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36 /*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
37 * \ingroup group_mdrun
39 * \brief Manages the decomposition of the simulation volume over MPI
40 * ranks to try to distribute work evenly with minimal communication
43 * \todo Get domdec stuff out of mdtypes/commrec.h
45 * \author Berk Hess <hess@kth.se>
49 /*! \libinternal \file
51 * \brief This file declares functions for mdrun to call to manage the
52 * details of its domain decomposition.
54 * \author Berk Hess <hess@kth.se>
56 * \ingroup module_domdec
59 #ifndef GMX_DOMDEC_DOMDEC_H
60 #define GMX_DOMDEC_DOMDEC_H
64 #include "gromacs/math/vectypes.h"
65 #include "gromacs/utility/arrayref.h"
66 #include "gromacs/utility/basedefinitions.h"
67 #include "gromacs/utility/real.h"
72 struct gmx_domdec_zones_t;
73 struct gmx_localtop_t;
88 class ForceWithShiftForces;
90 class RangePartitioning;
93 /*! \brief Returns the global topology atom number belonging to local atom index i.
95 * This function is intended for writing ASCII output
96 * and returns atom numbers starting at 1.
97 * When dd=NULL returns i+1.
99 int ddglatnr(const gmx_domdec_t *dd, int i);
101 /*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
102 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t &dd);
104 /*! \brief Store the global cg indices of the home cgs in state,
106 * This means it can be reset, even after a new DD partitioning.
108 void dd_store_state(struct gmx_domdec_t *dd, t_state *state);
110 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
111 struct gmx_domdec_zones_t *domdec_zones(struct gmx_domdec_t *dd);
113 /*! \brief Returns the range for atoms in zones*/
114 int dd_numAtomsZones(const gmx_domdec_t &dd);
116 /*! \brief Returns the number of home atoms */
117 int dd_numHomeAtoms(const gmx_domdec_t &dd);
119 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
120 int dd_natoms_mdatoms(const gmx_domdec_t *dd);
122 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
123 int dd_natoms_vsite(const gmx_domdec_t *dd);
125 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
126 void dd_get_constraint_range(const gmx_domdec_t *dd,
127 int *at_start, int *at_end);
129 /*! \libinternal \brief Struct for passing around the number of PME domains */
132 int x; //!< The number of PME domains along dimension x
133 int y; //!< The number of PME domains along dimension y
136 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
137 NumPmeDomains getNumPmeDomains(const gmx_domdec_t *dd);
139 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
140 std::vector<int> get_pme_ddranks(const t_commrec *cr, int pmenodeid);
142 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
143 int dd_pme_maxshift_x(const gmx_domdec_t *dd);
145 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
146 int dd_pme_maxshift_y(const gmx_domdec_t *dd);
148 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
149 bool ddHaveSplitConstraints(const gmx_domdec_t &dd);
151 /*! \brief Return whether the DD has a single dimension with a single pulse
153 * The GPU halo exchange code requires a 1D single-pulse DD, and its
154 * setup code can use the returned value to understand what it should
156 bool is1DAnd1PulseDD(const gmx_domdec_t &dd);
158 /*! \brief Initialize data structures for bonded interactions */
159 void dd_init_bondeds(FILE *fplog,
161 const gmx_mtop_t *mtop,
162 const gmx_vsite_t *vsite,
163 const t_inputrec *ir,
165 cginfo_mb_t *cginfo_mb);
167 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
168 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t &dd);
170 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
171 gmx_bool dd_bonded_molpbc(const gmx_domdec_t *dd, int ePBC);
173 /*! \brief Change the DD non-bonded communication cut-off.
175 * This could fail when trying to increase the cut-off,
176 * then FALSE will be returned and the cut-off is not modified.
178 * \param[in] cr Communication recrod
179 * \param[in] box Box matrix, used for computing the dimensions of the system
180 * \param[in] x Position vector, used for computing the dimensions of the system
181 * \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
183 gmx_bool change_dd_cutoff(t_commrec *cr,
185 gmx::ArrayRef<const gmx::RVec> x,
186 real cutoffRequested);
188 /*! \brief Set up communication for averaging GPU wait times over domains
190 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
191 * are meaningless, as it depends on the order in which tasks on the same
192 * GPU finish. Therefore there wait times need to be averaged over the ranks
193 * sharing the same GPU. This function sets up the communication for that.
