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 <memory>
  51 #include <vector>
  52
  53 #include "gromacs/math/vectypes.h"
  54 #include "gromacs/topology/block.h"
  55 #include "gromacs/utility/basedefinitions.h"
  56 #include "gromacs/utility/gmxmpi.h"
  57 #include "gromacs/utility/real.h"
  58
  59 //! Max number of zones in domain decomposition
  60 #define DD_MAXZONE  8
  61 //! Max number of izones in domain decomposition
  62 #define DD_MAXIZONE 4
  63
  64 struct AtomDistribution;
  65 struct gmx_domdec_comm_t;
  66 struct gmx_domdec_constraints_t;
  67 struct gmx_domdec_specat_comm_t;
  68 class gmx_ga2la_t;
  69 struct gmx_pme_comm_n_box_t;
  70 struct gmx_reverse_top_t;
  71 struct t_inputrec;
  72
  73 namespace gmx
  74 {
  75 template <typename T> class HashedMap;
  76 class LocalAtomSetManager;
  77 }
  78
  79 typedef struct {
  80     /* j-zone start               */
  81     int  j0 = 0;
  82     /* j-zone end                 */
  83     int  j1 = 0;
  84     /* i-charge-group end         */
  85     int  cg1 = 0;
  86     /* j-charge-group start       */
  87     int  jcg0 = 0;
  88     /* j-charge-group end         */
  89     int  jcg1 = 0;
  90     /* Minimum shifts to consider */
  91     ivec shift0 = { };
  92     /* Maximum shifts to consider */
  93     ivec shift1 = { };
  94 } gmx_domdec_ns_ranges_t;
  95
  96 typedef struct {
  97     /* Zone lower corner in triclinic coordinates         */
  98     rvec x0 = { };
  99     /* Zone upper corner in triclinic coordinates         */
 100     rvec x1 = { };
 101     /* Zone bounding box lower corner in Cartesian coords */
 102     rvec bb_x0 = { };
 103     /* Zone bounding box upper corner in Cartesian coords */
 104     rvec bb_x1 = { };
 105 } gmx_domdec_zone_size_t;
 106
 107 struct gmx_domdec_zones_t {
 108     /* The number of zones including the home zone */
 109     int                    n = 0;
 110     /* The shift of the zones with respect to the home zone */
 111     ivec                   shift[DD_MAXZONE] = { };
 112     /* The charge group boundaries for the zones */
 113     int                    cg_range[DD_MAXZONE+1] = { };
 114     /* The number of neighbor search zones with i-particles */
 115     int                    nizone = 0;
 116     /* The neighbor search charge group ranges for each i-zone */
 117     gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
 118     /* Boundaries of the zones */
 119     gmx_domdec_zone_size_t size[DD_MAXZONE];
 120     /* The cg density of the home zone */
 121     real                   dens_zone0 = 0;
 122 };
 123
 124 struct gmx_ddbox_t {
 125     int  npbcdim;
 126     int  nboundeddim;
 127     rvec box0;
 128     rvec box_size;
 129     /* Tells if the box is skewed for each of the three cartesian directions */
 130     ivec tric_dir;
 131     rvec skew_fac;
 132     /* Orthogonal vectors for triclinic cells, Cartesian index */
 133     rvec v[DIM][DIM];
 134     /* Normal vectors for the cells walls */
 135     rvec normal[DIM];
 136 };
 137
 138 /*! \internal \brief Provides information about properties of the unit cell */
 139 struct UnitCellInfo
 140 {
 141     //! Constructor
 142     UnitCellInfo(const t_inputrec &ir);
 143
 144     //! We have PBC from dim 0 (X) up to npbcdim
 145     int  npbcdim;
 146     //! The system is bounded from 0 (X) to numBoundedDimensions
 147     int  numBoundedDimensions;
 148     //! Tells whether the box bounding the atoms is dynamic
 149     bool ddBoxIsDynamic;
 150     //! Screw PBC?
