src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c

   1 /*
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   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
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  11  * as published by the Free Software Foundation; either version 2.1
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40
  41 #include "types/simple.h"
  42 #include "gromacs/math/utilities.h"
  43 #include "vec.h"
  44 #include "typedefs.h"
  45 #include "force.h"
  46 #include "nbnxn_kernel_gpu_ref.h"
  47 #include "../nbnxn_consts.h"
  48 #include "nbnxn_kernel_common.h"
  49
  50 #define NCL_PER_SUPERCL         (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
  51 #define CL_SIZE                 (NBNXN_GPU_CLUSTER_SIZE)
  52
  53 void
  54 nbnxn_kernel_gpu_ref(const nbnxn_pairlist_t     *nbl,
  55                      const nbnxn_atomdata_t     *nbat,
  56                      const interaction_const_t  *iconst,
  57                      rvec                       *shift_vec,
  58                      int                         force_flags,
  59                      int                         clearF,
  60                      real  *                     f,
  61                      real  *                     fshift,
  62                      real  *                     Vc,
  63                      real  *                     Vvdw)
  64 {
  65     const nbnxn_sci_t  *nbln;
  66     const real         *x;
  67     gmx_bool            bEner;
  68     gmx_bool            bEwald;
  69     const real         *Ftab = NULL;
  70     real                rcut2, rvdw2, rlist2;
  71     int                 ntype;
  72     real                facel;
  73     int                 n;
  74     int                 ish3;
  75     int                 sci;
  76     int                 cj4_ind0, cj4_ind1, cj4_ind;
  77     int                 ci, cj;
  78     int                 ic, jc, ia, ja, is, ifs, js, jfs, im, jm;
  79     int                 n0;
  80     int                 ggid;
  81     real                shX, shY, shZ;
  82     real                fscal, tx, ty, tz;
  83     real                rinvsq;
  84     real                iq;
  85     real                qq, vcoul = 0, krsq, vctot;
  86     int                 nti;
  87     int                 tj;
  88     real                rt, r, eps;
  89     real                rinvsix;
  90     real                Vvdwtot;
  91     real                Vvdw_rep, Vvdw_disp;
  92     real                ix, iy, iz, fix, fiy, fiz;
  93     real                jx, jy, jz;
  94     real                dx, dy, dz, rsq, rinv;
  95     int                 int_bit;
  96     real                fexcl;
  97     real                c6, c12, cexp1, cexp2, br;
  98     const real       *  shiftvec;
  99     real       *        vdwparam;
 100     int       *         shift;
 101     int       *         type;
 102     const nbnxn_excl_t *excl[2];
 103
 104     int                 npair_tot, npair;
 105     int                 nhwu, nhwu_pruned;
 106
 107     if (nbl->na_ci != CL_SIZE)
 108     {
 109         gmx_fatal(FARGS, "The neighborlist cluster size in the GPU reference kernel is %d, expected it to be %d", nbl->na_ci, CL_SIZE);
 110     }
 111
 112     if (clearF == enbvClearFYes)
 113     {
 114         clear_f(nbat, 0, f);
 115     }
 116
 117     bEner = (force_flags & GMX_FORCE_ENERGY);
 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     type                = nbat->type;
 131     facel               = iconst->epsfac;
 132     shiftvec            = shift_vec[0];
 133     vdwparam            = nbat->nbfp;
 134     ntype               = nbat->ntype;
 135
 136     x = nbat->x;
 137
 138     npair_tot   = 0;
 139     nhwu        = 0;
 140     nhwu_pruned = 0;
 141
 142     for (n = 0; n < nbl->nsci; n++)
 143     {
 144         nbln = &nbl->sci[n];
 145
 146         ish3             = 3*nbln->shift;
 147         shX              = shiftvec[ish3];
 148         shY              = shiftvec[ish3+1];
 149         shZ              = shiftvec[ish3+2];
 150         cj4_ind0         = nbln->cj4_ind_start;
 151         cj4_ind1         = nbln->cj4_ind_end;
 152         sci              = nbln->sci;
 153         vctot            = 0;
 154         Vvdwtot          = 0;
 155
 156         if (nbln->shift == CENTRAL &&
 157             nbl->cj4[cj4_ind0].cj[0] == sci*NCL_PER_SUPERCL)
 158         {
 159             /* we have the diagonal:
 160              * add the charge self interaction energy term
