src/gromacs/gmxlib/nonbonded/nb_generic.c

   1 /*
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   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2012,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  37 #include "gmxpre.h"
  38
  39 #include "nb_generic.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
  44 #include "gromacs/legacyheaders/nonbonded.h"
  45 #include "gromacs/legacyheaders/nrnb.h"
  46 #include "gromacs/legacyheaders/typedefs.h"
  47 #include "gromacs/legacyheaders/types/simple.h"
  48 #include "gromacs/math/vec.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           nri, ntype, table_nelements, ielec, ivdw;
  61     real          facel, gbtabscale;
  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 *         shift;
  82     int *         type;
  83     real *        fshift;
  84     real *        velecgrp;
  85     real *        vvdwgrp;
  86     real          tabscale;
  87     real *        VFtab;
  88     real *        x;
  89     real *        f;
  90     int           ewitab;
  91     real          ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace;
  92     real *        ewtab;
  93     real          rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion;
  94     real          rcutoff, rcutoff2;
  95     real          rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr;
  96     real          elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
  97     real          vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
  98     real          ewclj, ewclj2, ewclj6, ewcljrsq, poly, exponent, sh_lj_ewald;
  99     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
 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     tabscale            = kernel_data->table_elec_vdw->scale;
 110     VFtab               = kernel_data->table_elec_vdw->data;
 111
 112     sh_ewald            = fr->ic->sh_ewald;
 113     ewtab               = fr->ic->tabq_coul_FDV0;
 114     ewtabscale          = fr->ic->tabq_scale;
 115     ewtabhalfspace      = 0.5/ewtabscale;
 116
 117     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 118     rvdw                = fr->rvdw;
 119     rvdw2               = rvdw*rvdw;
 120     sh_dispersion       = fr->ic->dispersion_shift.cpot;
 121     sh_repulsion        = fr->ic->repulsion_shift.cpot;
 122     sh_lj_ewald         = fr->ic->sh_lj_ewald;
 123
 124     ewclj               = fr->ewaldcoeff_lj;
 125     ewclj2              = ewclj*ewclj;
 126     ewclj6              = ewclj2*ewclj2*ewclj2;
 127
 128     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 129     {
 130         d               = fr->rcoulomb-fr->rcoulomb_switch;
 131         elec_swV3       = -10.0/(d*d*d);
 132         elec_swV4       =  15.0/(d*d*d*d);
 133         elec_swV5       =  -6.0/(d*d*d*d*d);
 134         elec_swF2       = -30.0/(d*d*d);
 135         elec_swF3       =  60.0/(d*d*d*d);
 136         elec_swF4       = -30.0/(d*d*d*d*d);
 137     }
 138     else
 139     {
 140         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 141         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 142     }
 143     if (fr->vdw_modifier == eintmodPOTSWITCH)
 144     {
 145         d               = fr->rvdw-fr->rvdw_switch;
 146         vdw_swV3        = -10.0/(d*d*d);
 147         vdw_swV4        =  15.0/(d*d*d*d);
 148         vdw_swV5        =  -6.0/(d*d*d*d*d);
 149         vdw_swF2        = -30.0/(d*d*d);
 150         vdw_swF3        =  60.0/(d*d*d*d);
 151         vdw_swF4        = -30.0/(d*d*d*d*d);
 152     }
 153     else
 154     {
 155         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 156         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 157     }
 158
 159     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 160     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 161     bExactCutoff        = bExactElecCutoff && bExactVdwCutoff;
 162
 163     if (bExactCutoff)
 164     {
 165         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 166         rcutoff2 = rcutoff*rcutoff;
 167     }
 168     else
 169     {
 170         /* Fix warnings for stupid compilers */
 171         rcutoff = rcutoff2 = 1e30;
 172     }
 173
 174     /* avoid compiler warnings for cases that cannot happen */
 175     nnn                 = 0;
 176     eps                 = 0.0;
 177     eps2                = 0.0;
 178
 179     /* 3 VdW parameters for Buckingham, otherwise 2 */
 180     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 181     table_nelements     = 12;
 182
 183     charge              = mdatoms->chargeA;
 184     type                = mdatoms->typeA;
 185     facel               = fr->epsfac;
 186     shiftvec            = fr->shift_vec[0];
 187     vdwparam            = fr->nbfp;
 188     ntype               = fr->ntype;
 189     vdwgridparam        = fr->ljpme_c6grid;
 190
 191     for (n = 0; (n < nlist->nri); n++)
 192     {
 193         is3              = 3*nlist->shift[n];
 194         shX              = shiftvec[is3];
 195         shY              = shiftvec[is3+1];
 196         shZ              = shiftvec[is3+2];
 197         nj0              = nlist->jindex[n];
 198         nj1              = nlist->jindex[n+1];
 199         ii               = nlist->iinr[n];
 200         ii3              = 3*ii;
 201         ix               = shX + x[ii3+0];
 202         iy               = shY + x[ii3+1];
 203         iz               = shZ + x[ii3+2];
 204         iq               = facel*charge[ii];
 205         nti              = nvdwparam*ntype*type[ii];
 206         vctot            = 0;
 207         vvdwtot          = 0;
 208         fix              = 0;
 209         fiy              = 0;
 210         fiz              = 0;
 211
 212         for (k = nj0; (k < nj1); k++)
 213         {
 214             jnr              = nlist->jjnr[k];
 215             j3               = 3*jnr;
 216             jx               = x[j3+0];
 217             jy               = x[j3+1];
 218             jz               = x[j3+2];
 219             dx               = ix - jx;
 220             dy               = iy - jy;
 221             dz               = iz - jz;
 222             rsq              = dx*dx+dy*dy+dz*dz;
 223             rinv             = gmx_invsqrt(rsq);
