src/gromacs/gmxlib/nonbonded/nb_generic.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include "nb_generic.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/mdtypes/md_enums.h"
  49 #include "gromacs/utility/fatalerror.h"
  50
  51 void
  52 gmx_nb_generic_kernel(t_nblist *                nlist,
  53                       rvec *                    xx,
  54                       rvec *                    ff,
  55                       t_forcerec *              fr,
  56                       t_mdatoms *               mdatoms,
  57                       nb_kernel_data_t *        kernel_data,
  58                       t_nrnb *                  nrnb)
  59 {
  60     int           ntype, table_nelements, ielec, ivdw;
  61     real          facel;
  62     int           n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0;
  63     real          shX, shY, shZ;
  64     real          fscal, felec, fvdw, velec, vvdw, tx, ty, tz;
  65     real          rinvsq;
  66     real          iq;
  67     real          qq, 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, c6grid, cexp1, cexp2, br;
  78     real *        charge;
  79     real *        shiftvec;
  80     real *        vdwparam, *vdwgridparam;
  81     int *         type;
  82     real *        fshift;
  83     real *        velecgrp;
  84     real *        vvdwgrp;
  85     real          tabscale;
  86     real *        VFtab;
  87     real *        x;
  88     real *        f;
  89     int           ewitab;
  90     real          ewtabscale, eweps, ewrt, ewtabhalfspace;
  91     real *        ewtab;
  92     real          rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion;
  93     real          rcutoff, rcutoff2;
  94     real          d, d2, sw, dsw, rinvcorr;
  95     real          elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
  96     real          vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
  97     real          ewclj, ewclj2, ewclj6, ewcljrsq, poly, exponent, sh_lj_ewald;
  98     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
  99     gmx_bool      do_tab;
 100
 101     x                   = xx[0];
 102     f                   = ff[0];
 103     ielec               = nlist->ielec;
 104     ivdw                = nlist->ivdw;
 105
 106     fshift              = fr->fshift[0];
 107     velecgrp            = kernel_data->energygrp_elec;
 108     vvdwgrp             = kernel_data->energygrp_vdw;
 109
 110     do_tab = (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE ||
 111               ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE);
 112     if (do_tab)
 113     {
 114         tabscale         = kernel_data->table_elec_vdw->scale;
 115         VFtab            = kernel_data->table_elec_vdw->data;
 116     }
 117     else
 118     {
 119         tabscale        = 0;
 120         VFtab           = nullptr;
 121     }
 122     ewtab               = fr->ic->tabq_coul_FDV0;
 123     ewtabscale          = fr->ic->tabq_scale;
 124     ewtabhalfspace      = 0.5/ewtabscale;
 125
 126     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 127     rvdw                = fr->rvdw;
 128     rvdw2               = rvdw*rvdw;
 129     sh_dispersion       = fr->ic->dispersion_shift.cpot;
 130     sh_repulsion        = fr->ic->repulsion_shift.cpot;
 131     sh_lj_ewald         = fr->ic->sh_lj_ewald;
 132
 133     ewclj               = fr->ewaldcoeff_lj;
 134     ewclj2              = ewclj*ewclj;
 135     ewclj6              = ewclj2*ewclj2*ewclj2;
 136
 137     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 138     {
 139         d               = fr->rcoulomb-fr->rcoulomb_switch;
 140         elec_swV3       = -10.0/(d*d*d);
 141         elec_swV4       =  15.0/(d*d*d*d);
 142         elec_swV5       =  -6.0/(d*d*d*d*d);
 143         elec_swF2       = -30.0/(d*d*d);
 144         elec_swF3       =  60.0/(d*d*d*d);
 145         elec_swF4       = -30.0/(d*d*d*d*d);
 146     }
 147     else
 148     {
 149         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 150         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 151     }
 152     if (fr->vdw_modifier == eintmodPOTSWITCH)
 153     {
 154         d               = fr->rvdw-fr->rvdw_switch;
 155         vdw_swV3        = -10.0/(d*d*d);
 156         vdw_swV4        =  15.0/(d*d*d*d);
 157         vdw_swV5        =  -6.0/(d*d*d*d*d);
 158         vdw_swF2        = -30.0/(d*d*d);
 159         vdw_swF3        =  60.0/(d*d*d*d);
 160         vdw_swF4        = -30.0/(d*d*d*d*d);
 161     }
 162     else
 163     {
 164         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 165         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 166     }
 167
 168     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 169     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 170     bExactCutoff        = bExactElecCutoff && bExactVdwCutoff;
 171
 172     if (bExactCutoff)
 173     {
