src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014, 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,
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  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
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  34  */
  35 #include "gmxpre.h"
  36
  37 #include "config.h"
  38
  39 #include <math.h>
  40 #include <assert.h>
  41
  42 #include "gromacs/legacyheaders/typedefs.h"
  43 #include "gromacs/legacyheaders/force.h"
  44 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/pbcutil/ishift.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 #include "nbnxn_kernel_ref.h"
  51 #include "../nbnxn_consts.h"
  52 #include "nbnxn_kernel_common.h"
  53 #include "gromacs/mdlib/nb_verlet.h"
  54
  55 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  56  */
  57
  58 typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t     *nbl,
  59                                   const nbnxn_atomdata_t     *nbat,
  60                                   const interaction_const_t  *ic,
  61                                   rvec                       *shift_vec,
  62                                   real                       *f,
  63                                   real                       *fshift);
  64
  65 typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
  66                                 const nbnxn_atomdata_t     *nbat,
  67                                 const interaction_const_t  *ic,
  68                                 rvec                       *shift_vec,
  69                                 real                       *f,
  70                                 real                       *fshift,
  71                                 real                       *Vvdw,
  72                                 real                       *Vc);
  73
  74 /* Analytical reaction-field kernels */
  75 #define CALC_COUL_RF
  76 #define LJ_CUT
  77 #include "nbnxn_kernel_ref_includes.h"
  78 #undef LJ_CUT
  79 #define LJ_FORCE_SWITCH
  80 #include "nbnxn_kernel_ref_includes.h"
  81 #undef LJ_FORCE_SWITCH
  82 #define LJ_POT_SWITCH
  83 #include "nbnxn_kernel_ref_includes.h"
  84 #undef LJ_POT_SWITCH
  85 #define LJ_EWALD
  86 #define LJ_CUT
  87 #define LJ_EWALD_COMB_GEOM
  88 #include "nbnxn_kernel_ref_includes.h"
  89 #undef LJ_EWALD_COMB_GEOM
  90 #define LJ_EWALD_COMB_LB
  91 #include "nbnxn_kernel_ref_includes.h"
  92 #undef LJ_EWALD_COMB_LB
  93 #undef LJ_CUT
  94 #undef LJ_EWALD
  95 #undef CALC_COUL_RF
  96
  97
  98 /* Tabulated exclusion interaction electrostatics kernels */
  99 #define CALC_COUL_TAB
 100 #define LJ_CUT
 101 #include "nbnxn_kernel_ref_includes.h"
 102 #undef LJ_CUT
 103 #define LJ_FORCE_SWITCH
 104 #include "nbnxn_kernel_ref_includes.h"
 105 #undef LJ_FORCE_SWITCH
 106 #define LJ_POT_SWITCH
 107 #include "nbnxn_kernel_ref_includes.h"
 108 #undef LJ_POT_SWITCH
 109 #define LJ_EWALD
 110 #define LJ_CUT
 111 #define LJ_EWALD_COMB_GEOM
 112 #include "nbnxn_kernel_ref_includes.h"
 113 #undef LJ_EWALD_COMB_GEOM
 114 #define LJ_EWALD_COMB_LB
 115 #include "nbnxn_kernel_ref_includes.h"
 116 #undef LJ_EWALD_COMB_LB
 117 #undef LJ_CUT
 118 #undef LJ_EWALD
 119 /* Twin-range cut-off kernels */
 120 #define VDW_CUTOFF_CHECK
 121 #define LJ_CUT
 122 #include "nbnxn_kernel_ref_includes.h"
 123 #undef LJ_CUT
 124 #define LJ_FORCE_SWITCH
 125 #include "nbnxn_kernel_ref_includes.h"
 126 #undef LJ_FORCE_SWITCH
 127 #define LJ_POT_SWITCH
 128 #include "nbnxn_kernel_ref_includes.h"
 129 #undef LJ_POT_SWITCH
 130 #define LJ_EWALD
 131 #define LJ_CUT
 132 #define LJ_EWALD_COMB_GEOM
 133 #include "nbnxn_kernel_ref_includes.h"
 134 #undef LJ_EWALD_COMB_GEOM
 135 #define LJ_EWALD_COMB_LB
 136 #include "nbnxn_kernel_ref_includes.h"
 137 #undef LJ_EWALD_COMB_LB
 138 #undef LJ_CUT
 139 #undef LJ_EWALD
 140 #undef VDW_CUTOFF_CHECK
 141 #undef CALC_COUL_TAB
 142
 143
 144 enum {
 145     coultRF, coultTAB, coultTAB_TWIN, coultNR
 146 };
 147
 148 enum {
 149     vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
 150 };
 151
 152 p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
 153 {
 154     { nbnxn_kernel_ElecRF_VdwLJ_F_ref,           nbnxn_kernel_ElecRF_VdwLJFsw_F_ref,           nbnxn_kernel_ElecRF_VdwLJPsw_F_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref           },
 155     { nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,        nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref,        nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref        },
 156     { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref }
 157 };
 158
 159 p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
 160 {
 161     { nbnxn_kernel_ElecRF_VdwLJ_VF_ref,           nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref,           nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref            },
 162     { nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,        nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref,        nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref         },
 163     { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref  }
 164 };
 165
 166 p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
 167 {
 168     { nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,           nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref,           nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref,           nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref           },