 161              */
 162             for (im = 0; im < NCL_PER_SUPERCL; im++)
 163             {
 164                 ci = sci*NCL_PER_SUPERCL + im;
 165                 for (ic = 0; ic < CL_SIZE; ic++)
 166                 {
 167                     ia     = ci*CL_SIZE + ic;
 168                     iq     = x[ia*nbat->xstride+3];
 169                     vctot += iq*iq;
 170                 }
 171             }
 172             if (!bEwald)
 173             {
 174                 vctot *= -facel*0.5*iconst->c_rf;
 175             }
 176             else
 177             {
 178                 /* last factor 1/sqrt(pi) */
 179                 vctot *= -facel*iconst->ewaldcoeff_q*M_1_SQRTPI;
 180             }
 181         }
 182
 183         for (cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
 184         {
 185             excl[0]           = &nbl->excl[nbl->cj4[cj4_ind].imei[0].excl_ind];
 186             excl[1]           = &nbl->excl[nbl->cj4[cj4_ind].imei[1].excl_ind];
 187
 188             for (jm = 0; jm < NBNXN_GPU_JGROUP_SIZE; jm++)
 189             {
 190                 cj               = nbl->cj4[cj4_ind].cj[jm];
 191
 192                 for (im = 0; im < NCL_PER_SUPERCL; im++)
 193                 {
 194                     /* We're only using the first imask,
 195                      * but here imei[1].imask is identical.
 196                      */
 197                     if ((nbl->cj4[cj4_ind].imei[0].imask >> (jm*NCL_PER_SUPERCL+im)) & 1)
 198                     {
 199                         gmx_bool within_rlist;
 200
 201                         ci               = sci*NCL_PER_SUPERCL + im;
 202
 203                         within_rlist     = FALSE;
 204                         npair            = 0;
 205                         for (ic = 0; ic < CL_SIZE; ic++)
 206                         {
 207                             ia               = ci*CL_SIZE + ic;
 208
 209                             is               = ia*nbat->xstride;
 210                             ifs              = ia*nbat->fstride;
 211                             ix               = shX + x[is+0];
 212                             iy               = shY + x[is+1];
 213                             iz               = shZ + x[is+2];
 214                             iq               = facel*x[is+3];
 215                             nti              = ntype*2*type[ia];
 216
 217                             fix              = 0;
 218                             fiy              = 0;
 219                             fiz              = 0;
 220
 221                             for (jc = 0; jc < CL_SIZE; jc++)
 222                             {
 223                                 ja               = cj*CL_SIZE + jc;
 224
 225                                 if (nbln->shift == CENTRAL &&
 226                                     ci == cj && ja <= ia)
 227                                 {
 228                                     continue;
 229                                 }
 230
 231                                 int_bit = ((excl[jc>>2]->pair[(jc & 3)*CL_SIZE+ic] >> (jm*NCL_PER_SUPERCL+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                                 /* avoid NaN for excluded pairs at r=0 */
 257                                 rsq             += (1.0 - int_bit)*NBNXN_AVOID_SING_R2_INC;
 258
 259                                 rinv             = gmx_invsqrt(rsq);
 260                                 rinvsq           = rinv*rinv;
 261                                 fscal            = 0;
 262
 263                                 qq               = iq*x[js+3];
 264                                 if (!bEwald)
 265                                 {
 266                                     /* Reaction-field */
 267                                     krsq  = iconst->k_rf*rsq;
 268                                     fscal = qq*(int_bit*rinv - 2*krsq)*rinvsq;
 269                                     if (bEner)
 270                                     {
 271                                         vcoul = qq*(int_bit*rinv + krsq - iconst->c_rf);
 272                                     }
 273                                 }
 274                                 else
 275                                 {
 276                                     r     = rsq*rinv;
 277                                     rt    = r*iconst->tabq_scale;
 278                                     n0    = rt;
 279                                     eps   = rt - n0;
