src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "nbnxn_kernel_gpu_ref.h"
  38
  39 #include "config.h"
  40
  41 #include <cmath>
  42
  43 #include <algorithm>
  44
  45 #include "gromacs/math/functions.h"
  46 #include "gromacs/math/utilities.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/mdlib/force_flags.h"
  49 #include "gromacs/mdlib/nb_verlet.h"
  50 #include "gromacs/mdlib/nbnxn_consts.h"
  51 #include "gromacs/mdtypes/md_enums.h"
  52 #include "gromacs/pbcutil/ishift.h"
  53 #include "gromacs/utility/fatalerror.h"
  54
  55 #include "nbnxn_kernel_common.h"
  56
  57 static const int c_numClPerSupercl = c_nbnxnGpuNumClusterPerSupercluster;
  58 static const int c_clSize          = c_nbnxnGpuClusterSize;
  59
  60 void
  61 nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu     *nbl,
  62                      const nbnxn_atomdata_t     *nbat,
  63                      const interaction_const_t  *iconst,
  64                      rvec                       *shift_vec,
  65                      int                         force_flags,
  66                      int                         clearF,
  67                      gmx::ArrayRef<real>         f,
  68                      real  *                     fshift,
  69                      real  *                     Vc,
  70                      real  *                     Vvdw)
  71 {
  72     gmx_bool            bEner;
  73     gmx_bool            bEwald;
  74     const real         *Ftab = nullptr;
  75     real                rcut2, rvdw2, rlist2;
  76     int                 ntype;
  77     real                facel;
  78     int                 ish3;
  79     int                 sci;
  80     int                 cj4_ind0, cj4_ind1, cj4_ind;
  81     int                 ci, cj;
  82     int                 ic, jc, ia, ja, is, ifs, js, jfs, im, jm;
  83     int                 n0;
  84     int                 ggid;
  85     real                shX, shY, shZ;
  86     real                fscal, tx, ty, tz;
  87     real                rinvsq;
  88     real                iq;
  89     real                qq, vcoul = 0, krsq, vctot;
  90     int                 nti;
  91     int                 tj;
  92     real                rt, r, eps;
  93     real                rinvsix;
  94     real                Vvdwtot;
  95     real                Vvdw_rep, Vvdw_disp;
  96     real                ix, iy, iz, fix, fiy, fiz;
  97     real                jx, jy, jz;
  98     real                dx, dy, dz, rsq, rinv;
  99     int                 int_bit;
 100     real                fexcl;
 101     real                c6, c12;
 102     const nbnxn_excl_t *excl[2];
 103
 104     int                 npair_tot, npair;
 105     int                 nhwu, nhwu_pruned;
 106
 107     if (nbl->na_ci != c_clSize)
 108     {
 109         gmx_fatal(FARGS, "The neighborlist cluster size in the GPU reference kernel is %d, expected it to be %d", nbl->na_ci, c_clSize);
 110     }
 111
 112     if (clearF == enbvClearFYes)
 113     {
 114         clear_f(nbat, 0, f.data());
 115     }
 116
 117     bEner = ((force_flags & GMX_FORCE_ENERGY) != 0);
 118
 119     bEwald = EEL_FULL(iconst->eeltype);
 120     if (bEwald)
 121     {
 122         Ftab = iconst->tabq_coul_F;
 123     }
 124
 125     rcut2                = iconst->rcoulomb*iconst->rcoulomb;
 126     rvdw2                = iconst->rvdw*iconst->rvdw;
 127
 128     rlist2               = nbl->rlist*nbl->rlist;
 129
 130     const int  *type     = nbat->params().type.data();
 131     facel                = iconst->epsfac;
 132     const real *shiftvec = shift_vec[0];
 133     const real *vdwparam = nbat->params().nbfp.data();
 134     ntype                = nbat->params().numTypes;
 135
 136     const real *x        = nbat->x().data();
 137
 138     npair_tot   = 0;
 139     nhwu        = 0;
 140     nhwu_pruned = 0;
 141
 142     for (const nbnxn_sci_t &nbln : nbl->sci)
 143     {
 144         ish3             = 3*nbln.shift;
 145         shX              = shiftvec[ish3];
 146         shY              = shiftvec[ish3+1];
 147         shZ              = shiftvec[ish3+2];
 148         cj4_ind0         = nbln.cj4_ind_start;
 149         cj4_ind1         = nbln.cj4_ind_end;
 150         sci              = nbln.sci;
 151         vctot            = 0;
 152         Vvdwtot          = 0;
 153
 154         if (nbln.shift == CENTRAL &&
 155             nbl->cj4[cj4_ind0].cj[0] == sci*c_numClPerSupercl)
 156         {
 157             /* we have the diagonal:
 158              * add the charge self interaction energy term
 159              */
 160             for (im = 0; im < c_numClPerSupercl; im++)
 161             {
 162                 ci = sci*c_numClPerSupercl + im;
 163                 for (ic = 0; ic < c_clSize; ic++)
 164                 {
 165                     ia     = ci*c_clSize + ic;
 166                     iq     = x[ia*nbat->xstride+3];
 167                     vctot += iq*iq;
 168                 }
 169             }