 169     { nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,        nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref,        nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref,        nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref        },
 170     { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref }
 171 };
 172
 173 void
 174 nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
 175                  const nbnxn_atomdata_t     *nbat,
 176                  const interaction_const_t  *ic,
 177                  rvec                       *shift_vec,
 178                  int                         force_flags,
 179                  int                         clearF,
 180                  real                       *fshift,
 181                  real                       *Vc,
 182                  real                       *Vvdw)
 183 {
 184     int                nnbl;
 185     nbnxn_pairlist_t **nbl;
 186     int                coult;
 187     int                vdwt;
 188     int                nb;
 189
 190     nnbl = nbl_list->nnbl;
 191     nbl  = nbl_list->nbl;
 192
 193     if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
 194     {
 195         coult = coultRF;
 196     }
 197     else
 198     {
 199         if (ic->rcoulomb == ic->rvdw)
 200         {
 201             coult = coultTAB;
 202         }
 203         else
 204         {
 205             coult = coultTAB_TWIN;
 206         }
 207     }
 208
 209     if (ic->vdwtype == evdwCUT)
 210     {
 211         switch (ic->vdw_modifier)
 212         {
 213             case eintmodPOTSHIFT:
 214             case eintmodNONE:
 215                 vdwt = vdwtCUT;
 216                 break;
 217             case eintmodFORCESWITCH:
 218                 vdwt = vdwtFSWITCH;
 219                 break;
 220             case eintmodPOTSWITCH:
 221                 vdwt = vdwtPSWITCH;
 222                 break;
 223             default:
 224                 gmx_incons("Unsupported VdW modifier");
 225                 break;
 226         }
 227     }
 228     else if (ic->vdwtype == evdwPME)
 229     {
 230         if (ic->ljpme_comb_rule == ljcrGEOM)
 231         {
 232             assert(nbat->comb_rule == ljcrGEOM);
 233             vdwt = vdwtEWALDGEOM;
 234         }
 235         else
 236         {
 237             assert(nbat->comb_rule == ljcrLB);
 238             vdwt = vdwtEWALDLB;
 239         }
 240     }
 241     else
 242     {
 243         gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
 244     }
 245
 246 #pragma omp parallel for schedule(static) num_threads(gmx_omp_nthreads_get(emntNonbonded))
 247     for (nb = 0; nb < nnbl; nb++)
 248     {
 249         nbnxn_atomdata_output_t *out;
 250         real                    *fshift_p;
 251
 252         out = &nbat->out[nb];
 253
 254         if (clearF == enbvClearFYes)
 255         {
 256             clear_f(nbat, nb, out->f);
 257         }
 258
 259         if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
 260         {
 261             fshift_p = fshift;
 262         }
 263         else
 264         {
 265             fshift_p = out->fshift;
 266
 267             if (clearF == enbvClearFYes)
 268             {
 269                 clear_fshift(fshift_p);
 270             }
 271         }
 272
 273         if (!(force_flags & GMX_FORCE_ENERGY))
 274         {
 275             /* Don't calculate energies */
 276             p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
 277                                         ic,
 278                                         shift_vec,
 279                                         out->f,
 280                                         fshift_p);
 281         }
 282         else if (out->nV == 1)
 283         {
 284             /* No energy groups */
 285             out->Vvdw[0] = 0;
 286             out->Vc[0]   = 0;
 287
 288             p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
 289                                       ic,
 290                                       shift_vec,
 291                                       out->f,
 292                                       fshift_p,
 293                                       out->Vvdw,
 294                                       out->Vc);
 295         }
 296         else
 297         {
 298             /* Calculate energy group contributions */
 299             int i;
 300
 301             for (i = 0; i < out->nV; i++)
 302             {
 303                 out->Vvdw[i] = 0;
 304             }
 305             for (i = 0; i < out->nV; i++)
 306             {
 307                 out->Vc[i] = 0;
 308             }
 309
 310             p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
 311                                          ic,
 312                                          shift_vec,
 313                                          out->f,
 314                                          fshift_p,
 315                                          out->Vvdw,
 316                                          out->Vc);
 317         }
 318     }
 319
 320     if (force_flags & GMX_FORCE_ENERGY)
 321     {
 322         reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
 323     }
 324 }