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
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   8  *
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  11  * as published by the Free Software Foundation; either version 2.1
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  35 #include "gmxpre.h"
  36
  37 #include "nbnxn_kernel_gpu_ref.h"
  38
  39 #include "config.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/legacyheaders/force.h"
  44 #include "gromacs/legacyheaders/typedefs.h"
  45 #include "gromacs/legacyheaders/types/simple.h"
  46 #include "gromacs/math/utilities.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
  53 #define NCL_PER_SUPERCL         (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
  54 #define CL_SIZE                 (NBNXN_GPU_CLUSTER_SIZE)
  55
  56 void
  57 nbnxn_kernel_gpu_ref(const nbnxn_pairlist_t     *nbl,
  58                      const nbnxn_atomdata_t     *nbat,
  59                      const interaction_const_t  *iconst,
  60                      rvec                       *shift_vec,
  61                      int                         force_flags,
  62                      int                         clearF,
  63                      real  *                     f,
  64                      real  *                     fshift,
  65                      real  *                     Vc,
  66                      real  *                     Vvdw)
  67 {
  68     const nbnxn_sci_t  *nbln;
  69     const real         *x;
  70     gmx_bool            bEner;
  71     gmx_bool            bEwald;
  72     const real         *Ftab = NULL;
  73     real                rcut2, rvdw2, rlist2;
  74     int                 ntype;
  75     real                facel;
  76     int                 n;
  77     int                 ish3;
  78     int                 sci;
  79     int                 cj4_ind0, cj4_ind1, cj4_ind;
  80     int                 ci, cj;
  81     int                 ic, jc, ia, ja, is, ifs, js, jfs, im, jm;
  82     int                 n0;
  83     int                 ggid;
  84     real                shX, shY, shZ;
  85     real                fscal, tx, ty, tz;
  86     real                rinvsq;
  87     real                iq;
  88     real                qq, vcoul = 0, krsq, vctot;
  89     int                 nti;
  90     int                 tj;
  91     real                rt, r, eps;
  92     real                rinvsix;
  93     real                Vvdwtot;
  94     real                Vvdw_rep, Vvdw_disp;
  95     real                ix, iy, iz, fix, fiy, fiz;
  96     real                jx, jy, jz;
  97     real                dx, dy, dz, rsq, rinv;
  98     int                 int_bit;
  99     real                fexcl;
 100     real                c6, c12, cexp1, cexp2, br;
 101     const real       *  shiftvec;
 102     real       *        vdwparam;
 103     int       *         shift;
 104     int       *         type;
 105     const nbnxn_excl_t *excl[2];
 106
 107     int                 npair_tot, npair;
 108     int                 nhwu, nhwu_pruned;
 109
 110     if (nbl->na_ci != CL_SIZE)
 111     {
 112         gmx_fatal(FARGS, "The neighborlist cluster size in the GPU reference kernel is %d, expected it to be %d", nbl->na_ci, CL_SIZE);
 113     }
 114
 115     if (clearF == enbvClearFYes)
 116     {
 117         clear_f(nbat, 0, f);
 118     }
 119
 120     bEner = (force_flags & GMX_FORCE_ENERGY);
 121
 122     bEwald = EEL_FULL(iconst->eeltype);
 123     if (bEwald)
 124     {
 125         Ftab = iconst->tabq_coul_F;
 126     }
 127
 128     rcut2               = iconst->rcoulomb*iconst->rcoulomb;
 129     rvdw2               = iconst->rvdw*iconst->rvdw;
 130
 131     rlist2              = nbl->rlist*nbl->rlist;
 132
 133     type                = nbat->type;
 134     facel               = iconst->epsfac;
 135     shiftvec            = shift_vec[0];
 136     vdwparam            = nbat->nbfp;
 137     ntype               = nbat->ntype;
 138
 139     x = nbat->x;
 140
 141     npair_tot   = 0;
 142     nhwu        = 0;
 143     nhwu_pruned = 0;
 144
 145     for (n = 0; n < nbl->nsci; n++)
 146     {
 147         nbln = &nbl->sci[n];
 148
 149         ish3             = 3*nbln->shift;
 150         shX              = shiftvec[ish3];
 151         shY              = shiftvec[ish3+1];
 152         shZ              = shiftvec[ish3+2];
 153         cj4_ind0         = nbln->cj4_ind_start;
 154         cj4_ind1         = nbln->cj4_ind_end;
 155         sci              = nbln->sci;
 156         vctot            = 0;
 157         Vvdwtot          = 0;
 158
 159         if (nbln->shift == CENTRAL &&
 160             nbl->cj4[cj4_ind0].cj[0] == sci*NCL_PER_SUPERCL)
 161         {
 162             /* we have the diagonal:
 163              * add the charge self interaction energy term
 164              */
 165             for (im = 0; im < NCL_PER_SUPERCL; im++)
 166             {
 167                 ci = sci*NCL_PER_SUPERCL + im;