 224             rinvsq           = rinv*rinv;
 225             felec            = 0;
 226             fvdw             = 0;
 227             velec            = 0;
 228             vvdw             = 0;
 229
 230             if (bExactCutoff && rsq >= rcutoff2)
 231             {
 232                 continue;
 233             }
 234
 235             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 236             {
 237                 r                = rsq*rinv;
 238                 rt               = r*tabscale;
 239                 n0               = rt;
 240                 eps              = rt-n0;
 241                 eps2             = eps*eps;
 242                 nnn              = table_nelements*n0;
 243             }
 244
 245             /* Coulomb interaction. ielec==0 means no interaction */
 246             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 247             {
 248                 qq               = iq*charge[jnr];
 249
 250                 switch (ielec)
 251                 {
 252                     case GMX_NBKERNEL_ELEC_NONE:
 253                         break;
 254
 255                     case GMX_NBKERNEL_ELEC_COULOMB:
 256                         /* Vanilla cutoff coulomb */
 257                         velec            = qq*rinv;
 258                         felec            = velec*rinvsq;
 259                         /* The shift for the Coulomb potential is stored in
 260                          * the RF parameter c_rf, which is 0 without shift
 261                          */
 262                         velec           -= qq*fr->ic->c_rf;
 263                         break;
 264
 265                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 266                         /* Reaction-field */
 267                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 268                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 269                         break;
 270
 271                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 272                         /* Tabulated coulomb */
 273                         Y                = VFtab[nnn];
 274                         F                = VFtab[nnn+1];
 275                         Geps             = eps*VFtab[nnn+2];
 276                         Heps2            = eps2*VFtab[nnn+3];
 277                         Fp               = F+Geps+Heps2;
 278                         VV               = Y+eps*Fp;
 279                         FF               = Fp+Geps+2.0*Heps2;
 280                         velec            = qq*VV;
 281                         felec            = -qq*FF*tabscale*rinv;
 282                         break;
 283
 284                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 285                         /* GB */
 286                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 287                         break;
 288
 289                     case GMX_NBKERNEL_ELEC_EWALD:
 290                         ewrt             = rsq*rinv*ewtabscale;
 291                         ewitab           = ewrt;
 292                         eweps            = ewrt-ewitab;
 293                         ewitab           = 4*ewitab;
 294                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 295                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 296                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 297                         felec            = qq*rinv*(rinvsq-felec);
 298                         break;
 299
 300                     default:
 301                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 302                         break;
 303                 }
 304                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 305                 {
 306                     d                = rsq*rinv-fr->rcoulomb_switch;
 307                     d                = (d > 0.0) ? d : 0.0;
 308                     d2               = d*d;
 309                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 310                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 311                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 312                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 313                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 314                      */
 315                     felec            = felec*sw - rinv*velec*dsw;
 316                     /* Once we have used velec to update felec we can modify velec too */
 317                     velec           *= sw;
 318                 }
 319                 if (bExactElecCutoff)
 320                 {
 321                     felec            = (rsq < rcoulomb2) ? felec : 0.0;
 322                     velec            = (rsq < rcoulomb2) ? velec : 0.0;
 323                 }
 324                 vctot           += velec;
 325             } /* End of coulomb interactions */
 326
 327
 328             /* VdW interaction. ivdw==0 means no interaction */
 329             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 330             {
 331                 tj               = nti+nvdwparam*type[jnr];
 332
 333                 switch (ivdw)
 334                 {
 335                     case GMX_NBKERNEL_VDW_NONE:
 336                         break;
 337
 338                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 339                         /* Vanilla Lennard-Jones cutoff */
 340                         c6               = vdwparam[tj];
 341                         c12              = vdwparam[tj+1];
 342                         rinvsix          = rinvsq*rinvsq*rinvsq;
 343                         vvdw_disp        = c6*rinvsix;
 344                         vvdw_rep         = c12*rinvsix*rinvsix;
 345                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 346                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 347                         {
 348                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
 349                         }
 350                         else
 351                         {
 352                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 353                         }
