src/gromacs/gmxlib/nonbonded/nb_generic.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40
  41 #include "types/simple.h"
  42 #include "vec.h"
  43 #include "typedefs.h"
  44 #include "nb_generic.h"
  45 #include "nrnb.h"
  46
  47 #include "nonbonded.h"
  48 #include "nb_kernel.h"
  49
  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, cexp1, cexp2, br;
  78     real *        charge;
  79     real *        shiftvec;
  80     real *        vdwparam;
  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_invrc6;
  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     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
  99
 100     x                   = xx[0];
 101     f                   = ff[0];
 102     ielec               = nlist->ielec;
 103     ivdw                = nlist->ivdw;
 104
 105     fshift              = fr->fshift[0];
 106     velecgrp            = kernel_data->energygrp_elec;
 107     vvdwgrp             = kernel_data->energygrp_vdw;
 108     tabscale            = kernel_data->table_elec_vdw->scale;
 109     VFtab               = kernel_data->table_elec_vdw->data;
 110
 111     sh_ewald            = fr->ic->sh_ewald;
 112     ewtab               = fr->ic->tabq_coul_FDV0;
 113     ewtabscale          = fr->ic->tabq_scale;
 114     ewtabhalfspace      = 0.5/ewtabscale;
 115
 116     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 117     rvdw                = fr->rvdw;
 118     rvdw2               = rvdw*rvdw;
 119     sh_invrc6           = fr->ic->sh_invrc6;
 120
 121     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 122     {
 123         d               = fr->rcoulomb-fr->rcoulomb_switch;
 124         elec_swV3       = -10.0/(d*d*d);
 125         elec_swV4       =  15.0/(d*d*d*d);
 126         elec_swV5       =  -6.0/(d*d*d*d*d);
 127         elec_swF2       = -30.0/(d*d*d);
 128         elec_swF3       =  60.0/(d*d*d*d);
 129         elec_swF4       = -30.0/(d*d*d*d*d);
 130     }
 131     else
 132     {
 133         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 134         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 135     }
 136     if (fr->vdw_modifier == eintmodPOTSWITCH)
 137     {
 138         d               = fr->rvdw-fr->rvdw_switch;
 139         vdw_swV3        = -10.0/(d*d*d);
 140         vdw_swV4        =  15.0/(d*d*d*d);
 141         vdw_swV5        =  -6.0/(d*d*d*d*d);
 142         vdw_swF2        = -30.0/(d*d*d);
 143         vdw_swF3        =  60.0/(d*d*d*d);
 144         vdw_swF4        = -30.0/(d*d*d*d*d);
 145     }
 146     else
 147     {
 148         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 149         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 150     }
 151
 152     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 153     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 154     bExactCutoff        = bExactElecCutoff || bExactVdwCutoff;
 155
 156     if (bExactCutoff)
 157     {
 158         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 159         rcutoff2 = rcutoff*rcutoff;
 160     }
 161     else
 162     {
 163         /* Fix warnings for stupid compilers */
 164         rcutoff = rcutoff2 = 1e30;
 165     }
 166
 167     /* avoid compiler warnings for cases that cannot happen */
 168     nnn                 = 0;
 169     eps                 = 0.0;
 170     eps2                = 0.0;
 171
 172     /* 3 VdW parameters for buckingham, otherwise 2 */
 173     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 174     table_nelements     = 12;
 175
 176     charge              = mdatoms->chargeA;
 177     type                = mdatoms->typeA;
 178     facel               = fr->epsfac;
 179     shiftvec            = fr->shift_vec[0];
 180     vdwparam            = fr->nbfp;
 181     ntype               = fr->ntype;
 182
 183     for (n = 0; (n < nlist->nri); n++)
 184     {
 185         is3              = 3*nlist->shift[n];
 186         shX              = shiftvec[is3];
 187         shY              = shiftvec[is3+1];
 188         shZ              = shiftvec[is3+2];
 189         nj0              = nlist->jindex[n];
 190         nj1              = nlist->jindex[n+1];
 191         ii               = nlist->iinr[n];
 192         ii3              = 3*ii;
 193         ix               = shX + x[ii3+0];
 194         iy               = shY + x[ii3+1];
 195         iz               = shZ + x[ii3+2];
 196         iq               = facel*charge[ii];
 197         nti              = nvdwparam*ntype*type[ii];
 198         vctot            = 0;
 199         vvdwtot          = 0;
 200         fix              = 0;
 201         fiy              = 0;
 202         fiz              = 0;
 203
 204         for (k = nj0; (k < nj1); k++)
 205         {
 206             jnr              = nlist->jjnr[k];
 207             j3               = 3*jnr;
 208             jx               = x[j3+0];
 209             jy               = x[j3+1];
 210             jz               = x[j3+2];
 211             dx               = ix - jx;
 212             dy               = iy - jy;
 213             dz               = iz - jz;
 214             rsq              = dx*dx+dy*dy+dz*dz;
 215             rinv             = gmx_invsqrt(rsq);
 216             rinvsq           = rinv*rinv;
 217             felec            = 0;
 218             fvdw             = 0;
 219             velec            = 0;
 220             vvdw             = 0;
