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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
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"
59 //! Max number of zones in domain decomposition
61 //! Max number of izones in domain decomposition
64 struct AtomDistribution;
65 struct gmx_domdec_comm_t;
66 struct gmx_domdec_constraints_t;
67 struct gmx_domdec_specat_comm_t;
69 struct gmx_pme_comm_n_box_t;
70 struct gmx_reverse_top_t;
75 template <typename T> class HashedMap;
76 class LocalAtomSetManager;
77 class GpuHaloExchange;
85 /* i-charge-group end */
87 /* j-charge-group start */
89 /* j-charge-group end */
91 /* Minimum shifts to consider */
93 /* Maximum shifts to consider */
95 } gmx_domdec_ns_ranges_t;
98 /* Zone lower corner in triclinic coordinates */
100 /* Zone upper corner in triclinic coordinates */
102 /* Zone bounding box lower corner in Cartesian coords */
104 /* Zone bounding box upper corner in Cartesian coords */
106 } gmx_domdec_zone_size_t;
108 struct gmx_domdec_zones_t {
109 /* The number of zones including the home zone */
111 /* The shift of the zones with respect to the home zone */
112 ivec shift[DD_MAXZONE] = { };
113 /* The charge group boundaries for the zones */
114 int cg_range[DD_MAXZONE+1] = { };
115 /* The number of neighbor search zones with i-particles */
117 /* The neighbor search charge group ranges for each i-zone */
118 gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
119 /* Boundaries of the zones */
120 gmx_domdec_zone_size_t size[DD_MAXZONE];
121 /* The cg density of the home zone */
130 /* Tells if the box is skewed for each of the three cartesian directions */
133 /* Orthogonal vectors for triclinic cells, Cartesian index */
135 /* Normal vectors for the cells walls */
139 /*! \internal \brief Provides information about properties of the unit cell */
143 UnitCellInfo(const t_inputrec &ir);
145 //! We have PBC from dim 0 (X) up to npbcdim
147 //! The system is bounded from 0 (X) to numBoundedDimensions
148 int numBoundedDimensions;
149 //! Tells whether the box bounding the atoms is dynamic
155 struct gmx_domdec_t { //NOLINT(clang-analyzer-optin.performance.Padding)
156 //! Constructor, only partial for now
157 gmx_domdec_t(const t_inputrec &ir);
159 /* The DD particle-particle nodes only */
160 /* The communication setup within the communicator all
161 * defined in dd->comm in domdec.c
164 MPI_Comm mpi_comm_all = MPI_COMM_NULL;
165 /* The local DD cell index and rank */
166 ivec ci = { 0, 0, 0 };
168 ivec master_ci = { 0, 0, 0 };
170 /* Communication with the PME only nodes */
172 gmx_bool pme_receive_vir_ener = false;
173 gmx_pme_comm_n_box_t *cnb = nullptr;
175 MPI_Request req_pme[8];
177 /* Properties of the unit cell */
178 UnitCellInfo unitCellInfo;
180 /* The communication setup, identical for each cell, cartesian index */
181 ivec nc = { 0, 0, 0 };
183 ivec dim = { 0, 0, 0 }; /* indexed by 0 to ndim */
185 /* Forward and backward neighboring cells, indexed by 0 to ndim */
186 int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
188 /* Only available on the master node */
189 std::unique_ptr<AtomDistribution> ma;
191 /* Global atom number to interaction list */
192 gmx_reverse_top_t *reverse_top = nullptr;
193 int nbonded_global = 0;
194 int nbonded_local = 0;
196 /* The number of inter charge-group exclusions */
197 int n_intercg_excl = 0;
200 gmx::HashedMap<int> *ga2la_vsite = nullptr;
201 gmx_domdec_specat_comm_t *vsite_comm = nullptr;
202 std::vector<int> vsite_requestedGlobalAtomIndices;
204 /* Constraint stuff */
205 gmx_domdec_constraints_t *constraints = nullptr;
206 gmx_domdec_specat_comm_t *constraint_comm = nullptr;
208 /* The number of home atom groups */
210 /* Global atom group indices for the home and all non-home groups */
211 std::vector<int> globalAtomGroupIndices;
213 /* Index from the local atoms to the global atoms, covers home and received zones */
214 std::vector<int> globalAtomIndices;
216 /* Global atom number to local atom number list */
217 gmx_ga2la_t *ga2la = nullptr;
219 /* Communication stuff */
220 gmx_domdec_comm_t *comm = nullptr;
222 /* The partioning count, to keep track of the state */
223 int64_t ddp_count = 0;
225 /* The managed atom sets that are updated in domain decomposition */
226 gmx::LocalAtomSetManager * atomSets = nullptr;
228 /* gmx_pme_recv_f buffer */
229 std::vector<gmx::RVec> pmeForceReceiveBuffer;
231 /* GPU halo exchange object */
232 std::unique_ptr<gmx::GpuHaloExchange> gpuHaloExchange;
235 //! Are we the master node for domain decomposition
236 static inline bool DDMASTER(const gmx_domdec_t &dd)
238 return dd.rank == dd.masterrank;
241 //! Are we the master node for domain decomposition, deprecated
242 static inline bool DDMASTER(const gmx_domdec_t *dd)
244 return dd->rank == dd->masterrank;