src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 #include "gmxpre.h"
  36
  37 #include "nbnxn_kernel_ref.h"
  38
  39 #include "config.h"
  40
  41 #include <assert.h>
  42
  43 #include <cmath>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/math/functions.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/mdlib/force.h"
  50 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  51 #include "gromacs/mdlib/nb_verlet.h"
  52 #include "gromacs/mdlib/nbnxn_consts.h"
  53 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
  54 #include "gromacs/mdtypes/md_enums.h"
  55 #include "gromacs/pbcutil/ishift.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  60  */
  61
  62 typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t     *nbl,
  63                                   const nbnxn_atomdata_t     *nbat,
  64                                   const interaction_const_t  *ic,
  65                                   rvec                       *shift_vec,
  66                                   real                       *f,
  67                                   real                       *fshift);
  68
  69 typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
  70                                 const nbnxn_atomdata_t     *nbat,
  71                                 const interaction_const_t  *ic,
  72                                 rvec                       *shift_vec,
  73                                 real                       *f,
  74                                 real                       *fshift,
  75                                 real                       *Vvdw,
  76                                 real                       *Vc);
  77
  78 /* Analytical reaction-field kernels */
  79 #define CALC_COUL_RF
  80 #define LJ_CUT
  81 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  82 #undef LJ_CUT
  83 #define LJ_FORCE_SWITCH
  84 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  85 #undef LJ_FORCE_SWITCH
  86 #define LJ_POT_SWITCH
  87 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  88 #undef LJ_POT_SWITCH
  89 #define LJ_EWALD
  90 #define LJ_CUT
  91 #define LJ_EWALD_COMB_GEOM
  92 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  93 #undef LJ_EWALD_COMB_GEOM
  94 #define LJ_EWALD_COMB_LB
  95 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
  96 #undef LJ_EWALD_COMB_LB
  97 #undef LJ_CUT
  98 #undef LJ_EWALD
  99 #undef CALC_COUL_RF
 100
 101
 102 /* Tabulated exclusion interaction electrostatics kernels */
 103 #define CALC_COUL_TAB
 104 #define LJ_CUT
 105 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 106 #undef LJ_CUT
 107 #define LJ_FORCE_SWITCH
 108 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 109 #undef LJ_FORCE_SWITCH
 110 #define LJ_POT_SWITCH
 111 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 112 #undef LJ_POT_SWITCH
 113 #define LJ_EWALD
 114 #define LJ_CUT
 115 #define LJ_EWALD_COMB_GEOM
 116 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 117 #undef LJ_EWALD_COMB_GEOM
 118 #define LJ_EWALD_COMB_LB
 119 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 120 #undef LJ_EWALD_COMB_LB
 121 #undef LJ_CUT
 122 #undef LJ_EWALD
 123 /* Twin-range cut-off kernels */
 124 #define VDW_CUTOFF_CHECK
 125 #define LJ_CUT
 126 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 127 #undef LJ_CUT
 128 #define LJ_FORCE_SWITCH
 129 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 130 #undef LJ_FORCE_SWITCH
 131 #define LJ_POT_SWITCH
 132 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 133 #undef LJ_POT_SWITCH
 134 #define LJ_EWALD
 135 #define LJ_CUT
 136 #define LJ_EWALD_COMB_GEOM
 137 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 138 #undef LJ_EWALD_COMB_GEOM
 139 #define LJ_EWALD_COMB_LB
 140 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 141 #undef LJ_EWALD_COMB_LB
 142 #undef LJ_CUT
 143 #undef LJ_EWALD
 144 #undef VDW_CUTOFF_CHECK
 145 #undef CALC_COUL_TAB
 146
 147
 148 enum {
 149     coultRF, coultTAB, coultTAB_TWIN, coultNR
 150 };
 151
 152 enum {
 153     vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
 154 };
 155
 156 p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
 157 {
 158     { 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           },
 159     { 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        },
 160     { 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 }
 161 };
 162
 163 p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
 164 {
 165     { 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            },
 166     { 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         },
 167     { 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  }
 168 };
 169
 170 p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
 171 {
 172     { 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           },
 173     { 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        },
 174     { 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 }
 175 };
 176
 177 void
 178 nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
