src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "nb_generic_cg.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/gmxlib/nrnb.h"
  44 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
  45 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/utility/fatalerror.h"
  49
  50 void
  51 gmx_nb_generic_cg_kernel(t_nblist *                nlist,
  52                          rvec *                    xx,
  53                          rvec *                    ff,
  54                          t_forcerec *              fr,
  55                          t_mdatoms *               mdatoms,
  56                          nb_kernel_data_t *        kernel_data,
  57                          t_nrnb *                  nrnb)
  58 {
  59     int           ntype, table_nelements, ielec, ivdw;
  60     real          facel;
  61     int           n, is3, i3, k, nj0, nj1, j3, ggid, nnn, n0;
  62     int           ai0, ai1, ai, aj0, aj1, aj;
  63     real          shX, shY, shZ;
  64     real          fscal, tx, ty, tz;
  65     real          rinvsq;
  66     real          iq;
  67     real          qq, vcoul, krsq, vctot;
  68     int           nti, nvdwparam;
  69     int           tj;
  70     real          rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
  71     real          rinvsix;
  72     real          Vvdwtot;
  73     real          Vvdw_rep, Vvdw_disp;
  74     real          ix, iy, iz, fix, fiy, fiz;
  75     real          jx, jy, jz;
  76     real          dx, dy, dz, rsq, rinv;
  77     real          c6, c12, cexp1, cexp2, br;
  78     real *        charge;
  79     real *        shiftvec;
  80     real *        vdwparam;
  81     int *         type;
  82     t_excl *      excl;
  83     real *        fshift;
  84     real *        Vc;
  85     real *        Vvdw;
  86     real          tabscale;
  87     real *        VFtab;
  88     real *        x;
  89     real *        f;
  90     gmx_bool      do_tab;
  91
  92     x                   = xx[0];
  93     f                   = ff[0];
  94     ielec               = nlist->ielec;
  95     ivdw                = nlist->ivdw;
  96
  97     fshift              = fr->fshift[0];
  98     Vc                  = kernel_data->energygrp_elec;
  99     Vvdw                = kernel_data->energygrp_vdw;
 100
 101     do_tab = (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE ||
 102               ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE);
 103     if (do_tab)
 104     {
 105         tabscale         = kernel_data->table_elec_vdw->scale;
 106         VFtab            = kernel_data->table_elec_vdw->data;
 107     }
 108     else
 109     {
 110         tabscale        = 0;
 111         VFtab           = nullptr;
 112     }
 113
 114     /* avoid compiler warnings for cases that cannot happen */
 115     nnn                 = 0;
 116     eps                 = 0.0;
 117     eps2                = 0.0;
 118
 119     /* 3 VdW parameters for buckingham, otherwise 2 */
 120     nvdwparam           = (nlist->ivdw == 2) ? 3 : 2;
 121     table_nelements     = (ielec == 3) ? 4 : 0;
 122     table_nelements    += (ivdw == 3) ? 8 : 0;
 123
 124     charge              = mdatoms->chargeA;
 125     type                = mdatoms->typeA;
 126     facel               = fr->ic->epsfac;
 127     shiftvec            = fr->shift_vec[0];
 128     vdwparam            = fr->nbfp;
 129     ntype               = fr->ntype;
 130
 131     for (n = 0; (n < nlist->nri); n++)
 132     {
 133         is3              = 3*nlist->shift[n];
 134         shX              = shiftvec[is3];
 135         shY              = shiftvec[is3+1];
 136         shZ              = shiftvec[is3+2];
 137         nj0              = nlist->jindex[n];
 138         nj1              = nlist->jindex[n+1];
 139         ai0              = nlist->iinr[n];
 140         ai1              = nlist->iinr_end[n];
 141         vctot            = 0;
 142         Vvdwtot          = 0;
 143         fix              = 0;
 144         fiy              = 0;
 145         fiz              = 0;
 146
 147         for (k = nj0; (k < nj1); k++)
 148         {
 149             aj0              = nlist->jjnr[k];
 150             aj1              = nlist->jjnr_end[k];
 151             excl             = &nlist->excl[k*MAX_CGCGSIZE];
 152
 153             for (ai = ai0; (ai < ai1); ai++)
 154             {
 155                 i3               = ai*3;
 156                 ix               = shX + x[i3+0];
 157                 iy               = shY + x[i3+1];
 158                 iz               = shZ + x[i3+2];
 159                 iq               = facel*charge[ai];
 160                 nti              = nvdwparam*ntype*type[ai];
 161
 162                 /* Note that this code currently calculates
 163                  * all LJ and Coulomb interactions,
 164                  * even if the LJ parameters or charges are zero.
 165                  * If required, this can be optimized.
