src/gromacs/mdlib/nbnxn_atomdata.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35
  36 #ifndef _nbnxn_atomdata_h
  37 #define _nbnxn_atomdata_h
  38
  39 #include <cstdio>
  40
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/mdlib/nbnxn_pairlist.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44 #include "gromacs/utility/real.h"
  45
  46 namespace gmx
  47 {
  48 class MDLogger;
  49 }
  50
  51 struct t_mdatoms;
  52 struct gmx_wallcycle;
  53
  54 /* Default nbnxn allocation routine, allocates 32 byte aligned,
  55  * which works for plain C and aligned SSE and AVX loads/stores.
  56  */
  57 void nbnxn_alloc_aligned(void **ptr, size_t nbytes);
  58
  59 /* Free function for memory allocated with nbnxn_alloc_aligned */
  60 void nbnxn_free_aligned(void *ptr);
  61
  62 /* Reallocation wrapper function for nbnxn data structures */
  63 void nbnxn_realloc_void(void **ptr,
  64                         size_t nbytes_copy, size_t nbytes_new,
  65                         nbnxn_alloc_t *ma,
  66                         nbnxn_free_t  *mf);
  67
  68 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
  69 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
  70
  71 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
  72  * and fills up to na_round with coordinates that are far away.
  73  */
  74 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
  75                             const rvec *x, int nbatFormat,
  76                             real *xnb, int a0);
  77
  78 enum {
  79     enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
  80 };
  81
  82 /* Initialize the non-bonded atom data structure.
  83  * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
  84  * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
  85  * to the atom data structure.
  86  * enbnxninitcombrule sets what combination rule data gets stored in nbat.
  87  */
  88 void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
  89                          nbnxn_atomdata_t *nbat,
  90                          int nb_kernel_type,
  91                          int enbnxninitcombrule,
  92                          int ntype, const real *nbfp,
  93                          int n_energygroups,
  94                          int nout,
  95                          nbnxn_alloc_t *alloc,
  96                          nbnxn_free_t  *free);
  97
  98 /* Copy the atom data to the non-bonded atom data structure */
  99 void nbnxn_atomdata_set(nbnxn_atomdata_t    *nbat,
 100                         const nbnxn_search  *nbs,
 101                         const t_mdatoms     *mdatoms,
 102                         const int           *atinfo);
 103
 104 /* Copy the shift vectors to nbat */
 105 void nbnxn_atomdata_copy_shiftvec(gmx_bool          dynamic_box,
 106                                   rvec             *shift_vec,
 107                                   nbnxn_atomdata_t *nbat);
 108
 109 /* Copy x to nbat->x.
 110  * FillLocal tells if the local filler particle coordinates should be zeroed.
 111  */
 112 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search  *nbs,
 113                                      int                  locality,
 114                                      gmx_bool             FillLocal,
 115                                      rvec                *x,
 116                                      nbnxn_atomdata_t    *nbat,
 117                                      gmx_wallcycle       *wcycle);
 118
 119 /* Add the forces stored in nbat to f, zeros the forces in nbat */
 120 void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search           *nbs,
 121                                     int                     locality,
 122                                     const nbnxn_atomdata_t *nbat,
 123                                     rvec                   *f,
 124                                     gmx_wallcycle          *wcycle);
 125
 126 /* Add the fshift force stored in nbat to fshift */
 127 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,
 128                                               rvec                   *fshift);
 129
 130 #endif