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 "gmxpre.h"
  36
  37 #include "nbnxn_kernel_ref.h"
  38
  39 #include "config.h"
  40
  41 #include <assert.h>
  42 #include <math.h>
  43
  44 #include "gromacs/legacyheaders/force.h"
  45 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
  46 #include "gromacs/legacyheaders/typedefs.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/mdlib/nb_verlet.h"
  49 #include "gromacs/mdlib/nbnxn_consts.h"
  50 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
  51 #include "gromacs/pbcutil/ishift.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  55  */
  56
  57 typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t     *nbl,
  58                                   const nbnxn_atomdata_t     *nbat,
  59                                   const interaction_const_t  *ic,
  60                                   rvec                       *shift_vec,
  61                                   real                       *f,
  62                                   real                       *fshift);
  63
  64 typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
  65                                 const nbnxn_atomdata_t     *nbat,
  66                                 const interaction_const_t  *ic,
  67                                 rvec                       *shift_vec,
  68                                 real                       *f,
  69                                 real                       *fshift,
  70                                 real                       *Vvdw,
  71                                 real                       *Vc);
  72
  73 /* Analytical reaction-field kernels */
  74 #define CALC_COUL_RF
  75 #define LJ_CUT
  76 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  77 #undef LJ_CUT
  78 #define LJ_FORCE_SWITCH
  79 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  80 #undef LJ_FORCE_SWITCH
  81 #define LJ_POT_SWITCH
  82 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  83 #undef LJ_POT_SWITCH
  84 #define LJ_EWALD
  85 #define LJ_CUT
  86 #define LJ_EWALD_COMB_GEOM
  87 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  88 #undef LJ_EWALD_COMB_GEOM
  89 #define LJ_EWALD_COMB_LB
  90 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  91 #undef LJ_EWALD_COMB_LB
  92 #undef LJ_CUT
  93 #undef LJ_EWALD
  94 #undef CALC_COUL_RF
  95
  96
  97 /* Tabulated exclusion interaction electrostatics kernels */
  98 #define CALC_COUL_TAB
  99 #define LJ_CUT
 100 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 101 #undef LJ_CUT
 102 #define LJ_FORCE_SWITCH
 103 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 104 #undef LJ_FORCE_SWITCH
 105 #define LJ_POT_SWITCH
 106 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 107 #undef LJ_POT_SWITCH
 108 #define LJ_EWALD
 109 #define LJ_CUT
 110 #define LJ_EWALD_COMB_GEOM
 111 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 112 #undef LJ_EWALD_COMB_GEOM
 113 #define LJ_EWALD_COMB_LB
 114 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 115 #undef LJ_EWALD_COMB_LB
 116 #undef LJ_CUT
 117 #undef LJ_EWALD
 118 /* Twin-range cut-off kernels */
 119 #define VDW_CUTOFF_CHECK
 120 #define LJ_CUT
 121 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 122 #undef LJ_CUT
 123 #define LJ_FORCE_SWITCH
 124 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 125 #undef LJ_FORCE_SWITCH
 126 #define LJ_POT_SWITCH
 127 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 128 #undef LJ_POT_SWITCH
 129 #define LJ_EWALD
 130 #define LJ_CUT
 131 #define LJ_EWALD_COMB_GEOM
 132 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 133 #undef LJ_EWALD_COMB_GEOM
 134 #define LJ_EWALD_COMB_LB
 135 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 136 #undef LJ_EWALD_COMB_LB
 137 #undef LJ_CUT
 138 #undef LJ_EWALD
 139 #undef VDW_CUTOFF_CHECK
 140 #undef CALC_COUL_TAB
 141
 142
 143 enum {
 144     coultRF, coultTAB, coultTAB_TWIN, coultNR
 145 };
 146
 147 enum {
 148     vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
 149 };
 150
 151 p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
 152 {
 153     { 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           },
 154     { 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        },
 155     { 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 }
 156 };
 157
 158 p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
 159 {
 160     { 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            },
 161     { 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         },
 162     { 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  }
 163 };
 164
 165 p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
 166 {
 167     { 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           },
 168     { 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        },
 169     { 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 }
 170 };
 171
 172 void
 173 nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
 174                  const nbnxn_atomdata_t     *nbat,
 175                  const interaction_const_t  *ic,
 176                  rvec                       *shift_vec,
 177                  int                         force_flags,
 178                  int                         clearF,
 179                  real                       *fshift,
 180                  real                       *Vc,
 181                  real                       *Vvdw)
 182 {
 183     int                nnbl;
 184     nbnxn_pairlist_t **nbl;
 185     int                coult;
 186     int                vdwt;
 187     int                nb;
 188     int                nthreads gmx_unused;
 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     nthreads = gmx_omp_nthreads_get(emntNonbonded);
 247 #pragma omp parallel for schedule(static) num_threads(nthreads)
 248     for (nb = 0; nb < nnbl; nb++)
 249     {
 250         nbnxn_atomdata_output_t *out;
 251         real                    *fshift_p;
 252
 253         out = &nbat->out[nb];
 254
 255         if (clearF == enbvClearFYes)
 256         {
 257             clear_f(nbat, nb, out->f);
 258         }
 259
 260         if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
 261         {
 262             fshift_p = fshift;
 263         }
 264         else
 265         {
 266             fshift_p = out->fshift;
 267
 268             if (clearF == enbvClearFYes)
 269             {
 270                 clear_fshift(fshift_p);
 271             }
 272         }
 273
 274         if (!(force_flags & GMX_FORCE_ENERGY))
 275         {
 276             /* Don't calculate energies */
 277             p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
 278                                         ic,
 279                                         shift_vec,
 280                                         out->f,
 281                                         fshift_p);
 282         }
 283         else if (out->nV == 1)
 284         {
 285             /* No energy groups */
 286             out->Vvdw[0] = 0;
 287             out->Vc[0]   = 0;
 288
 289             p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
 290                                       ic,
 291                                       shift_vec,
 292                                       out->f,
 293                                       fshift_p,
 294                                       out->Vvdw,
 295                                       out->Vc);
 296         }
 297         else
 298         {
 299             /* Calculate energy group contributions */
 300             int i;
 301
 302             for (i = 0; i < out->nV; i++)
 303             {
 304                 out->Vvdw[i] = 0;
 305             }
 306             for (i = 0; i < out->nV; i++)
 307             {
 308                 out->Vc[i] = 0;
 309             }
 310
 311             p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
 312                                          ic,
 313                                          shift_vec,
 314                                          out->f,
 315                                          fshift_p,
 316                                          out->Vvdw,
 317                                          out->Vc);
 318         }
 319     }
 320
 321     if (force_flags & GMX_FORCE_ENERGY)
 322     {
 323         reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
 324     }
 325 }