src/gromacs/domdec/domdec_struct.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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 <memory>
  51 #include <vector>
  52
  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"
  58
  59 //! Max number of zones in domain decomposition
  60 #define DD_MAXZONE  8
  61 //! Max number of izones in domain decomposition
  62 #define DD_MAXIZONE 4
  63
  64 struct AtomDistribution;
  65 struct gmx_domdec_comm_t;
  66 struct gmx_domdec_constraints_t;
  67 struct gmx_domdec_specat_comm_t;
  68 class gmx_ga2la_t;
  69 struct gmx_pme_comm_n_box_t;
  70 struct gmx_reverse_top_t;
  71
  72 namespace gmx
  73 {
  74 template <typename T> class HashedMap;
  75 class LocalAtomSetManager;
  76 }
  77
  78 typedef struct {
  79     /* j-zone start               */
  80     int  j0 = 0;
  81     /* j-zone end                 */
  82     int  j1 = 0;
  83     /* i-charge-group end         */
  84     int  cg1 = 0;
  85     /* j-charge-group start       */
  86     int  jcg0 = 0;
  87     /* j-charge-group end         */
  88     int  jcg1 = 0;
  89     /* Minimum shifts to consider */
  90     ivec shift0 = { };
  91     /* Maximum shifts to consider */
  92     ivec shift1 = { };
  93 } gmx_domdec_ns_ranges_t;
  94
  95 typedef struct {
  96     /* Zone lower corner in triclinic coordinates         */
  97     rvec x0 = { };
  98     /* Zone upper corner in triclinic coordinates         */
  99     rvec x1 = { };
 100     /* Zone bounding box lower corner in Cartesian coords */
 101     rvec bb_x0 = { };
 102     /* Zone bounding box upper corner in Cartesian coords */
 103     rvec bb_x1 = { };
 104 } gmx_domdec_zone_size_t;
 105
 106 struct gmx_domdec_zones_t {
 107     /* The number of zones including the home zone */
 108     int                    n = 0;
 109     /* The shift of the zones with respect to the home zone */
 110     ivec                   shift[DD_MAXZONE] = { };
 111     /* The charge group boundaries for the zones */
 112     int                    cg_range[DD_MAXZONE+1] = { };
 113     /* The number of neighbor search zones with i-particles */
 114     int                    nizone = 0;
 115     /* The neighbor search charge group ranges for each i-zone */
 116     gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
 117     /* Boundaries of the zones */
 118     gmx_domdec_zone_size_t size[DD_MAXZONE];
 119     /* The cg density of the home zone */
 120     real                   dens_zone0 = 0;
 121 };
 122
 123 struct gmx_ddbox_t {
 124     int  npbcdim;
 125     int  nboundeddim;
 126     rvec box0;
 127     rvec box_size;
 128     /* Tells if the box is skewed for each of the three cartesian directions */
 129     ivec tric_dir;
 130     rvec skew_fac;
 131     /* Orthogonal vectors for triclinic cells, Cartesian index */
 132     rvec v[DIM][DIM];
 133     /* Normal vectors for the cells walls */
 134     rvec normal[DIM];
 135 };
 136
 137
 138 struct gmx_domdec_t { //NOLINT(clang-analyzer-optin.performance.Padding)
 139     /* The DD particle-particle nodes only */
 140     /* The communication setup within the communicator all
 141      * defined in dd->comm in domdec.c
 142      */
 143     int                    nnodes;
 144     MPI_Comm               mpi_comm_all;
 145     /* Use MPI_Sendrecv communication instead of non-blocking calls */
 146     gmx_bool               bSendRecv2;
 147     /* The local DD cell index and rank */
 148     ivec                   ci;
 149     int                    rank;
 150     ivec                   master_ci;
 151     int                    masterrank;
 152     /* Communication with the PME only nodes */
 153     int                    pme_nodeid;
 154     gmx_bool               pme_receive_vir_ener;
 155     gmx_pme_comm_n_box_t  *cnb      = nullptr;
 156     int                    nreq_pme = 0;
 157     MPI_Request            req_pme[8];
 158
 159
 160     /* The communication setup, identical for each cell, cartesian index */
 161     ivec     nc;
 162     int      ndim;
 163     ivec     dim; /* indexed by 0 to ndim */
 164
 165     /* TODO: Move the next 4, and more from domdec_internal.h, to a simulation system */
 166
 167     /* PBC from dim 0 (X) to npbcdim */
 168     int  npbcdim;
 169     /* The system is bounded from 0 (X) to numBoundedDimensions */
 170     int  numBoundedDimensions;
 171     /* Does the box size change during the simulaton? */
 172     bool haveDynamicBox;
 173
 174     /* Screw PBC? */
 175     gmx_bool bScrewPBC;
 176
 177     /* Forward and backward neighboring cells, indexed by 0 to ndim */
 178     int  neighbor[DIM][2];
 179
 180     /* Only available on the master node */
 181     std::unique_ptr<AtomDistribution> ma;
 182
 183     /* Can atoms connected by constraints be assigned to different domains? */
 184     bool splitConstraints;
 185     /* Can atoms connected by settles be assigned to different domains? */
 186     bool splitSettles;
 187
 188     /* Global atom number to interaction list */
 189     gmx_reverse_top_t  *reverse_top;
 190     int                 nbonded_global;
 191     int                 nbonded_local;
 192
 193     /* The number of inter charge-group exclusions */
 194     int  n_intercg_excl;
 195
 196     /* Vsite stuff */
 197     gmx::HashedMap<int>       *ga2la_vsite = nullptr;
 198     gmx_domdec_specat_comm_t  *vsite_comm  = nullptr;
 199     std::vector<int>           vsite_requestedGlobalAtomIndices;
 200
 201     /* Constraint stuff */
 202     gmx_domdec_constraints_t *constraints     = nullptr;
 203     gmx_domdec_specat_comm_t *constraint_comm = nullptr;
 204
 205     /* The number of home atom groups */
 206     int                           ncg_home = 0;
 207     /* Global atom group indices for the home and all non-home groups */
 208     std::vector<int>              globalAtomGroupIndices;
 209
 210     /* Index from the local atoms to the global atoms, covers home and received zones */
 211     std::vector<int> globalAtomIndices;
 212
 213     /* Global atom number to local atom number list */
 214     gmx_ga2la_t  *ga2la = nullptr;
 215
 216     /* Communication stuff */
 217     gmx_domdec_comm_t *comm;
 218
 219     /* The partioning count, to keep track of the state */
 220     int64_t ddp_count;
 221
 222     /* The managed atom sets that are updated in domain decomposition */
 223     gmx::LocalAtomSetManager * atomSets;
 224
 225     /* gmx_pme_recv_f buffer */
 226     int   pme_recv_f_alloc = 0;
 227     rvec *pme_recv_f_buf   = nullptr;
 228 };
 229
 230 //! Are we the master node for domain decomposition
 231 static inline bool DDMASTER(const gmx_domdec_t &dd)
 232 {
 233     return dd.rank == dd.masterrank;
 234 };
 235
 236 //! Are we the master node for domain decomposition, deprecated
 237 static inline bool DDMASTER(const gmx_domdec_t *dd)
 238 {
 239     return dd->rank == dd->masterrank;
 240 };
 241
 242 #endif