 174         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 175         rcutoff2 = rcutoff*rcutoff;
 176     }
 177     else
 178     {
 179         /* Fix warnings for stupid compilers */
 180         rcutoff2 = 1e30;
 181     }
 182
 183     /* avoid compiler warnings for cases that cannot happen */
 184     nnn                 = 0;
 185     eps                 = 0.0;
 186     eps2                = 0.0;
 187
 188     /* 3 VdW parameters for Buckingham, otherwise 2 */
 189     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 190     table_nelements     = 12;
 191
 192     charge              = mdatoms->chargeA;
 193     type                = mdatoms->typeA;
 194     facel               = fr->epsfac;
 195     shiftvec            = fr->shift_vec[0];
 196     vdwparam            = fr->nbfp;
 197     ntype               = fr->ntype;
 198     vdwgridparam        = fr->ljpme_c6grid;
 199
 200     for (n = 0; (n < nlist->nri); n++)
 201     {
 202         is3              = 3*nlist->shift[n];
 203         shX              = shiftvec[is3];
 204         shY              = shiftvec[is3+1];
 205         shZ              = shiftvec[is3+2];
 206         nj0              = nlist->jindex[n];
 207         nj1              = nlist->jindex[n+1];
 208         ii               = nlist->iinr[n];
 209         ii3              = 3*ii;
 210         ix               = shX + x[ii3+0];
 211         iy               = shY + x[ii3+1];
 212         iz               = shZ + x[ii3+2];
 213         iq               = facel*charge[ii];
 214         nti              = nvdwparam*ntype*type[ii];
 215         vctot            = 0;
 216         vvdwtot          = 0;
 217         fix              = 0;
 218         fiy              = 0;
 219         fiz              = 0;
 220
 221         for (k = nj0; (k < nj1); k++)
 222         {
 223             jnr              = nlist->jjnr[k];
 224             j3               = 3*jnr;
 225             jx               = x[j3+0];
 226             jy               = x[j3+1];
 227             jz               = x[j3+2];
 228             dx               = ix - jx;
 229             dy               = iy - jy;
 230             dz               = iz - jz;
 231             rsq              = dx*dx+dy*dy+dz*dz;
 232             rinv             = gmx::invsqrt(rsq);
 233             rinvsq           = rinv*rinv;
 234             felec            = 0;
 235             fvdw             = 0;
 236             velec            = 0;
 237             vvdw             = 0;
 238
 239             if (bExactCutoff && rsq >= rcutoff2)
 240             {
 241                 continue;
 242             }
 243
 244             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 245             {
 246                 r                = rsq*rinv;
 247                 rt               = r*tabscale;
 248                 n0               = rt;
 249                 eps              = rt-n0;
 250                 eps2             = eps*eps;
 251                 nnn              = table_nelements*n0;
 252             }
 253
 254             /* Coulomb interaction. ielec==0 means no interaction */
 255             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 256             {
 257                 qq               = iq*charge[jnr];
 258
 259                 switch (ielec)
 260                 {
 261                     case GMX_NBKERNEL_ELEC_NONE:
 262                         break;
 263
 264                     case GMX_NBKERNEL_ELEC_COULOMB:
 265                         /* Vanilla cutoff coulomb */
 266                         velec            = qq*rinv;
 267                         felec            = velec*rinvsq;
 268                         /* The shift for the Coulomb potential is stored in
 269                          * the RF parameter c_rf, which is 0 without shift
 270                          */
 271                         velec           -= qq*fr->ic->c_rf;
 272                         break;
 273
 274                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 275                         /* Reaction-field */
 276                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 277                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 278                         break;
 279
 280                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 281                         /* Tabulated coulomb */
 282                         Y                = VFtab[nnn];
 283                         F                = VFtab[nnn+1];
 284                         Geps             = eps*VFtab[nnn+2];
 285                         Heps2            = eps2*VFtab[nnn+3];
 286                         Fp               = F+Geps+Heps2;
 287                         VV               = Y+eps*Fp;
 288                         FF               = Fp+Geps+2.0*Heps2;
 289                         velec            = qq*VV;
 290                         felec            = -qq*FF*tabscale*rinv;