 170             if (!bEwald)
 171             {
 172                 vctot *= -facel*0.5*iconst->c_rf;
 173             }
 174             else
 175             {
 176                 /* last factor 1/sqrt(pi) */
 177                 vctot *= -facel*iconst->ewaldcoeff_q*M_1_SQRTPI;
 178             }
 179         }
 180
 181         for (cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
 182         {
 183             excl[0]           = &nbl->excl[nbl->cj4[cj4_ind].imei[0].excl_ind];
 184             excl[1]           = &nbl->excl[nbl->cj4[cj4_ind].imei[1].excl_ind];
 185
 186             for (jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
 187             {
 188                 cj               = nbl->cj4[cj4_ind].cj[jm];
 189
 190                 for (im = 0; im < c_numClPerSupercl; im++)
 191                 {
 192                     /* We're only using the first imask,
 193                      * but here imei[1].imask is identical.
 194                      */
 195                     if ((nbl->cj4[cj4_ind].imei[0].imask >> (jm*c_numClPerSupercl + im)) & 1)
 196                     {
 197                         gmx_bool within_rlist;
 198
 199                         ci               = sci*c_numClPerSupercl + im;
 200
 201                         within_rlist     = FALSE;
 202                         npair            = 0;
 203                         for (ic = 0; ic < c_clSize; ic++)
 204                         {
 205                             ia               = ci*c_clSize + ic;
 206
 207                             is               = ia*nbat->xstride;
 208                             ifs              = ia*nbat->fstride;
 209                             ix               = shX + x[is+0];
 210                             iy               = shY + x[is+1];
 211                             iz               = shZ + x[is+2];
 212                             iq               = facel*x[is+3];
 213                             nti              = ntype*2*type[ia];
 214
 215                             fix              = 0;
 216                             fiy              = 0;
 217                             fiz              = 0;
 218
 219                             for (jc = 0; jc < c_clSize; jc++)
 220                             {
 221                                 ja               = cj*c_clSize + jc;
 222
 223                                 if (nbln.shift == CENTRAL &&
 224                                     ci == cj && ja <= ia)
 225                                 {
 226                                     continue;
 227                                 }
 228
 229                                 constexpr int clusterPerSplit = c_nbnxnGpuClusterSize/c_nbnxnGpuClusterpairSplit;
 230                                 int_bit = ((excl[jc/clusterPerSplit]->pair[(jc & (clusterPerSplit - 1))*c_clSize + ic]
 231                                             >> (jm*c_numClPerSupercl + im)) & 1);
 232
 233                                 js               = ja*nbat->xstride;
 234                                 jfs              = ja*nbat->fstride;
 235                                 jx               = x[js+0];
 236                                 jy               = x[js+1];
 237                                 jz               = x[js+2];
 238                                 dx               = ix - jx;
 239                                 dy               = iy - jy;
 240                                 dz               = iz - jz;
 241                                 rsq              = dx*dx + dy*dy + dz*dz;
 242                                 if (rsq < rlist2)
 243                                 {
 244                                     within_rlist = TRUE;
 245                                 }
 246                                 if (rsq >= rcut2)
 247                                 {
 248                                     continue;
 249                                 }
 250
 251                                 if (type[ia] != ntype-1 && type[ja] != ntype-1)
 252                                 {
 253                                     npair++;
 254                                 }
 255
 256                                 // Ensure distance do not become so small that r^-12 overflows
 257                                 rsq              = std::max(rsq, NBNXN_MIN_RSQ);
 258
 259                                 rinv             = gmx::invsqrt(rsq);
 260                                 rinvsq           = rinv*rinv;
 261
 262                                 qq               = iq*x[js+3];
 263                                 if (!bEwald)
 264                                 {
 265                                     /* Reaction-field */
 266                                     krsq  = iconst->k_rf*rsq;
 267                                     fscal = qq*(int_bit*rinv - 2*krsq)*rinvsq;
 268                                     if (bEner)
 269                                     {
 270                                         vcoul = qq*(int_bit*rinv + krsq - iconst->c_rf);
