src/gromacs/gmxlib/nonbonded/nb_generic.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   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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  13  * as published by the Free Software Foundation; either version 2.1
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  37 #include "gmxpre.h"
  38
  39 #include <math.h>
  40
  41 #include "gromacs/legacyheaders/types/simple.h"
  42 #include "gromacs/math/vec.h"
  43 #include "gromacs/legacyheaders/typedefs.h"
  44 #include "nb_generic.h"
  45 #include "gromacs/legacyheaders/nrnb.h"
  46
  47 #include "gromacs/utility/fatalerror.h"
  48
  49 #include "gromacs/legacyheaders/nonbonded.h"
  50 #include "nb_kernel.h"
  51
  52 void
  53 gmx_nb_generic_kernel(t_nblist *                nlist,
  54                       rvec *                    xx,
  55                       rvec *                    ff,
  56                       t_forcerec *              fr,
  57                       t_mdatoms *               mdatoms,
  58                       nb_kernel_data_t *        kernel_data,
  59                       t_nrnb *                  nrnb)
  60 {
  61     int           nri, ntype, table_nelements, ielec, ivdw;
  62     real          facel, gbtabscale;
  63     int           n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0;
  64     real          shX, shY, shZ;
  65     real          fscal, felec, fvdw, velec, vvdw, tx, ty, tz;
  66     real          rinvsq;
  67     real          iq;
  68     real          qq, vctot;
  69     int           nti, nvdwparam;
  70     int           tj;
  71     real          rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
  72     real          rinvsix;
  73     real          vvdwtot;
  74     real          vvdw_rep, vvdw_disp;
  75     real          ix, iy, iz, fix, fiy, fiz;
  76     real          jx, jy, jz;
  77     real          dx, dy, dz, rsq, rinv;
  78     real          c6, c12, c6grid, cexp1, cexp2, br;
  79     real *        charge;
  80     real *        shiftvec;
  81     real *        vdwparam, *vdwgridparam;
  82     int *         shift;
  83     int *         type;
  84     real *        fshift;
  85     real *        velecgrp;
  86     real *        vvdwgrp;
  87     real          tabscale;
  88     real *        VFtab;
  89     real *        x;
  90     real *        f;
  91     int           ewitab;
  92     real          ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace;
  93     real *        ewtab;
  94     real          rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion;
  95     real          rcutoff, rcutoff2;
  96     real          rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr;
  97     real          elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
  98     real          vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
  99     real          ewclj, ewclj2, ewclj6, ewcljrsq, poly, exponent, sh_lj_ewald;
 100     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
 101
 102     x                   = xx[0];
 103     f                   = ff[0];
 104     ielec               = nlist->ielec;
 105     ivdw                = nlist->ivdw;
 106
 107     fshift              = fr->fshift[0];
 108     velecgrp            = kernel_data->energygrp_elec;
 109     vvdwgrp             = kernel_data->energygrp_vdw;
 110     tabscale            = kernel_data->table_elec_vdw->scale;
 111     VFtab               = kernel_data->table_elec_vdw->data;
 112
 113     sh_ewald            = fr->ic->sh_ewald;
 114     ewtab               = fr->ic->tabq_coul_FDV0;
 115     ewtabscale          = fr->ic->tabq_scale;
 116     ewtabhalfspace      = 0.5/ewtabscale;
 117
 118     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 119     rvdw                = fr->rvdw;
 120     rvdw2               = rvdw*rvdw;
 121     sh_dispersion       = fr->ic->dispersion_shift.cpot;
 122     sh_repulsion        = fr->ic->repulsion_shift.cpot;
 123     sh_lj_ewald         = fr->ic->sh_lj_ewald;
 124
 125     ewclj               = fr->ewaldcoeff_lj;
 126     ewclj2              = ewclj*ewclj;
 127     ewclj6              = ewclj2*ewclj2*ewclj2;
 128
 129     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 130     {
 131         d               = fr->rcoulomb-fr->rcoulomb_switch;
 132         elec_swV3       = -10.0/(d*d*d);
 133         elec_swV4       =  15.0/(d*d*d*d);
 134         elec_swV5       =  -6.0/(d*d*d*d*d);
 135         elec_swF2       = -30.0/(d*d*d);
 136         elec_swF3       =  60.0/(d*d*d*d);
 137         elec_swF4       = -30.0/(d*d*d*d*d);
 138     }
 139     else
 140     {
 141         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 142         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 143     }
 144     if (fr->vdw_modifier == eintmodPOTSWITCH)
 145     {
 146         d               = fr->rvdw-fr->rvdw_switch;
 147         vdw_swV3        = -10.0/(d*d*d);
 148         vdw_swV4        =  15.0/(d*d*d*d);
 149         vdw_swV5        =  -6.0/(d*d*d*d*d);
 150         vdw_swF2        = -30.0/(d*d*d);
