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37 /*! \libinternal \file
38 * \brief Declares structures related to domain decomposition.
40 * \author Berk Hess <hess@kth.se>
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
43 * \ingroup module_domdec
45 #ifndef GMX_DOMDEC_DOMDEC_STRUCT_H
46 #define GMX_DOMDEC_DOMDEC_STRUCT_H
54 #include "gromacs/math/vectypes.h"
55 #include "gromacs/topology/block.h"
56 #include "gromacs/utility/gmxmpi.h"
57 #include "gromacs/utility/range.h"
58 #include "gromacs/utility/real.h"
60 //! Max number of zones in domain decomposition
62 //! Max number of izones in domain decomposition
65 struct AtomDistribution;
66 struct gmx_domdec_comm_t;
67 struct gmx_domdec_constraints_t;
68 struct gmx_domdec_specat_comm_t;
70 struct gmx_pme_comm_n_box_t;
72 struct gmx_reverse_top_t;
74 struct ReverseTopOptions;
80 class LocalAtomSetManager;
81 class GpuHaloExchange;
85 * \brief Pair interaction zone and atom range for an i-zone
87 struct DDPairInteractionRanges
89 //! The index of this i-zone in the i-zone list
91 //! The range of j-zones
92 gmx::Range<int> jZoneRange;
94 gmx::Range<int> iAtomRange;
96 gmx::Range<int> jAtomRange;
97 //! Minimum shifts to consider
98 gmx::IVec shift0 = { 0, 0, 0 };
99 //! Maximum shifts to consider
100 gmx::IVec shift1 = { 0, 0, 0 };
103 typedef struct gmx_domdec_zone_size
105 /* Zone lower corner in triclinic coordinates */
106 gmx::RVec x0 = { 0, 0, 0 };
107 /* Zone upper corner in triclinic coordinates */
108 gmx::RVec x1 = { 0, 0, 0 };
109 /* Zone bounding box lower corner in Cartesian coords */
110 gmx::RVec bb_x0 = { 0, 0, 0 };
111 /* Zone bounding box upper corner in Cartesian coords */
112 gmx::RVec bb_x1 = { 0, 0, 0 };
113 } gmx_domdec_zone_size_t;
115 struct gmx_domdec_zones_t
117 /* The number of zones including the home zone */
119 /* The shift of the zones with respect to the home zone */
120 std::array<ivec, DD_MAXZONE> shift;
121 /* The charge group boundaries for the zones */
122 std::array<int, DD_MAXZONE + 1> cg_range;
123 /* The pair interaction zone and atom ranges per each i-zone */
124 std::vector<DDPairInteractionRanges> iZones;
125 /* Boundaries of the zones */
126 std::array<gmx_domdec_zone_size_t, DD_MAXZONE> size;
127 /* The cg density of the home zone */
135 gmx::RVec box0 = { 0, 0, 0 };
136 gmx::RVec box_size = { 0, 0, 0 };
137 /* Tells if the box is skewed for each of the three cartesian directions */
138 gmx::IVec tric_dir = { 0, 0, 0 };
139 gmx::RVec skew_fac = { 0, 0, 0 };
140 /* Orthogonal vectors for triclinic cells, Cartesian index */
142 /* Normal vectors for the cells walls */
146 /*! \internal \brief Provides information about properties of the unit cell */
150 UnitCellInfo(const t_inputrec& ir);
152 //! We have PBC from dim 0 (X) up to npbcdim
154 //! The system is bounded from 0 (X) to numBoundedDimensions
155 int numBoundedDimensions;
156 //! Tells whether the box bounding the atoms is dynamic
163 { //NOLINT(clang-analyzer-optin.performance.Padding)
164 //! Constructor, only partial for now
165 gmx_domdec_t(const t_inputrec& ir);
168 /* The DD particle-particle nodes only */
169 /* The communication setup within the communicator all
170 * defined in dd->comm in domdec.c
173 MPI_Comm mpi_comm_all = MPI_COMM_NULL;
174 /* The local DD cell index and rank */
175 gmx::IVec ci = { 0, 0, 0 };
177 gmx::IVec master_ci = { 0, 0, 0 };
179 /* Communication with the PME only nodes */
181 gmx_bool pme_receive_vir_ener = false;
182 gmx_pme_comm_n_box_t* cnb = nullptr;
184 MPI_Request req_pme[8];
186 /* Properties of the unit cell */
187 UnitCellInfo unitCellInfo;
189 /* The communication setup, identical for each cell, cartesian index */
190 //! Todo: refactor nbnxm to not rely on this sometimes being a nullptr so this can be IVec
191 ivec numCells = { 0, 0, 0 };
193 gmx::IVec dim = { 0, 0, 0 }; /* indexed by 0 to ndim */
195 /* Forward and backward neighboring cells, indexed by 0 to ndim */
196 int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
198 /* Only available on the master node */
199 std::unique_ptr<AtomDistribution> ma;
201 /* Global atom number to interaction list */
202 std::unique_ptr<gmx_reverse_top_t> reverse_top;
203 int nbonded_global = 0;
204 int nbonded_local = 0;
206 /* Whether we have non-self exclusion */
207 bool haveExclusions = false;
210 gmx::HashedMap<int>* ga2la_vsite = nullptr;
211 gmx_domdec_specat_comm_t* vsite_comm = nullptr;
212 std::vector<int> vsite_requestedGlobalAtomIndices;
214 /* Constraint stuff */
215 gmx_domdec_constraints_t* constraints = nullptr;
216 gmx_domdec_specat_comm_t* constraint_comm = nullptr;
218 /* The number of home atom groups */
220 /* Global atom group indices for the home and all non-home groups */
221 std::vector<int> globalAtomGroupIndices;
223 /* Index from the local atoms to the global atoms, covers home and received zones */
224 std::vector<int> globalAtomIndices;
226 /* Global atom number to local atom number list */
227 gmx_ga2la_t* ga2la = nullptr;
229 /* Communication stuff */
230 gmx_domdec_comm_t* comm = nullptr;
232 /* The partioning count, to keep track of the state */
233 int64_t ddp_count = 0;
235 /* The managed atom sets that are updated in domain decomposition */
236 gmx::LocalAtomSetManager* atomSets = nullptr;
238 /* gmx_pme_recv_f buffer */
239 std::vector<gmx::RVec> pmeForceReceiveBuffer;
241 /* GPU halo exchange objects: this structure supports a vector of pulses for each dimension */
242 std::vector<std::unique_ptr<gmx::GpuHaloExchange>> gpuHaloExchange[DIM];
245 //! Are we the master node for domain decomposition
246 static inline bool DDMASTER(const gmx_domdec_t& dd)
248 return dd.rank == dd.masterrank;
251 //! Are we the master node for domain decomposition, deprecated
252 static inline bool DDMASTER(const gmx_domdec_t* dd)
254 return dd->rank == dd->masterrank;