 179                  const nbnxn_atomdata_t     *nbat,
 180                  const interaction_const_t  *ic,
 181                  rvec                       *shift_vec,
 182                  int                         force_flags,
 183                  int                         clearF,
 184                  real                       *fshift,
 185                  real                       *Vc,
 186                  real                       *Vvdw)
 187 {
 188     int                nnbl;
 189     nbnxn_pairlist_t **nbl;
 190     int                coult;
 191     int                vdwt;
 192     int                nb;
 193     int                nthreads gmx_unused;
 194
 195     nnbl = nbl_list->nnbl;
 196     nbl  = nbl_list->nbl;
 197
 198     if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
 199     {
 200         coult = coultRF;
 201     }
 202     else
 203     {
 204         if (ic->rcoulomb == ic->rvdw)
 205         {
 206             coult = coultTAB;
 207         }
 208         else
 209         {
 210             coult = coultTAB_TWIN;
 211         }
 212     }
 213
 214     if (ic->vdwtype == evdwCUT)
 215     {
 216         switch (ic->vdw_modifier)
 217         {
 218             case eintmodPOTSHIFT:
 219             case eintmodNONE:
 220                 vdwt = vdwtCUT;
 221                 break;
 222             case eintmodFORCESWITCH:
 223                 vdwt = vdwtFSWITCH;
 224                 break;
 225             case eintmodPOTSWITCH:
 226                 vdwt = vdwtPSWITCH;
 227                 break;
 228             default:
 229                 gmx_incons("Unsupported VdW modifier");
 230                 break;
 231         }
 232     }
 233     else if (ic->vdwtype == evdwPME)
 234     {
 235         if (ic->ljpme_comb_rule == ljcrGEOM)
 236         {
 237             assert(nbat->comb_rule == ljcrGEOM);
 238             vdwt = vdwtEWALDGEOM;
 239         }
 240         else
 241         {
 242             assert(nbat->comb_rule == ljcrLB);
 243             vdwt = vdwtEWALDLB;
 244         }
 245     }
 246     else
 247     {
 248         gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
 249     }
 250
 251     // cppcheck-suppress unreadVariable
 252     nthreads = gmx_omp_nthreads_get(emntNonbonded);
 253 #pragma omp parallel for schedule(static) num_threads(nthreads)
 254     for (nb = 0; nb < nnbl; nb++)
 255     {
 256         // Presently, the kernels do not call C++ code that can throw, so
 257         // no need for a try/catch pair in this OpenMP region.
 258         nbnxn_atomdata_output_t *out;
 259         real                    *fshift_p;
 260
 261         out = &nbat->out[nb];
 262
 263         if (clearF == enbvClearFYes)
 264         {
 265             clear_f(nbat, nb, out->f);
 266         }
 267
 268         if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
 269         {
 270             fshift_p = fshift;
 271         }
 272         else
 273         {
 274             fshift_p = out->fshift;
 275
 276             if (clearF == enbvClearFYes)
 277             {
 278                 clear_fshift(fshift_p);
 279             }
 280         }
 281
 282         if (!(force_flags & GMX_FORCE_ENERGY))
 283         {
 284             /* Don't calculate energies */
 285             p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
 286                                         ic,
 287                                         shift_vec,
 288                                         out->f,
 289                                         fshift_p);
 290         }
 291         else if (out->nV == 1)
 292         {
 293             /* No energy groups */
 294             out->Vvdw[0] = 0;
 295             out->Vc[0]   = 0;
 296
 297             p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
 298                                       ic,
 299                                       shift_vec,
 300                                       out->f,
 301                                       fshift_p,
 302                                       out->Vvdw,
 303                                       out->Vc);
 304         }
 305         else
 306         {
 307             /* Calculate energy group contributions */
 308             int i;
 309
 310             for (i = 0; i < out->nV; i++)
 311             {
 312                 out->Vvdw[i] = 0;
 313             }
 314             for (i = 0; i < out->nV; i++)
 315             {
 316                 out->Vc[i] = 0;
 317             }
 318
 319             p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
 320                                          ic,
 321                                          shift_vec,
 322                                          out->f,
 323                                          fshift_p,
 324                                          out->Vvdw,
 325                                          out->Vc);
 326         }
 327     }
 328
 329     if (force_flags & GMX_FORCE_ENERGY)
 330     {
 331         reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
 332     }
 333 }