 291                         break;
 292
 293                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 294                         /* GB */
 295                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 296                         break;
 297
 298                     case GMX_NBKERNEL_ELEC_EWALD:
 299                         ewrt             = rsq*rinv*ewtabscale;
 300                         ewitab           = ewrt;
 301                         eweps            = ewrt-ewitab;
 302                         ewitab           = 4*ewitab;
 303                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 304                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 305                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 306                         felec            = qq*rinv*(rinvsq-felec);
 307                         break;
 308
 309                     default:
 310                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 311                         break;
 312                 }
 313                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 314                 {
 315                     d                = rsq*rinv-fr->rcoulomb_switch;
 316                     d                = (d > 0.0) ? d : 0.0;
 317                     d2               = d*d;
 318                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 319                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 320                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 321                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 322                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 323                      */
 324                     felec            = felec*sw - rinv*velec*dsw;
 325                     /* Once we have used velec to update felec we can modify velec too */
 326                     velec           *= sw;
 327                 }
 328                 if (bExactElecCutoff)
 329                 {
 330                     felec            = (rsq < rcoulomb2) ? felec : 0.0;
 331                     velec            = (rsq < rcoulomb2) ? velec : 0.0;
 332                 }
 333                 vctot           += velec;
 334             } /* End of coulomb interactions */
 335
 336
 337             /* VdW interaction. ivdw==0 means no interaction */
 338             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 339             {
 340                 tj               = nti+nvdwparam*type[jnr];
 341
 342                 switch (ivdw)
 343                 {
 344                     case GMX_NBKERNEL_VDW_NONE:
 345                         break;
 346
 347                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 348                         /* Vanilla Lennard-Jones cutoff */
 349                         c6               = vdwparam[tj];
 350                         c12              = vdwparam[tj+1];
 351                         rinvsix          = rinvsq*rinvsq*rinvsq;
 352                         vvdw_disp        = c6*rinvsix;
 353                         vvdw_rep         = c12*rinvsix*rinvsix;
 354                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 355                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 356                         {
 357                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
 358                         }
 359                         else
 360                         {
 361                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 362                         }
 363                         break;
 364
 365                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 366                         /* Buckingham */
 367                         c6               = vdwparam[tj];
 368                         cexp1            = vdwparam[tj+1];
 369                         cexp2            = vdwparam[tj+2];
 370
 371                         rinvsix          = rinvsq*rinvsq*rinvsq;
 372                         vvdw_disp        = c6*rinvsix;
 373                         br               = cexp2*rsq*rinv;
 374                         vvdw_rep         = cexp1*std::exp(-br);
 375                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 376                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 377                         {
 378                             vvdw             = (vvdw_rep-cexp1*std::exp(-cexp2*rvdw))-(vvdw_disp + c6*sh_dispersion)/6.0;
 379                         }
 380                         else
 381                         {
 382                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 383                         }
 384                         break;
 385
 386                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 387                         /* Tabulated VdW */
 388                         c6               = vdwparam[tj];
