185     ivec     dim  = { 0, 0, 0 }; /* indexed by 0 to ndim */
 186
 187     /* Forward and backward neighboring cells, indexed by 0 to ndim */
 188     int  neighbor[DIM][2] = { { 0, 0 },  { 0, 0 },  { 0, 0 } };
 189
 190     /* Only available on the master node */
 191     std::unique_ptr<AtomDistribution> ma;
 192
 193     /* Global atom number to interaction list */
 194     gmx_reverse_top_t  *reverse_top    = nullptr;
 195     int                 nbonded_global = 0;
 196     int                 nbonded_local  = 0;
 197
 198     /* Whether we have non-self exclusion */
 199     bool haveExclusions = false;
 200
 201     /* Vsite stuff */
 202     gmx::HashedMap<int>       *ga2la_vsite = nullptr;
 203     gmx_domdec_specat_comm_t  *vsite_comm  = nullptr;
 204     std::vector<int>           vsite_requestedGlobalAtomIndices;
 205
 206     /* Constraint stuff */
 207     gmx_domdec_constraints_t *constraints     = nullptr;
 208     gmx_domdec_specat_comm_t *constraint_comm = nullptr;
 209
 210     /* The number of home atom groups */
 211     int                           ncg_home = 0;
 212     /* Global atom group indices for the home and all non-home groups */
 213     std::vector<int>              globalAtomGroupIndices;
 214
 215     /* Index from the local atoms to the global atoms, covers home and received zones */
 216     std::vector<int> globalAtomIndices;
 217
 218     /* Global atom number to local atom number list */
 219     gmx_ga2la_t  *ga2la = nullptr;
 220
 221     /* Communication stuff */
 222     gmx_domdec_comm_t *comm = nullptr;
 223
 224     /* The partioning count, to keep track of the state */
 225     int64_t ddp_count = 0;
 226
 227     /* The managed atom sets that are updated in domain decomposition */
 228     gmx::LocalAtomSetManager * atomSets = nullptr;
 229
 230     /* gmx_pme_recv_f buffer */
 231     std::vector<gmx::RVec> pmeForceReceiveBuffer;
 232
 233     /* GPU halo exchange object */
 234     std::unique_ptr<gmx::GpuHaloExchange> gpuHaloExchange;
 235 };
 236
 237 //! Are we the master node for domain decomposition
 238 static inline bool DDMASTER(const gmx_domdec_t &dd)
 239 {
 240     return dd.rank == dd.masterrank;
 241 };
 242
 243 //! Are we the master node for domain decomposition, deprecated
 244 static inline bool DDMASTER(const gmx_domdec_t *dd)
 245 {
 246     return dd->rank == dd->masterrank;
 247 };
 248
 249 #endif