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
 189     nnbl = nbl_list->nnbl;
 190     nbl  = nbl_list->nbl;
 191
 192     if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
 193     {
 194         coult = coultRF;
 195     }
 196     else
 197     {
 198         if (ic->rcoulomb == ic->rvdw)
 199         {
 200             coult = coultTAB;
 201         }
 202         else
 203         {
 204             coult = coultTAB_TWIN;
 205         }
 206     }
 207
 208     if (ic->vdwtype == evdwCUT)
 209     {
 210         switch (ic->vdw_modifier)
 211         {
 212             case eintmodPOTSHIFT:
 213             case eintmodNONE:
 214                 vdwt = vdwtCUT;
 215                 break;
 216             case eintmodFORCESWITCH:
 217                 vdwt = vdwtFSWITCH;
 218                 break;
 219             case eintmodPOTSWITCH:
 220                 vdwt = vdwtPSWITCH;
 221                 break;
 222             default:
 223                 gmx_incons("Unsupported VdW modifier");
 224                 break;
 225         }
 226     }
 227     else if (ic->vdwtype == evdwPME)
 228     {
 229         if (ic->ljpme_comb_rule == ljcrGEOM)
 230         {
 231             assert(nbat->comb_rule == ljcrGEOM);
 232             vdwt = vdwtEWALDGEOM;
 233         }
 234         else
 235         {
 236             assert(nbat->comb_rule == ljcrLB);
 237             vdwt = vdwtEWALDLB;
 238         }
 239     }
 240     else
 241     {
 242         gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
 243     }
 244
 245 #pragma omp parallel for schedule(static) num_threads(gmx_omp_nthreads_get(emntNonbonded))
 246     for (nb = 0; nb < nnbl; nb++)
 247     {
 248         nbnxn_atomdata_output_t *out;
 249         real                    *fshift_p;
 250
 251         out = &nbat->out[nb];
 252
 253         if (clearF == enbvClearFYes)
 254         {
 255             clear_f(nbat, nb, out->f);
 256         }
 257
 258         if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
 259         {
 260             fshift_p = fshift;
 261         }
 262         else
 263         {
 264             fshift_p = out->fshift;
 265
 266             if (clearF == enbvClearFYes)
 267             {
 268                 clear_fshift(fshift_p);
 269             }
 270         }
 271
 272         if (!(force_flags & GMX_FORCE_ENERGY))
 273         {
 274             /* Don't calculate energies */
 275             p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
 276                                         ic,
 277                                         shift_vec,
 278                                         out->f,
 279                                         fshift_p);
 280         }
 281         else if (out->nV == 1)
 282         {
 283             /* No energy groups */
 284             out->Vvdw[0] = 0;
 285             out->Vc[0]   = 0;
 286
 287             p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
 288                                       ic,
 289                                       shift_vec,
 290                                       out->f,
 291                                       fshift_p,
 292                                       out->Vvdw,
 293                                       out->Vc);
 294         }
 295         else
 296         {
 297             /* Calculate energy group contributions */
 298             int i;
 299
 300             for (i = 0; i < out->nV; i++)
 301             {
 302                 out->Vvdw[i] = 0;
 303             }
 304             for (i = 0; i < out->nV; i++)
 305             {
 306                 out->Vc[i] = 0;
 307             }
 308
 309             p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
 310                                          ic,
 311                                          shift_vec,
 312                                          out->f,
 313                                          fshift_p,
 314                                          out->Vvdw,
 315                                          out->Vc);
 316         }
 317     }
 318
 319     if (force_flags & GMX_FORCE_ENERGY)
 320     {
 321         reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
 322     }
 323 }