 221
 222             if (bExactCutoff && rsq > rcutoff2)
 223             {
 224                 continue;
 225             }
 226
 227             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 228             {
 229                 r                = rsq*rinv;
 230                 rt               = r*tabscale;
 231                 n0               = rt;
 232                 eps              = rt-n0;
 233                 eps2             = eps*eps;
 234                 nnn              = table_nelements*n0;
 235             }
 236
 237             /* Coulomb interaction. ielec==0 means no interaction */
 238             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 239             {
 240                 qq               = iq*charge[jnr];
 241
 242                 switch (ielec)
 243                 {
 244                     case GMX_NBKERNEL_ELEC_NONE:
 245                         break;
 246
 247                     case GMX_NBKERNEL_ELEC_COULOMB:
 248                         /* Vanilla cutoff coulomb */
 249                         velec            = qq*rinv;
 250                         felec            = velec*rinvsq;
 251                         break;
 252
 253                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 254                         /* Reaction-field */
 255                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 256                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 257                         break;
 258
 259                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 260                         /* Tabulated coulomb */
 261                         Y                = VFtab[nnn];
 262                         F                = VFtab[nnn+1];
 263                         Geps             = eps*VFtab[nnn+2];
 264                         Heps2            = eps2*VFtab[nnn+3];
 265                         Fp               = F+Geps+Heps2;
 266                         VV               = Y+eps*Fp;
 267                         FF               = Fp+Geps+2.0*Heps2;
 268                         velec            = qq*VV;
 269                         felec            = -qq*FF*tabscale*rinv;
 270                         break;
 271
 272                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 273                         /* GB */
 274                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 275                         break;
 276
 277                     case GMX_NBKERNEL_ELEC_EWALD:
 278                         ewrt             = rsq*rinv*ewtabscale;
 279                         ewitab           = ewrt;
 280                         eweps            = ewrt-ewitab;
 281                         ewitab           = 4*ewitab;
 282                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 283                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 284                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 285                         felec            = qq*rinv*(rinvsq-felec);
 286                         break;
 287
 288                     default:
 289                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 290                         break;
 291                 }
 292                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 293                 {
 294                     d                = rsq*rinv-fr->rcoulomb_switch;
 295                     d                = (d > 0.0) ? d : 0.0;
 296                     d2               = d*d;
 297                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 298                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 299                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 300                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 301                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 302                      */
 303                     felec            = felec*sw - rinv*velec*dsw;
 304                     /* Once we have used velec to update felec we can modify velec too */
 305                     velec           *= sw;
 306                 }
 307                 if (bExactElecCutoff)
 308                 {
 309                     felec            = (rsq <= rcoulomb2) ? felec : 0.0;
 310                     velec            = (rsq <= rcoulomb2) ? velec : 0.0;
 311                 }
 312                 vctot           += velec;
 313             } /* End of coulomb interactions */
 314
 315
 316             /* VdW interaction. ivdw==0 means no interaction */
 317             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 318             {
 319                 tj               = nti+nvdwparam*type[jnr];
 320
 321                 switch (ivdw)
 322                 {
 323                     case GMX_NBKERNEL_VDW_NONE:
 324                         break;
 325
 326                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 327                         /* Vanilla Lennard-Jones cutoff */
 328                         c6               = vdwparam[tj];
 329                         c12              = vdwparam[tj+1];
 330                         rinvsix          = rinvsq*rinvsq*rinvsq;
 331                         vvdw_disp        = c6*rinvsix;
 332                         vvdw_rep         = c12*rinvsix*rinvsix;