 168                 for (ic = 0; ic < CL_SIZE; ic++)
 169                 {
 170                     ia     = ci*CL_SIZE + ic;
 171                     iq     = x[ia*nbat->xstride+3];
 172                     vctot += iq*iq;
 173                 }
 174             }
 175             if (!bEwald)
 176             {
 177                 vctot *= -facel*0.5*iconst->c_rf;
 178             }
 179             else
 180             {
 181                 /* last factor 1/sqrt(pi) */
 182                 vctot *= -facel*iconst->ewaldcoeff_q*M_1_SQRTPI;
 183             }
 184         }
 185
 186         for (cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
 187         {
 188             excl[0]           = &nbl->excl[nbl->cj4[cj4_ind].imei[0].excl_ind];
 189             excl[1]           = &nbl->excl[nbl->cj4[cj4_ind].imei[1].excl_ind];
 190
 191             for (jm = 0; jm < NBNXN_GPU_JGROUP_SIZE; jm++)
 192             {
 193                 cj               = nbl->cj4[cj4_ind].cj[jm];
 194
 195                 for (im = 0; im < NCL_PER_SUPERCL; im++)
 196                 {
 197                     /* We're only using the first imask,
 198                      * but here imei[1].imask is identical.
 199                      */
 200                     if ((nbl->cj4[cj4_ind].imei[0].imask >> (jm*NCL_PER_SUPERCL+im)) & 1)
 201                     {
 202                         gmx_bool within_rlist;
 203
 204                         ci               = sci*NCL_PER_SUPERCL + im;
 205
 206                         within_rlist     = FALSE;
 207                         npair            = 0;
 208                         for (ic = 0; ic < CL_SIZE; ic++)
 209                         {
 210                             ia               = ci*CL_SIZE + ic;
 211
 212                             is               = ia*nbat->xstride;
 213                             ifs              = ia*nbat->fstride;
 214                             ix               = shX + x[is+0];
 215                             iy               = shY + x[is+1];
 216                             iz               = shZ + x[is+2];
 217                             iq               = facel*x[is+3];
 218                             nti              = ntype*2*type[ia];
 219
 220                             fix              = 0;
 221                             fiy              = 0;
 222                             fiz              = 0;
 223
 224                             for (jc = 0; jc < CL_SIZE; jc++)
 225                             {
 226                                 ja               = cj*CL_SIZE + jc;
 227
 228                                 if (nbln->shift == CENTRAL &&
 229                                     ci == cj && ja <= ia)
 230                                 {
 231                                     continue;
 232                                 }
 233
 234                                 int_bit = ((excl[jc>>2]->pair[(jc & 3)*CL_SIZE+ic] >> (jm*NCL_PER_SUPERCL+im)) & 1);
 235
 236                                 js               = ja*nbat->xstride;
 237                                 jfs              = ja*nbat->fstride;
 238                                 jx               = x[js+0];
 239                                 jy               = x[js+1];
 240                                 jz               = x[js+2];
 241                                 dx               = ix - jx;
 242                                 dy               = iy - jy;
 243                                 dz               = iz - jz;
 244                                 rsq              = dx*dx + dy*dy + dz*dz;
 245                                 if (rsq < rlist2)
 246                                 {
 247                                     within_rlist = TRUE;
 248                                 }
 249                                 if (rsq >= rcut2)
 250                                 {
 251                                     continue;
 252                                 }
 253
 254                                 if (type[ia] != ntype-1 && type[ja] != ntype-1)
 255                                 {
 256                                     npair++;
 257                                 }
 258
 259                                 /* avoid NaN for excluded pairs at r=0 */
 260                                 rsq             += (1.0 - int_bit)*NBNXN_AVOID_SING_R2_INC;
 261
 262                                 rinv             = gmx_invsqrt(rsq);
 263                                 rinvsq           = rinv*rinv;
 264                                 fscal            = 0;
 265
 266                                 qq               = iq*x[js+3];
 267                                 if (!bEwald)
 268                                 {
 269                                     /* Reaction-field */
 270                                     krsq  = iconst->k_rf*rsq;
 271                                     fscal = qq*(int_bit*rinv - 2*krsq)*rinvsq;
 272                                     if (bEner)
