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>
  78 class HashedMap;
  79 class LocalAtomSetManager;
  80 class GpuHaloExchange;
  81 } // namespace gmx
  82
  83 /*! \internal
  84  * \brief Pair interaction zone and atom range for an i-zone
  85  */
  86 struct DDPairInteractionRanges
  87 {
  88     //! The index of this i-zone in the i-zone list
  89     int iZoneIndex = -1;
  90     //! The range of j-zones
  91     gmx::Range<int> jZoneRange;
  92     //! The i-atom range
  93     gmx::Range<int> iAtomRange;
  94     //! The j-atom range
  95     gmx::Range<int> jAtomRange;
  96     //! Minimum shifts to consider
  97     gmx::IVec shift0 = { 0, 0, 0 };
  98     //! Maximum shifts to consider
  99     gmx::IVec shift1 = { 0, 0, 0 };
 100 };
 101
 102 typedef struct gmx_domdec_zone_size
 103 {
 104     /* Zone lower corner in triclinic coordinates         */
 105     gmx::RVec x0 = { 0, 0, 0 };
 106     /* Zone upper corner in triclinic coordinates         */
 107     gmx::RVec x1 = { 0, 0, 0 };
 108     /* Zone bounding box lower corner in Cartesian coords */
 109     gmx::RVec bb_x0 = { 0, 0, 0 };
 110     /* Zone bounding box upper corner in Cartesian coords */
 111     gmx::RVec bb_x1 = { 0, 0, 0 };
 112 } gmx_domdec_zone_size_t;
 113
 114 struct gmx_domdec_zones_t
 115 {
 116     /* The number of zones including the home zone */
 117     int n = 0;
 118     /* The shift of the zones with respect to the home zone */
 119     ivec shift[DD_MAXZONE] = {};
 120     /* The charge group boundaries for the zones */
 121     int cg_range[DD_MAXZONE + 1] = {};
 122     /* The pair interaction zone and atom ranges per each i-zone */
 123     std::vector<DDPairInteractionRanges> iZones;
 124     /* Boundaries of the zones */
 125     gmx_domdec_zone_size_t size[DD_MAXZONE];
 126     /* The cg density of the home zone */
 127     real dens_zone0 = 0;
 128 };
 129
 130 struct gmx_ddbox_t
 131 {
 132     int       npbcdim;
 133     int       nboundeddim;
 134     gmx::RVec box0     = { 0, 0, 0 };
 135     gmx::RVec box_size = { 0, 0, 0 };
 136     /* Tells if the box is skewed for each of the three cartesian directions */
 137     gmx::IVec tric_dir = { 0, 0, 0 };
 138     gmx::RVec skew_fac = { 0, 0, 0 };
 139     /* Orthogonal vectors for triclinic cells, Cartesian index */
 140     rvec v[DIM][DIM];
 141     /* Normal vectors for the cells walls */
 142     rvec normal[DIM];
 143 };
 144
 145 /*! \internal \brief Provides information about properties of the unit cell */
 146 struct UnitCellInfo
 147 {
 148     //! Constructor
 149     UnitCellInfo(const t_inputrec& ir);
 150
 151     //! We have PBC from dim 0 (X) up to npbcdim
 152     int npbcdim;
 153     //! The system is bounded from 0 (X) to numBoundedDimensions
 154     int numBoundedDimensions;
 155     //! Tells whether the box bounding the atoms is dynamic
 156     bool ddBoxIsDynamic;
 157     //! Screw PBC?
 158     bool haveScrewPBC;
 159 };
 160
 161 struct gmx_domdec_t
 162 { //NOLINT(clang-analyzer-optin.performance.Padding)
 163     //! Constructor, only partial for now
 164     gmx_domdec_t(const t_inputrec& ir);
 165
 166     /* The DD particle-particle nodes only */
 167     /* The communication setup within the communicator all
 168      * defined in dd->comm in domdec.c
 169      */
 170     int      nnodes       = 0;
 171     MPI_Comm mpi_comm_all = MPI_COMM_NULL;
 172     /* The local DD cell index and rank */
 173     gmx::IVec ci         = { 0, 0, 0 };
 174     int       rank       = 0;
 175     gmx::IVec master_ci  = { 0, 0, 0 };
 176     int       masterrank = 0;
 177     /* Communication with the PME only nodes */
 178     int                   pme_nodeid           = 0;
 179     gmx_bool              pme_receive_vir_ener = false;
 180     gmx_pme_comm_n_box_t* cnb                  = nullptr;
 181     int                   nreq_pme             = 0;
 182     MPI_Request           req_pme[8];
 183
 184     /* Properties of the unit cell */
 185     UnitCellInfo unitCellInfo;
 186
 187     /* The communication setup, identical for each cell, cartesian index */
 188     //! Todo: refactor nbnxm to not rely on this sometimes being a nullptr so this can be IVec
 189     ivec      numCells = { 0, 0, 0 };
 190     int       ndim     = 0;
 191     gmx::IVec dim      = { 0, 0, 0 }; /* indexed by 0 to ndim */
 192
 193     /* Forward and backward neighboring cells, indexed by 0 to ndim */
 194     int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
 195
 196     /* Only available on the master node */
 197     std::unique_ptr<AtomDistribution> ma;
 198
 199     /* Global atom number to interaction list */
 200     gmx_reverse_top_t* reverse_top    = nullptr;
 201     int                nbonded_global = 0;
 202     int                nbonded_local  = 0;
 203
 204     /* Whether we have non-self exclusion */
 205     bool haveExclusions = false;
 206
 207     /* Vsite stuff */
 208     gmx::HashedMap<int>*      ga2la_vsite = nullptr;
 209     gmx_domdec_specat_comm_t* vsite_comm  = nullptr;
 210     std::vector<int>          vsite_requestedGlobalAtomIndices;
 211
 212     /* Constraint stuff */
 213     gmx_domdec_constraints_t* constraints     = nullptr;
 214     gmx_domdec_specat_comm_t* constraint_comm = nullptr;
 215
 216     /* The number of home atom groups */
 217     int ncg_home = 0;
 218     /* Global atom group indices for the home and all non-home groups */
 219     std::vector<int> globalAtomGroupIndices;
 220
 221     /* Index from the local atoms to the global atoms, covers home and received zones */
 222     std::vector<int> globalAtomIndices;
 223
 224     /* Global atom number to local atom number list */
 225     gmx_ga2la_t* ga2la = nullptr;
 226
 227     /* Communication stuff */
 228     gmx_domdec_comm_t* comm = nullptr;
 229
 230     /* The partioning count, to keep track of the state */
 231     int64_t ddp_count = 0;
 232
 233     /* The managed atom sets that are updated in domain decomposition */
 234     gmx::LocalAtomSetManager* atomSets = nullptr;
 235
 236     /* gmx_pme_recv_f buffer */
 237     std::vector<gmx::RVec> pmeForceReceiveBuffer;
 238
 239     /* GPU halo exchange objects: this structure supports a vector of pulses for each dimension */
 240     std::vector<std::unique_ptr<gmx::GpuHaloExchange>> gpuHaloExchange[DIM];
 241 };
 242
 243 //! Are we the master node for domain decomposition
 244 static inline bool DDMASTER(const gmx_domdec_t& dd)
 245 {
 246     return dd.rank == dd.masterrank;
 247 };
 248
 249 //! Are we the master node for domain decomposition, deprecated
 250 static inline bool DDMASTER(const gmx_domdec_t* dd)
 251 {
 252     return dd->rank == dd->masterrank;
 253 };
 254
 255 #endif