 333                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 334                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 335                         {
 336                             vvdw             = (vvdw_rep-c12*sh_invrc6*sh_invrc6)*(1.0/12.0)-(vvdw_disp-c6*sh_invrc6)*(1.0/6.0);
 337                         }
 338                         else
 339                         {
 340                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 341                         }
 342                         break;
 343
 344                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 345                         /* Buckingham */
 346                         c6               = vdwparam[tj];
 347                         cexp1            = vdwparam[tj+1];
 348                         cexp2            = vdwparam[tj+2];
 349
 350                         rinvsix          = rinvsq*rinvsq*rinvsq;
 351                         vvdw_disp        = c6*rinvsix;
 352                         br               = cexp2*rsq*rinv;
 353                         vvdw_rep         = cexp1*exp(-br);
 354                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 355                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 356                         {
 357                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp-c6*sh_invrc6)/6.0;
 358                         }
 359                         else
 360                         {
 361                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 362                         }
 363                         break;
 364
 365                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 366                         /* Tabulated VdW */
 367                         c6               = vdwparam[tj];
 368                         c12              = vdwparam[tj+1];
 369                         Y                = VFtab[nnn+4];
 370                         F                = VFtab[nnn+5];
 371                         Geps             = eps*VFtab[nnn+6];
 372                         Heps2            = eps2*VFtab[nnn+7];
 373                         Fp               = F+Geps+Heps2;
 374                         VV               = Y+eps*Fp;
 375                         FF               = Fp+Geps+2.0*Heps2;
 376                         vvdw_disp        = c6*VV;
 377                         fijD             = c6*FF;
 378                         Y                = VFtab[nnn+8];
 379                         F                = VFtab[nnn+9];
 380                         Geps             = eps*VFtab[nnn+10];
 381                         Heps2            = eps2*VFtab[nnn+11];
 382                         Fp               = F+Geps+Heps2;
 383                         VV               = Y+eps*Fp;
 384                         FF               = Fp+Geps+2.0*Heps2;
 385                         vvdw_rep         = c12*VV;
 386                         fijR             = c12*FF;
 387                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 388                         vvdw             = vvdw_disp + vvdw_rep;
 389                         break;
 390
 391                     default:
 392                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 393                         break;
 394                 }
 395                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 396                 {
 397                     d                = rsq*rinv-fr->rvdw_switch;
 398                     d                = (d > 0.0) ? d : 0.0;
 399                     d2               = d*d;
 400                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 401                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 402                     /* See coulomb interaction for the force-switch formula */
 403                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 404                     vvdw            *= sw;
 405                 }
 406                 if (bExactVdwCutoff)
 407                 {
 408                     fvdw             = (rsq <= rvdw2) ? fvdw : 0.0;
 409                     vvdw             = (rsq <= rvdw2) ? vvdw : 0.0;
 410                 }
 411                 vvdwtot         += vvdw;
 412             } /* end VdW interactions */
 413
 414             fscal            = felec+fvdw;
 415
 416             tx               = fscal*dx;
 417             ty               = fscal*dy;
 418             tz               = fscal*dz;
 419             fix              = fix + tx;
 420             fiy              = fiy + ty;
 421             fiz              = fiz + tz;
 422             f[j3+0]          = f[j3+0] - tx;
 423             f[j3+1]          = f[j3+1] - ty;
 424             f[j3+2]          = f[j3+2] - tz;
 425         }
 426
 427         f[ii3+0]         = f[ii3+0] + fix;
 428         f[ii3+1]         = f[ii3+1] + fiy;
 429         f[ii3+2]         = f[ii3+2] + fiz;
 430         fshift[is3]      = fshift[is3]+fix;
 431         fshift[is3+1]    = fshift[is3+1]+fiy;
 432         fshift[is3+2]    = fshift[is3+2]+fiz;
 433         ggid             = nlist->gid[n];
 434         velecgrp[ggid]  += vctot;
 435         vvdwgrp[ggid]   += vvdwtot;
 436     }
 437     /* Estimate flops, average for generic kernel:
 438      * 12 flops per outer iteration
 439      * 50 flops per inner iteration
 440      */
 441     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50);
 442 }