 151         vdw_swF3        =  60.0/(d*d*d*d);
 152         vdw_swF4        = -30.0/(d*d*d*d*d);
 153     }
 154     else
 155     {
 156         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 157         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 158     }
 159
 160     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 161     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 162     bExactCutoff        = bExactElecCutoff && bExactVdwCutoff;
 163
 164     if (bExactCutoff)
 165     {
 166         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 167         rcutoff2 = rcutoff*rcutoff;
 168     }
 169     else
 170     {
 171         /* Fix warnings for stupid compilers */
 172         rcutoff = rcutoff2 = 1e30;
 173     }
 174
 175     /* avoid compiler warnings for cases that cannot happen */
 176     nnn                 = 0;
 177     eps                 = 0.0;
 178     eps2                = 0.0;
 179
 180     /* 3 VdW parameters for Buckingham, otherwise 2 */
 181     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 182     table_nelements     = 12;
 183
 184     charge              = mdatoms->chargeA;
 185     type                = mdatoms->typeA;
 186     facel               = fr->epsfac;
 187     shiftvec            = fr->shift_vec[0];
 188     vdwparam            = fr->nbfp;
 189     ntype               = fr->ntype;
 190     vdwgridparam        = fr->ljpme_c6grid;
 191
 192     for (n = 0; (n < nlist->nri); n++)
 193     {
 194         is3              = 3*nlist->shift[n];
 195         shX              = shiftvec[is3];
 196         shY              = shiftvec[is3+1];
 197         shZ              = shiftvec[is3+2];
 198         nj0              = nlist->jindex[n];
 199         nj1              = nlist->jindex[n+1];
 200         ii               = nlist->iinr[n];
 201         ii3              = 3*ii;
 202         ix               = shX + x[ii3+0];
 203         iy               = shY + x[ii3+1];
 204         iz               = shZ + x[ii3+2];
 205         iq               = facel*charge[ii];
 206         nti              = nvdwparam*ntype*type[ii];
 207         vctot            = 0;
 208         vvdwtot          = 0;
 209         fix              = 0;
 210         fiy              = 0;
 211         fiz              = 0;
 212
 213         for (k = nj0; (k < nj1); k++)
 214         {
 215             jnr              = nlist->jjnr[k];
 216             j3               = 3*jnr;
 217             jx               = x[j3+0];
 218             jy               = x[j3+1];
 219             jz               = x[j3+2];
 220             dx               = ix - jx;
 221             dy               = iy - jy;
 222             dz               = iz - jz;
 223             rsq              = dx*dx+dy*dy+dz*dz;
 224             rinv             = gmx_invsqrt(rsq);
 225             rinvsq           = rinv*rinv;
 226             felec            = 0;
 227             fvdw             = 0;
 228             velec            = 0;
 229             vvdw             = 0;
 230
 231             if (bExactCutoff && rsq >= rcutoff2)
 232             {
 233                 continue;
 234             }
 235
 236             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 237             {
 238                 r                = rsq*rinv;
 239                 rt               = r*tabscale;
 240                 n0               = rt;
 241                 eps              = rt-n0;
 242                 eps2             = eps*eps;
 243                 nnn              = table_nelements*n0;
 244             }
 245
 246             /* Coulomb interaction. ielec==0 means no interaction */
 247             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 248             {
 249                 qq               = iq*charge[jnr];
 250
 251                 switch (ielec)
 252                 {
 253                     case GMX_NBKERNEL_ELEC_NONE:
 254                         break;
 255
 256                     case GMX_NBKERNEL_ELEC_COULOMB:
 257                         /* Vanilla cutoff coulomb */
 258                         velec            = qq*rinv;
 259                         felec            = velec*rinvsq;
 260                         /* The shift for the Coulomb potential is stored in
 261                          * the RF parameter c_rf, which is 0 without shift
 262                          */
 263                         velec           -= qq*fr->ic->c_rf;
 264                         break;
 265
 266                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 267                         /* Reaction-field */
 268                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 269                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 270                         break;
 271
 272                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 273                         /* Tabulated coulomb */
 274                         Y                = VFtab[nnn];
 275                         F                = VFtab[nnn+1];
 276                         Geps             = eps*VFtab[nnn+2];
