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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 class gmx_reverse_top_t;
74 struct ReverseTopOptions;
80 class LocalAtomSetManager;
81 struct LocalTopologyChecker;
82 class GpuHaloExchange;
86 * \brief Pair interaction zone and atom range for an i-zone
88 struct DDPairInteractionRanges
90 //! The index of this i-zone in the i-zone list
92 //! The range of j-zones
93 gmx::Range<int> jZoneRange;
95 gmx::Range<int> iAtomRange;
97 gmx::Range<int> jAtomRange;
98 //! Minimum shifts to consider
99 gmx::IVec shift0 = { 0, 0, 0 };
100 //! Maximum shifts to consider
101 gmx::IVec shift1 = { 0, 0, 0 };
104 typedef struct gmx_domdec_zone_size
106 /* Zone lower corner in triclinic coordinates */
107 gmx::RVec x0 = { 0, 0, 0 };
108 /* Zone upper corner in triclinic coordinates */
109 gmx::RVec x1 = { 0, 0, 0 };
110 /* Zone bounding box lower corner in Cartesian coords */
111 gmx::RVec bb_x0 = { 0, 0, 0 };
112 /* Zone bounding box upper corner in Cartesian coords */
113 gmx::RVec bb_x1 = { 0, 0, 0 };
114 } gmx_domdec_zone_size_t;
116 struct gmx_domdec_zones_t
118 /* The number of zones including the home zone */
120 /* The shift of the zones with respect to the home zone */
121 std::array<ivec, DD_MAXZONE> shift;
122 /* The charge group boundaries for the zones */
123 std::array<int, DD_MAXZONE + 1> cg_range;
124 /* The pair interaction zone and atom ranges per each i-zone */
125 std::vector<DDPairInteractionRanges> iZones;
126 /* Boundaries of the zones */
127 std::array<gmx_domdec_zone_size_t, DD_MAXZONE> size;
128 /* The cg density of the home zone */
136 gmx::RVec box0 = { 0, 0, 0 };
137 gmx::RVec box_size = { 0, 0, 0 };
138 /* Tells if the box is skewed for each of the three cartesian directions */
139 gmx::IVec tric_dir = { 0, 0, 0 };
140 gmx::RVec skew_fac = { 0, 0, 0 };
141 /* Orthogonal vectors for triclinic cells, Cartesian index */
143 /* Normal vectors for the cells walls */
147 /*! \internal \brief Provides information about properties of the unit cell */
151 UnitCellInfo(const t_inputrec& ir);
153 //! We have PBC from dim 0 (X) up to npbcdim
155 //! The system is bounded from 0 (X) to numBoundedDimensions
156 int numBoundedDimensions;
157 //! Tells whether the box bounding the atoms is dynamic
164 { //NOLINT(clang-analyzer-optin.performance.Padding)
165 //! Constructor, only partial for now
166 gmx_domdec_t(const t_inputrec& ir);
169 /* The DD particle-particle nodes only */
170 /* The communication setup within the communicator all
171 * defined in dd->comm in domdec.c
174 MPI_Comm mpi_comm_all = MPI_COMM_NULL;
175 /* The local DD cell index and rank */
176 gmx::IVec ci = { 0, 0, 0 };
178 gmx::IVec master_ci = { 0, 0, 0 };
180 /* Communication with the PME only nodes */
182 gmx_bool pme_receive_vir_ener = false;
183 gmx_pme_comm_n_box_t* cnb = nullptr;
185 MPI_Request req_pme[8];
187 /* Properties of the unit cell */
188 UnitCellInfo unitCellInfo;
190 /* The communication setup, identical for each cell, cartesian index */
191 //! Todo: refactor nbnxm to not rely on this sometimes being a nullptr so this can be IVec
192 ivec numCells = { 0, 0, 0 };
194 gmx::IVec dim = { 0, 0, 0 }; /* indexed by 0 to ndim */
196 /* Forward and backward neighboring cells, indexed by 0 to ndim */
197 int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
199 /* Only available on the master node */
200 std::unique_ptr<AtomDistribution> ma;
202 /* Global atom number to interaction list */
203 std::unique_ptr<gmx_reverse_top_t> reverse_top;
205 /* Whether we have non-self exclusion */
206 bool haveExclusions = false;
209 gmx::HashedMap<int>* ga2la_vsite = nullptr;
210 gmx_domdec_specat_comm_t* vsite_comm = nullptr;
211 std::vector<int> vsite_requestedGlobalAtomIndices;
213 /* Constraint stuff */
214 gmx_domdec_constraints_t* constraints = nullptr;
215 gmx_domdec_specat_comm_t* constraint_comm = nullptr;
217 /* The number of home atoms */
218 int numHomeAtoms = 0;
219 /* Global atom group indices for the home and all non-home groups */
220 std::vector<int> globalAtomGroupIndices;
222 /* Index from the local atoms to the global atoms, covers home and received zones */
223 std::vector<int> globalAtomIndices;
225 /* Global atom number to local atom number list */
226 gmx_ga2la_t* ga2la = nullptr;
228 /* Communication stuff */
229 gmx_domdec_comm_t* comm = nullptr;
231 /* The partioning count, to keep track of the state */
232 int64_t ddp_count = 0;
234 /* The managed atom sets that are updated in domain decomposition */
235 gmx::LocalAtomSetManager* atomSets = nullptr;
237 //! The handler for checking whether the local topology is missing interactions
238 std::unique_ptr<gmx::LocalTopologyChecker> localTopologyChecker;
240 /* gmx_pme_recv_f buffer */
241 std::vector<gmx::RVec> pmeForceReceiveBuffer;
243 /* GPU halo exchange objects: this structure supports a vector of pulses for each dimension */
244 std::vector<std::unique_ptr<gmx::GpuHaloExchange>> gpuHaloExchange[DIM];
247 //! Are we the master node for domain decomposition
248 static inline bool DDMASTER(const gmx_domdec_t& dd)
250 return dd.rank == dd.masterrank;
253 //! Are we the master node for domain decomposition, deprecated
254 static inline bool DDMASTER(const gmx_domdec_t* dd)
256 return dd->rank == dd->masterrank;