 280
 281                                     fexcl = (1 - eps)*Ftab[n0] + eps*Ftab[n0+1];
 282
 283                                     fscal = qq*(int_bit*rinvsq - fexcl)*rinv;
 284
 285                                     if (bEner)
 286                                     {
 287                                         vcoul = qq*((int_bit - gmx_erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
 288                                     }
 289                                 }
 290
 291                                 if (rsq < rvdw2)
 292                                 {
 293                                     tj        = nti + 2*type[ja];
 294
 295                                     /* Vanilla Lennard-Jones cutoff */
 296                                     c6        = vdwparam[tj];
 297                                     c12       = vdwparam[tj+1];
 298
 299                                     rinvsix   = int_bit*rinvsq*rinvsq*rinvsq;
 300                                     Vvdw_disp = c6*rinvsix;
 301                                     Vvdw_rep  = c12*rinvsix*rinvsix;
 302                                     fscal    += (Vvdw_rep - Vvdw_disp)*rinvsq;
 303
 304                                     if (bEner)
 305                                     {
 306                                         vctot   += vcoul;
 307
 308                                         Vvdwtot +=
 309                                             (Vvdw_rep - int_bit*c12*iconst->sh_invrc6*iconst->sh_invrc6)/12 -
 310                                             (Vvdw_disp - int_bit*c6*iconst->sh_invrc6)/6;
 311                                     }
 312                                 }
 313
 314                                 tx        = fscal*dx;
 315                                 ty        = fscal*dy;
 316                                 tz        = fscal*dz;
 317                                 fix       = fix + tx;
 318                                 fiy       = fiy + ty;
 319                                 fiz       = fiz + tz;
 320                                 f[jfs+0] -= tx;
 321                                 f[jfs+1] -= ty;
 322                                 f[jfs+2] -= tz;
 323                             }
 324
 325                             f[ifs+0]        += fix;
 326                             f[ifs+1]        += fiy;
 327                             f[ifs+2]        += fiz;
 328                             fshift[ish3]     = fshift[ish3]   + fix;
 329                             fshift[ish3+1]   = fshift[ish3+1] + fiy;
 330                             fshift[ish3+2]   = fshift[ish3+2] + fiz;
 331
 332                             /* Count in half work-units.
 333                              * In CUDA one work-unit is 2 warps.
 334                              */
 335                             if ((ic+1) % (CL_SIZE/2) == 0)
 336                             {
 337                                 npair_tot += npair;
 338
 339                                 nhwu++;
 340                                 if (within_rlist)
 341                                 {
 342                                     nhwu_pruned++;
 343                                 }
 344
 345                                 within_rlist = FALSE;
 346                                 npair        = 0;
 347                             }
 348                         }
 349                     }
 350                 }
 351             }
 352         }
 353
 354         if (bEner)
 355         {
 356             ggid             = 0;
 357             Vc[ggid]         = Vc[ggid]   + vctot;
 358             Vvdw[ggid]       = Vvdw[ggid] + Vvdwtot;
 359         }
 360     }
 361
 362     if (debug)
 363     {
 364         fprintf(debug, "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
 365                 nbl->na_ci, nbl->na_ci,
 366                 nhwu, nhwu_pruned, nhwu_pruned/(double)nhwu);
 367         fprintf(debug, "generic kernel pair interactions:            %d\n",
 368                 nhwu*nbl->na_ci/2*nbl->na_ci);
 369         fprintf(debug, "generic kernel post-prune pair interactions: %d\n",
 370                 nhwu_pruned*nbl->na_ci/2*nbl->na_ci);
 371         fprintf(debug, "generic kernel non-zero pair interactions:   %d\n",
 372                 npair_tot);
 373         fprintf(debug, "ratio non-zero/post-prune pair interactions: %4.2f\n",
 374                 npair_tot/(double)(nhwu_pruned*nbl->na_ci/2*nbl->na_ci));
 375     }
 376 }