 273                                     {
 274                                         vcoul = qq*(int_bit*rinv + krsq - iconst->c_rf);
 275                                     }
 276                                 }
 277                                 else
 278                                 {
 279                                     r     = rsq*rinv;
 280                                     rt    = r*iconst->tabq_scale;
 281                                     n0    = rt;
 282                                     eps   = rt - n0;
 283
 284                                     fexcl = (1 - eps)*Ftab[n0] + eps*Ftab[n0+1];
 285
 286                                     fscal = qq*(int_bit*rinvsq - fexcl)*rinv;
 287
 288                                     if (bEner)
 289                                     {
 290                                         vcoul = qq*((int_bit - gmx_erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
 291                                     }
 292                                 }
 293
 294                                 if (rsq < rvdw2)
 295                                 {
 296                                     tj        = nti + 2*type[ja];
 297
 298                                     /* Vanilla Lennard-Jones cutoff */
 299                                     c6        = vdwparam[tj];
 300                                     c12       = vdwparam[tj+1];
 301
 302                                     rinvsix   = int_bit*rinvsq*rinvsq*rinvsq;
 303                                     Vvdw_disp = c6*rinvsix;
 304                                     Vvdw_rep  = c12*rinvsix*rinvsix;
 305                                     fscal    += (Vvdw_rep - Vvdw_disp)*rinvsq;
 306
 307                                     if (bEner)
 308                                     {
 309                                         vctot   += vcoul;
 310
 311                                         Vvdwtot +=
 312                                             (Vvdw_rep - int_bit*c12*iconst->sh_invrc6*iconst->sh_invrc6)/12 -
 313                                             (Vvdw_disp - int_bit*c6*iconst->sh_invrc6)/6;
 314                                     }
 315                                 }
 316
 317                                 tx        = fscal*dx;
 318                                 ty        = fscal*dy;
 319                                 tz        = fscal*dz;
 320                                 fix       = fix + tx;
 321                                 fiy       = fiy + ty;
 322                                 fiz       = fiz + tz;
 323                                 f[jfs+0] -= tx;
 324                                 f[jfs+1] -= ty;
 325                                 f[jfs+2] -= tz;
 326                             }
 327
 328                             f[ifs+0]        += fix;
 329                             f[ifs+1]        += fiy;
 330                             f[ifs+2]        += fiz;
 331                             fshift[ish3]     = fshift[ish3]   + fix;
 332                             fshift[ish3+1]   = fshift[ish3+1] + fiy;
 333                             fshift[ish3+2]   = fshift[ish3+2] + fiz;
 334
 335                             /* Count in half work-units.
 336                              * In CUDA one work-unit is 2 warps.
 337                              */
 338                             if ((ic+1) % (CL_SIZE/2) == 0)
 339                             {
 340                                 npair_tot += npair;
 341
 342                                 nhwu++;
 343                                 if (within_rlist)
 344                                 {
 345                                     nhwu_pruned++;
 346                                 }
 347
 348                                 within_rlist = FALSE;
 349                                 npair        = 0;
 350                             }
 351                         }
 352                     }
 353                 }
 354             }
 355         }
 356
 357         if (bEner)
 358         {
 359             ggid             = 0;
 360             Vc[ggid]         = Vc[ggid]   + vctot;
 361             Vvdw[ggid]       = Vvdw[ggid] + Vvdwtot;
 362         }
 363     }
 364
 365     if (debug)
 366     {
 367         fprintf(debug, "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
 368                 nbl->na_ci, nbl->na_ci,
 369                 nhwu, nhwu_pruned, nhwu_pruned/(double)nhwu);
 370         fprintf(debug, "generic kernel pair interactions:            %d\n",
 371                 nhwu*nbl->na_ci/2*nbl->na_ci);
 372         fprintf(debug, "generic kernel post-prune pair interactions: %d\n",
 373                 nhwu_pruned*nbl->na_ci/2*nbl->na_ci);
 374         fprintf(debug, "generic kernel non-zero pair interactions:   %d\n",
 375                 npair_tot);
 376         fprintf(debug, "ratio non-zero/post-prune pair interactions: %4.2f\n",
 377                 npair_tot/(double)(nhwu_pruned*nbl->na_ci/2*nbl->na_ci));
 378     }
 379 }