 389                         c12              = vdwparam[tj+1];
 390                         Y                = VFtab[nnn+4];
 391                         F                = VFtab[nnn+5];
 392                         Geps             = eps*VFtab[nnn+6];
 393                         Heps2            = eps2*VFtab[nnn+7];
 394                         Fp               = F+Geps+Heps2;
 395                         VV               = Y+eps*Fp;
 396                         FF               = Fp+Geps+2.0*Heps2;
 397                         vvdw_disp        = c6*VV;
 398                         fijD             = c6*FF;
 399                         Y                = VFtab[nnn+8];
 400                         F                = VFtab[nnn+9];
 401                         Geps             = eps*VFtab[nnn+10];
 402                         Heps2            = eps2*VFtab[nnn+11];
 403                         Fp               = F+Geps+Heps2;
 404                         VV               = Y+eps*Fp;
 405                         FF               = Fp+Geps+2.0*Heps2;
 406                         vvdw_rep         = c12*VV;
 407                         fijR             = c12*FF;
 408                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 409                         vvdw             = vvdw_disp + vvdw_rep;
 410                         break;
 411
 412
 413                     case GMX_NBKERNEL_VDW_LJEWALD:
 414                         /* LJ-PME */
 415                         rinvsix          = rinvsq*rinvsq*rinvsq;
 416                         ewcljrsq         = ewclj2*rsq;
 417                         exponent         = std::exp(-ewcljrsq);
 418                         poly             = exponent*(1.0 + ewcljrsq + ewcljrsq*ewcljrsq*0.5);
 419                         c6               = vdwparam[tj];
 420                         c12              = vdwparam[tj+1];
 421                         c6grid           = vdwgridparam[tj];
 422                         vvdw_disp        = (c6-c6grid*(1.0-poly))*rinvsix;
 423                         vvdw_rep         = c12*rinvsix*rinvsix;
 424                         fvdw             = (vvdw_rep - vvdw_disp - c6grid*(1.0/6.0)*exponent*ewclj6)*rinvsq;
 425                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 426                         {
 427                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion - c6grid*sh_lj_ewald)/6.0;
 428                         }
 429                         else
 430                         {
 431                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 432                         }
 433                         break;
 434
 435                     default:
 436                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 437                         break;
 438                 }
 439                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 440                 {
 441                     d                = rsq*rinv-fr->rvdw_switch;
 442                     d                = (d > 0.0) ? d : 0.0;
 443                     d2               = d*d;
 444                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 445                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 446                     /* See coulomb interaction for the force-switch formula */
 447                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 448                     vvdw            *= sw;
 449                 }
 450                 if (bExactVdwCutoff)
 451                 {
 452                     fvdw             = (rsq < rvdw2) ? fvdw : 0.0;
 453                     vvdw             = (rsq < rvdw2) ? vvdw : 0.0;
 454                 }
 455                 vvdwtot         += vvdw;
 456             } /* end VdW interactions */
 457
 458             fscal            = felec+fvdw;
 459
 460             tx               = fscal*dx;
 461             ty               = fscal*dy;
 462             tz               = fscal*dz;
 463             fix              = fix + tx;
 464             fiy              = fiy + ty;
 465             fiz              = fiz + tz;
 466             f[j3+0]          = f[j3+0] - tx;
 467             f[j3+1]          = f[j3+1] - ty;
 468             f[j3+2]          = f[j3+2] - tz;
 469         }
 470
 471         f[ii3+0]         = f[ii3+0] + fix;
 472         f[ii3+1]         = f[ii3+1] + fiy;
 473         f[ii3+2]         = f[ii3+2] + fiz;
 474         fshift[is3]      = fshift[is3]+fix;
 475         fshift[is3+1]    = fshift[is3+1]+fiy;
 476         fshift[is3+2]    = fshift[is3+2]+fiz;
 477         ggid             = nlist->gid[n];
 478         velecgrp[ggid]  += vctot;
 479         vvdwgrp[ggid]   += vvdwtot;
 480     }
 481     /* Estimate flops, average for generic kernel:
 482      * 12 flops per outer iteration
 483      * 50 flops per inner iteration
 484      */
 485     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50);
 486 }