 151     bool haveScrewPBC;
 152 };
 153
 154 struct gmx_domdec_t { //NOLINT(clang-analyzer-optin.performance.Padding)
 155     //! Constructor, only partial for now
 156     gmx_domdec_t(const t_inputrec &ir);
 157
 158     /* The DD particle-particle nodes only */
 159     /* The communication setup within the communicator all
 160      * defined in dd->comm in domdec.c
 161      */
 162     int                    nnodes       = 0;
 163     MPI_Comm               mpi_comm_all = MPI_COMM_NULL;
 164     /* Use MPI_Sendrecv communication instead of non-blocking calls */
 165     gmx_bool               bSendRecv2 = FALSE;
 166     /* The local DD cell index and rank */
 167     ivec                   ci         = { 0, 0, 0 };
 168     int                    rank       = 0;
 169     ivec                   master_ci  = { 0, 0, 0 };
 170     int                    masterrank = 0;
 171     /* Communication with the PME only nodes */
 172     int                    pme_nodeid           = 0;
 173     gmx_bool               pme_receive_vir_ener = false;
 174     gmx_pme_comm_n_box_t  *cnb                  = nullptr;
 175     int                    nreq_pme             = 0;
 176     MPI_Request            req_pme[8];
 177
 178     /* Properties of the unit cell */
 179     UnitCellInfo unitCellInfo;
 180
 181     /* The communication setup, identical for each cell, cartesian index */
 182     ivec     nc   = { 0, 0, 0 };
 183     int      ndim = 0;
 184     ivec     dim  = { 0, 0, 0 }; /* indexed by 0 to ndim */
 185
 186     /* Forward and backward neighboring cells, indexed by 0 to ndim */
 187     int  neighbor[DIM][2] = { { 0, 0 },  { 0, 0 },  { 0, 0 } };
 188
 189     /* Only available on the master node */
 190     std::unique_ptr<AtomDistribution> ma;
 191
 192     /* Global atom number to interaction list */
 193     gmx_reverse_top_t  *reverse_top    = nullptr;
 194     int                 nbonded_global = 0;
 195     int                 nbonded_local  = 0;
 196
 197     /* The number of inter charge-group exclusions */
 198     int  n_intercg_excl = 0;
 199
 200     /* Vsite stuff */
 201     gmx::HashedMap<int>       *ga2la_vsite = nullptr;
 202     gmx_domdec_specat_comm_t  *vsite_comm  = nullptr;
 203     std::vector<int>           vsite_requestedGlobalAtomIndices;
 204
 205     /* Constraint stuff */
 206     gmx_domdec_constraints_t *constraints     = nullptr;
 207     gmx_domdec_specat_comm_t *constraint_comm = nullptr;
 208
 209     /* The number of home atom groups */
 210     int                           ncg_home = 0;
 211     /* Global atom group indices for the home and all non-home groups */
 212     std::vector<int>              globalAtomGroupIndices;
 213
 214     /* Index from the local atoms to the global atoms, covers home and received zones */
 215     std::vector<int> globalAtomIndices;
 216
 217     /* Global atom number to local atom number list */
 218     gmx_ga2la_t  *ga2la = nullptr;
 219
 220     /* Communication stuff */
 221     gmx_domdec_comm_t *comm = nullptr;
 222
 223     /* The partioning count, to keep track of the state */
 224     int64_t ddp_count = 0;
 225
 226     /* The managed atom sets that are updated in domain decomposition */
 227     gmx::LocalAtomSetManager * atomSets = nullptr;
 228
 229     /* gmx_pme_recv_f buffer */
 230     std::vector<gmx::RVec> pmeForceReceiveBuffer;
 231 };
 232
 233 //! Are we the master node for domain decomposition
 234 static inline bool DDMASTER(const gmx_domdec_t &dd)
 235 {
 236     return dd.rank == dd.masterrank;
 237 };
 238
 239 //! Are we the master node for domain decomposition, deprecated
 240 static inline bool DDMASTER(const gmx_domdec_t *dd)
 241 {
 242     return dd->rank == dd->masterrank;
 243 };
 244
 245 #endif