 354                         break;
 355
 356                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 357                         /* Buckingham */
 358                         c6               = vdwparam[tj];
 359                         cexp1            = vdwparam[tj+1];
 360                         cexp2            = vdwparam[tj+2];
 361
 362                         rinvsix          = rinvsq*rinvsq*rinvsq;
 363                         vvdw_disp        = c6*rinvsix;
 364                         br               = cexp2*rsq*rinv;
 365                         vvdw_rep         = cexp1*exp(-br);
 366                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 367                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 368                         {
 369                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp + c6*sh_dispersion)/6.0;
 370                         }
 371                         else
 372                         {
 373                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 374                         }
 375                         break;
 376
 377                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 378                         /* Tabulated VdW */
 379                         c6               = vdwparam[tj];
 380                         c12              = vdwparam[tj+1];
 381                         Y                = VFtab[nnn+4];
 382                         F                = VFtab[nnn+5];
 383                         Geps             = eps*VFtab[nnn+6];
 384                         Heps2            = eps2*VFtab[nnn+7];
 385                         Fp               = F+Geps+Heps2;
 386                         VV               = Y+eps*Fp;
 387                         FF               = Fp+Geps+2.0*Heps2;
 388                         vvdw_disp        = c6*VV;
 389                         fijD             = c6*FF;
 390                         Y                = VFtab[nnn+8];
 391                         F                = VFtab[nnn+9];
 392                         Geps             = eps*VFtab[nnn+10];
 393                         Heps2            = eps2*VFtab[nnn+11];
 394                         Fp               = F+Geps+Heps2;
 395                         VV               = Y+eps*Fp;
 396                         FF               = Fp+Geps+2.0*Heps2;
 397                         vvdw_rep         = c12*VV;
 398                         fijR             = c12*FF;
 399                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 400                         vvdw             = vvdw_disp + vvdw_rep;
 401                         break;
 402
 403
 404                     case GMX_NBKERNEL_VDW_LJEWALD:
 405                         /* LJ-PME */
 406                         rinvsix          = rinvsq*rinvsq*rinvsq;
 407                         ewcljrsq         = ewclj2*rsq;
 408                         exponent         = exp(-ewcljrsq);
 409                         poly             = exponent*(1.0 + ewcljrsq + ewcljrsq*ewcljrsq*0.5);
 410                         c6               = vdwparam[tj];
 411                         c12              = vdwparam[tj+1];
 412                         c6grid           = vdwgridparam[tj];
 413                         vvdw_disp        = (c6-c6grid*(1.0-poly))*rinvsix;
 414                         vvdw_rep         = c12*rinvsix*rinvsix;
 415                         fvdw             = (vvdw_rep - vvdw_disp - c6grid*(1.0/6.0)*exponent*ewclj6)*rinvsq;
 416                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 417                         {
 418                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion - c6grid*sh_lj_ewald)/6.0;
 419                         }
 420                         else
 421                         {
 422                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 423                         }
 424                         break;
 425
 426                     default:
 427                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 428                         break;
 429                 }
 430                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 431                 {
 432                     d                = rsq*rinv-fr->rvdw_switch;
 433                     d                = (d > 0.0) ? d : 0.0;
 434                     d2               = d*d;
 435                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 436                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 437                     /* See coulomb interaction for the force-switch formula */
 438                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 439                     vvdw            *= sw;
 440                 }
 441                 if (bExactVdwCutoff)
 442                 {
 443                     fvdw             = (rsq < rvdw2) ? fvdw : 0.0;
 444                     vvdw             = (rsq < rvdw2) ? vvdw : 0.0;
 445                 }
 446                 vvdwtot         += vvdw;
 447             } /* end VdW interactions */
 448
 449             fscal            = felec+fvdw;
 450
 451             tx               = fscal*dx;
 452             ty               = fscal*dy;
 453             tz               = fscal*dz;
 454             fix              = fix + tx;
 455             fiy              = fiy + ty;
 456             fiz              = fiz + tz;
 457             f[j3+0]          = f[j3+0] - tx;
 458             f[j3+1]          = f[j3+1] - ty;
 459             f[j3+2]          = f[j3+2] - tz;
 460         }
 461
 462         f[ii3+0]         = f[ii3+0] + fix;
 463         f[ii3+1]         = f[ii3+1] + fiy;
 464         f[ii3+2]         = f[ii3+2] + fiz;
 465         fshift[is3]      = fshift[is3]+fix;
 466         fshift[is3+1]    = fshift[is3+1]+fiy;
 467         fshift[is3+2]    = fshift[is3+2]+fiz;
 468         ggid             = nlist->gid[n];
 469         velecgrp[ggid]  += vctot;
 470         vvdwgrp[ggid]   += vvdwtot;
 471     }
 472     /* Estimate flops, average for generic kernel:
 473      * 12 flops per outer iteration
 474      * 50 flops per inner iteration
 475      */
 476     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50);
 477 }