 277                         Heps2            = eps2*VFtab[nnn+3];
 278                         Fp               = F+Geps+Heps2;
 279                         VV               = Y+eps*Fp;
 280                         FF               = Fp+Geps+2.0*Heps2;
 281                         velec            = qq*VV;
 282                         felec            = -qq*FF*tabscale*rinv;
 283                         break;
 284
 285                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 286                         /* GB */
 287                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 288                         break;
 289
 290                     case GMX_NBKERNEL_ELEC_EWALD:
 291                         ewrt             = rsq*rinv*ewtabscale;
 292                         ewitab           = ewrt;
 293                         eweps            = ewrt-ewitab;
 294                         ewitab           = 4*ewitab;
 295                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 296                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 297                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 298                         felec            = qq*rinv*(rinvsq-felec);
 299                         break;
 300
 301                     default:
 302                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 303                         break;
 304                 }
 305                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 306                 {
 307                     d                = rsq*rinv-fr->rcoulomb_switch;
 308                     d                = (d > 0.0) ? d : 0.0;
 309                     d2               = d*d;
 310                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 311                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 312                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 313                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 314                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 315                      */
 316                     felec            = felec*sw - rinv*velec*dsw;
 317                     /* Once we have used velec to update felec we can modify velec too */
 318                     velec           *= sw;
 319                 }
 320                 if (bExactElecCutoff)
 321                 {
 322                     felec            = (rsq < rcoulomb2) ? felec : 0.0;
 323                     velec            = (rsq < rcoulomb2) ? velec : 0.0;
 324                 }
 325                 vctot           += velec;
 326             } /* End of coulomb interactions */
 327
 328
 329             /* VdW interaction. ivdw==0 means no interaction */
 330             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 331             {
 332                 tj               = nti+nvdwparam*type[jnr];
 333
 334                 switch (ivdw)
 335                 {
 336                     case GMX_NBKERNEL_VDW_NONE:
 337                         break;
 338
 339                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 340                         /* Vanilla Lennard-Jones cutoff */
 341                         c6               = vdwparam[tj];
 342                         c12              = vdwparam[tj+1];
 343                         rinvsix          = rinvsq*rinvsq*rinvsq;
 344                         vvdw_disp        = c6*rinvsix;
 345                         vvdw_rep         = c12*rinvsix*rinvsix;
 346                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 347                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 348                         {
 349                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
 350                         }
 351                         else
 352                         {
 353                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 354                         }
 355                         break;
 356
 357                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 358                         /* Buckingham */
 359                         c6               = vdwparam[tj];
 360                         cexp1            = vdwparam[tj+1];
 361                         cexp2            = vdwparam[tj+2];
 362
 363                         rinvsix          = rinvsq*rinvsq*rinvsq;
 364                         vvdw_disp        = c6*rinvsix;
 365                         br               = cexp2*rsq*rinv;
 366                         vvdw_rep         = cexp1*exp(-br);
 367                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 368                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 369                         {
 370                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp + c6*sh_dispersion)/6.0;
 371                         }
 372                         else
 373                         {
 374                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 375                         }
 376                         break;
 377