 271                                     }
 272                                 }
 273                                 else
 274                                 {
 275                                     r     = rsq*rinv;
 276                                     rt    = r*iconst->tabq_scale;
 277                                     n0    = static_cast<int>(rt);
 278                                     eps   = rt - n0;
 279
 280                                     fexcl = (1 - eps)*Ftab[n0] + eps*Ftab[n0+1];
 281
 282                                     fscal = qq*(int_bit*rinvsq - fexcl)*rinv;
 283
 284                                     if (bEner)
 285                                     {
 286                                         vcoul = qq*((int_bit - std::erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
 287                                     }
 288                                 }
 289
 290                                 if (rsq < rvdw2)
 291                                 {
 292                                     tj        = nti + 2*type[ja];
 293
 294                                     /* Vanilla Lennard-Jones cutoff */
 295                                     c6        = vdwparam[tj];
 296                                     c12       = vdwparam[tj+1];
 297
 298                                     rinvsix   = int_bit*rinvsq*rinvsq*rinvsq;
 299                                     Vvdw_disp = c6*rinvsix;
 300                                     Vvdw_rep  = c12*rinvsix*rinvsix;
 301                                     fscal    += (Vvdw_rep - Vvdw_disp)*rinvsq;
 302
 303                                     if (bEner)
 304                                     {
 305                                         vctot   += vcoul;
 306
 307                                         Vvdwtot +=
 308                                             (Vvdw_rep - int_bit*c12*iconst->sh_invrc6*iconst->sh_invrc6)/12 -
 309                                             (Vvdw_disp - int_bit*c6*iconst->sh_invrc6)/6;
 310                                     }
 311                                 }
 312
 313                                 tx        = fscal*dx;
 314                                 ty        = fscal*dy;
 315                                 tz        = fscal*dz;
 316                                 fix       = fix + tx;
 317                                 fiy       = fiy + ty;
 318                                 fiz       = fiz + tz;
 319                                 f[jfs+0] -= tx;
 320                                 f[jfs+1] -= ty;
 321                                 f[jfs+2] -= tz;
 322                             }
 323
 324                             f[ifs+0]        += fix;
 325                             f[ifs+1]        += fiy;
 326                             f[ifs+2]        += fiz;
 327                             fshift[ish3]     = fshift[ish3]   + fix;
 328                             fshift[ish3+1]   = fshift[ish3+1] + fiy;
 329                             fshift[ish3+2]   = fshift[ish3+2] + fiz;
 330
 331                             /* Count in half work-units.
 332                              * In CUDA one work-unit is 2 warps.
 333                              */
 334                             if ((ic+1) % (c_clSize/c_nbnxnGpuClusterpairSplit) == 0)
 335                             {
 336                                 npair_tot += npair;
 337
 338                                 nhwu++;
 339                                 if (within_rlist)
 340                                 {
 341                                     nhwu_pruned++;
 342                                 }
 343
 344                                 within_rlist = FALSE;
 345                                 npair        = 0;
 346                             }
 347                         }
 348                     }
 349                 }
 350             }
 351         }
 352
 353         if (bEner)
 354         {
 355             ggid             = 0;
 356             Vc[ggid]         = Vc[ggid]   + vctot;
 357             Vvdw[ggid]       = Vvdw[ggid] + Vvdwtot;
 358         }
 359     }
 360
 361     if (debug)
 362     {
 363         fprintf(debug, "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
 364                 nbl->na_ci, nbl->na_ci,
 365                 nhwu, nhwu_pruned, nhwu_pruned/static_cast<double>(nhwu));
 366         fprintf(debug, "generic kernel pair interactions:            %d\n",
 367                 nhwu*nbl->na_ci/2*nbl->na_ci);
 368         fprintf(debug, "generic kernel post-prune pair interactions: %d\n",
 369                 nhwu_pruned*nbl->na_ci/2*nbl->na_ci);
 370         fprintf(debug, "generic kernel non-zero pair interactions:   %d\n",
 371                 npair_tot);
 372         fprintf(debug, "ratio non-zero/post-prune pair interactions: %4.2f\n",
 373                 npair_tot/static_cast<double>(nhwu_pruned*gmx::exactDiv(nbl->na_ci, 2)*nbl->na_ci));
 374     }
 375 }