 166                  */
 167
 168                 for (aj = aj0; (aj < aj1); aj++)
 169                 {
 170                     /* Check if this interaction is excluded */
 171                     if (excl[aj-aj0] & (1<<(ai-ai0)))
 172                     {
 173                         continue;
 174                     }
 175
 176                     j3               = aj*3;
 177                     jx               = x[j3+0];
 178                     jy               = x[j3+1];
 179                     jz               = x[j3+2];
 180                     dx               = ix - jx;
 181                     dy               = iy - jy;
 182                     dz               = iz - jz;
 183                     rsq              = dx*dx+dy*dy+dz*dz;
 184                     rinv             = gmx::invsqrt(rsq);
 185                     rinvsq           = rinv*rinv;
 186                     fscal            = 0;
 187
 188                     if (ielec == 3 || ivdw == 3)
 189                     {
 190                         r                = rsq*rinv;
 191                         rt               = r*tabscale;
 192                         n0               = rt;
 193                         eps              = rt-n0;
 194                         eps2             = eps*eps;
 195                         nnn              = table_nelements*n0;
 196                     }
 197
 198                     /* Coulomb interaction. ielec==0 means no interaction */
 199                     if (ielec > 0)
 200                     {
 201                         qq               = iq*charge[aj];
 202
 203                         switch (ielec)
 204                         {
 205                             case 1:
 206                                 /* Vanilla cutoff coulomb */
 207                                 vcoul            = qq*rinv;
 208                                 fscal            = vcoul*rinvsq;
 209                                 break;
 210
 211                             case 2:
 212                                 /* Reaction-field */
 213                                 krsq             = fr->ic->k_rf*rsq;
 214                                 vcoul            = qq*(rinv + krsq - fr->ic->c_rf);
 215                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 216                                 break;
 217
 218                             case 3:
 219                                 /* Tabulated coulomb */
 220                                 Y                = VFtab[nnn];
 221                                 F                = VFtab[nnn+1];
 222                                 Geps             = eps*VFtab[nnn+2];
 223                                 Heps2            = eps2*VFtab[nnn+3];
 224                                 nnn             += 4;
 225                                 Fp               = F+Geps+Heps2;
 226                                 VV               = Y+eps*Fp;
 227                                 FF               = Fp+Geps+2.0*Heps2;
 228                                 vcoul            = qq*VV;
 229                                 fscal            = -qq*FF*tabscale*rinv;
 230                                 break;
 231
 232                             case 4:
 233                                 /* GB */
 234                                 gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 235                             default:
 236                                 gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 237                         }
 238                         vctot            = vctot+vcoul;
 239                     }  /* End of coulomb interactions */
 240
 241
 242                     /* VdW interaction. ivdw==0 means no interaction */
 243                     if (ivdw > 0)
 244                     {
 245                         tj               = nti+nvdwparam*type[aj];
 246
 247                         switch (ivdw)
 248                         {
 249                             case 1:
 250                                 /* Vanilla Lennard-Jones cutoff */
 251                                 c6               = vdwparam[tj];
 252                                 c12              = vdwparam[tj+1];
 253
 254                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 255                                 Vvdw_disp        = c6*rinvsix;
 256                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 257                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 258                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 259                                 break;
 260
 261                             case 2:
 262                                 /* Buckingham */
 263                                 c6               = vdwparam[tj];
 264                                 cexp1            = vdwparam[tj+1];
 265                                 cexp2            = vdwparam[tj+2];
 266
 267                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 268                                 Vvdw_disp        = c6*rinvsix;
 269                                 br               = cexp2*rsq*rinv;
 270                                 Vvdw_rep         = cexp1*std::exp(-br);
 271                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 272                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 273                                 break;
 274
 275                             case 3:
 276                                 /* Tabulated VdW */
 277                                 c6               = vdwparam[tj];
 278                                 c12              = vdwparam[tj+1];
 279
 280                                 Y                = VFtab[nnn];
 281                                 F                = VFtab[nnn+1];
 282                                 Geps             = eps*VFtab[nnn+2];
 283                                 Heps2            = eps2*VFtab[nnn+3];
 284                                 Fp               = F+Geps+Heps2;
 285                                 VV               = Y+eps*Fp;
 286                                 FF               = Fp+Geps+2.0*Heps2;
 287                                 Vvdw_disp        = c6*VV;
 288                                 fijD             = c6*FF;
 289                                 nnn             += 4;
 290                                 Y                = VFtab[nnn];
 291                                 F                = VFtab[nnn+1];
 292                                 Geps             = eps*VFtab[nnn+2];
 293                                 Heps2            = eps2*VFtab[nnn+3];
 294                                 Fp               = F+Geps+Heps2;
 295                                 VV               = Y+eps*Fp;
 296                                 FF               = Fp+Geps+2.0*Heps2;
 297                                 Vvdw_rep         = c12*VV;
 298                                 fijR             = c12*FF;
 299                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 300                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 301                                 break;
 302
 303                             default:
 304                                 gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 305                         }
 306                     }  /* end VdW interactions */
 307
 308
 309                     tx               = fscal*dx;
 310                     ty               = fscal*dy;
 311                     tz               = fscal*dz;
 312                     f[i3+0]         += tx;
 313                     f[i3+1]         += ty;
 314                     f[i3+2]         += tz;
 315                     f[j3+0]         -= tx;
 316                     f[j3+1]         -= ty;
 317                     f[j3+2]         -= tz;
 318                     fix             += tx;
 319                     fiy             += ty;
 320                     fiz             += tz;
 321                 }
 322             }
 323         }
 324
 325         fshift[is3]     += fix;
 326         fshift[is3+1]   += fiy;
 327         fshift[is3+2]   += fiz;
 328         ggid             = nlist->gid[n];
 329         Vc[ggid]        += vctot;
 330         Vvdw[ggid]      += Vvdwtot;
 331     }
 332     /* Estimate flops, average for generic cg kernel:
 333      * 12  flops per outer iteration
 334      * 100 flops per inner iteration
 335      */
 336     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_CG, nlist->nri*12 + nlist->jindex[n]*100);
 337 }