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