195 void dd_setup_dlb_resource_sharing(const t_commrec *cr,
198 /*! \brief Cycle counter indices used internally in the domain decomposition */
200 ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
203 /*! \brief Add the wallcycle count to the DD counter */
204 void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl);
206 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
207 void dd_move_x(struct gmx_domdec_t *dd,
209 gmx::ArrayRef<gmx::RVec> x,
210 gmx_wallcycle *wcycle);
212 /*! \brief Sum the forces over the neighboring cells.
214 * When fshift!=NULL the shift forces are updated to obtain
215 * the correct virial from the single sum including f.
217 void dd_move_f(struct gmx_domdec_t *dd,
218 gmx::ForceWithShiftForces *forceWithShiftForces,
219 gmx_wallcycle *wcycle);
221 /*! \brief Communicate a real for each atom to the neighboring cells. */
222 void dd_atom_spread_real(struct gmx_domdec_t *dd, real v[]);
224 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
225 void dd_atom_sum_real(struct gmx_domdec_t *dd, real v[]);
227 /*! \brief Reset all the statistics and counters for total run counting */
228 void reset_dd_statistics_counters(struct gmx_domdec_t *dd);
230 /* In domdec_con.c */
232 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
233 void dd_move_f_vsites(struct gmx_domdec_t *dd, rvec *f, rvec *fshift);
235 /*! \brief Clears the forces for virtual sites */
236 void dd_clear_f_vsites(struct gmx_domdec_t *dd, rvec *f);
238 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
239 void dd_move_x_constraints(struct gmx_domdec_t *dd, const matrix box,
240 rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
242 /*! \brief Communicates the coordinates involved in virtual sites */
243 void dd_move_x_vsites(struct gmx_domdec_t *dd, const matrix box, rvec *x);
245 /*! \brief Returns the local atom count array for all constraints
247 * The local atom count for a constraint, possible values 2/1/0, is needed
248 * to avoid not/double-counting contributions linked to the Lagrange
249 * multiplier, such as the virial and free-energy derivatives.
251 * \note When \p dd = nullptr, an empty reference is returned.
253 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t *dd);
255 /* In domdec_top.c */
257 /*! \brief Print error output when interactions are missing */
259 void dd_print_missing_interactions(const gmx::MDLogger &mdlog,
262 const gmx_mtop_t *top_global,
263 const gmx_localtop_t *top_local,
267 /*! \brief Generate and store the reverse topology */
268 void dd_make_reverse_top(FILE *fplog,
269 gmx_domdec_t *dd, const gmx_mtop_t *mtop,
270 const gmx_vsite_t *vsite,
271 const t_inputrec *ir, gmx_bool bBCheck);
273 /*! \brief Generate the local topology and virtual site data */
274 void dd_make_local_top(struct gmx_domdec_t *dd,
275 struct gmx_domdec_zones_t *zones,
282 const gmx_mtop_t &top,
283 gmx_localtop_t *ltop);
285 /*! \brief Sort ltop->ilist when we are doing free energy. */
286 void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
287 gmx_localtop_t *ltop);
289 /*! \brief Initialize local topology
291 * \param[in] top_global Reference to global topology.
292 * \param[in,out] top Pointer to new local topology
294 void dd_init_local_top(const gmx_mtop_t &top_global,
295 gmx_localtop_t *top);
297 /*! \brief Construct local state */
298 void dd_init_local_state(struct gmx_domdec_t *dd,
299 const t_state *state_global, t_state *local_state);
301 /*! \brief Generate a list of links between atoms that are linked by bonded interactions
303 * Also stores whether atoms are linked in \p cginfo_mb.
305 t_blocka *makeBondedLinks(const gmx_mtop_t *mtop,
306 cginfo_mb_t *cginfo_mb);
308 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
309 void dd_bonded_cg_distance(const gmx::MDLogger &mdlog,
310 const gmx_mtop_t *mtop,
311 const t_inputrec *ir,
312 const rvec *x, const matrix box,
314 real *r_2b, real *r_mb);