 378                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 379                         /* Tabulated VdW */
 380                         c6               = vdwparam[tj];
 381                         c12              = vdwparam[tj+1];
 382                         Y                = VFtab[nnn+4];
 383                         F                = VFtab[nnn+5];
 384                         Geps             = eps*VFtab[nnn+6];
 385                         Heps2            = eps2*VFtab[nnn+7];
 386                         Fp               = F+Geps+Heps2;
 387                         VV               = Y+eps*Fp;
 388                         FF               = Fp+Geps+2.0*Heps2;
 389                         vvdw_disp        = c6*VV;
 390                         fijD             = c6*FF;
 391                         Y                = VFtab[nnn+8];
 392                         F                = VFtab[nnn+9];
 393                         Geps             = eps*VFtab[nnn+10];
 394                         Heps2            = eps2*VFtab[nnn+11];
 395                         Fp               = F+Geps+Heps2;
 396                         VV               = Y+eps*Fp;
 397                         FF               = Fp+Geps+2.0*Heps2;
 398                         vvdw_rep         = c12*VV;
 399                         fijR             = c12*FF;
 400                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 401                         vvdw             = vvdw_disp + vvdw_rep;
 402                         break;
 403
 404
 405                     case GMX_NBKERNEL_VDW_LJEWALD:
 406                         /* LJ-PME */
 407                         rinvsix          = rinvsq*rinvsq*rinvsq;
 408                         ewcljrsq         = ewclj2*rsq;
 409                         exponent         = exp(-ewcljrsq);
 410                         poly             = exponent*(1.0 + ewcljrsq + ewcljrsq*ewcljrsq*0.5);
 411                         c6               = vdwparam[tj];
 412                         c12              = vdwparam[tj+1];
 413                         c6grid           = vdwgridparam[tj];
 414                         vvdw_disp        = (c6-c6grid*(1.0-poly))*rinvsix;
 415                         vvdw_rep         = c12*rinvsix*rinvsix;
 416                         fvdw             = (vvdw_rep - vvdw_disp - c6grid*(1.0/6.0)*exponent*ewclj6)*rinvsq;
 417                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 418                         {
 419                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion - c6grid*sh_lj_ewald)/6.0;
 420                         }
 421                         else
 422                         {
 423                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 424                         }
 425                         break;
 426
 427                     default:
 428                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 429                         break;
 430                 }
 431                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 432                 {
 433                     d                = rsq*rinv-fr->rvdw_switch;
 434                     d                = (d > 0.0) ? d : 0.0;
 435                     d2               = d*d;
 436                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 437                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 438                     /* See coulomb interaction for the force-switch formula */
 439                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 440                     vvdw            *= sw;
 441                 }
 442                 if (bExactVdwCutoff)
 443                 {
 444                     fvdw             = (rsq < rvdw2) ? fvdw : 0.0;
 445                     vvdw             = (rsq < rvdw2) ? vvdw : 0.0;
 446                 }
 447                 vvdwtot         += vvdw;
 448             } /* end VdW interactions */
 449
 450             fscal            = felec+fvdw;
 451
 452             tx               = fscal*dx;
 453             ty               = fscal*dy;
 454             tz               = fscal*dz;
 455             fix              = fix + tx;
 456             fiy              = fiy + ty;
 457             fiz              = fiz + tz;
 458             f[j3+0]          = f[j3+0] - tx;
 459             f[j3+1]          = f[j3+1] - ty;
 460             f[j3+2]          = f[j3+2] - tz;
 461         }
 462
 463         f[ii3+0]         = f[ii3+0] + fix;
 464         f[ii3+1]         = f[ii3+1] + fiy;
 465         f[ii3+2]         = f[ii3+2] + fiz;
 466         fshift[is3]      = fshift[is3]+fix;
 467         fshift[is3+1]    = fshift[is3+1]+fiy;
 468         fshift[is3+2]    = fshift[is3+2]+fiz;
 469         ggid             = nlist->gid[n];
 470         velecgrp[ggid]  += vctot;
 471         vvdwgrp[ggid]   += vvdwtot;
 472     }
 473     /* Estimate flops, average for generic kernel:
 474      * 12 flops per outer iteration
 475      * 50 flops per inner iteration
 476      */
 477     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50);
 478 }