src/gromacs/gmxlib/nonbonded/nb_generic_cg.c

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   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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_cg.h"
  45 #include "gromacs/legacyheaders/nonbonded.h"
  46 #include "nb_kernel.h"
  47 #include "gromacs/legacyheaders/nrnb.h"
  48
  49 #include "gromacs/utility/fatalerror.h"
  50
  51 void
  52 gmx_nb_generic_cg_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, is3, i3, k, nj0, nj1, j3, ggid, nnn, n0;
  63     int           ai0, ai1, ai, aj0, aj1, aj;
  64     real          shX, shY, shZ;
  65     real          fscal, tx, ty, tz;
  66     real          rinvsq;
  67     real          iq;
  68     real          qq, vcoul, krsq, 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, cexp1, cexp2, br;
  79     real *        charge;
  80     real *        shiftvec;
  81     real *        vdwparam;
  82     int *         shift;
  83     int *         type;
  84     t_excl *      excl;
  85     real *        fshift;
  86     real *        Vc;
  87     real *        Vvdw;
  88     real          tabscale;
  89     real *        VFtab;
  90     real *        x;
  91     real *        f;
  92
  93     x                   = xx[0];
  94     f                   = ff[0];
  95     ielec               = nlist->ielec;
  96     ivdw                = nlist->ivdw;
  97
  98     fshift              = fr->fshift[0];
  99     Vc                  = kernel_data->energygrp_elec;
 100     Vvdw                = kernel_data->energygrp_vdw;
 101     tabscale            = kernel_data->table_elec_vdw->scale;
 102     VFtab               = kernel_data->table_elec_vdw->data;
 103
 104     /* avoid compiler warnings for cases that cannot happen */
 105     nnn                 = 0;
 106     vcoul               = 0.0;
 107     eps                 = 0.0;
 108     eps2                = 0.0;
 109
 110     /* 3 VdW parameters for buckingham, otherwise 2 */
 111     nvdwparam           = (nlist->ivdw == 2) ? 3 : 2;
 112     table_nelements     = (ielec == 3) ? 4 : 0;
 113     table_nelements    += (ivdw == 3) ? 8 : 0;
 114
 115     charge              = mdatoms->chargeA;
 116     type                = mdatoms->typeA;
 117     facel               = fr->epsfac;
 118     shiftvec            = fr->shift_vec[0];
 119     vdwparam            = fr->nbfp;
 120     ntype               = fr->ntype;
 121
 122     for (n = 0; (n < nlist->nri); n++)
 123     {
 124         is3              = 3*nlist->shift[n];
 125         shX              = shiftvec[is3];
 126         shY              = shiftvec[is3+1];
 127         shZ              = shiftvec[is3+2];
 128         nj0              = nlist->jindex[n];
 129         nj1              = nlist->jindex[n+1];
 130         ai0              = nlist->iinr[n];
 131         ai1              = nlist->iinr_end[n];
 132         vctot            = 0;
 133         Vvdwtot          = 0;
 134         fix              = 0;
 135         fiy              = 0;
 136         fiz              = 0;
 137
 138         for (k = nj0; (k < nj1); k++)
 139         {
 140             aj0              = nlist->jjnr[k];
 141             aj1              = nlist->jjnr_end[k];
 142             excl             = &nlist->excl[k*MAX_CGCGSIZE];
 143
 144             for (ai = ai0; (ai < ai1); ai++)
 145             {
 146                 i3               = ai*3;
 147                 ix               = shX + x[i3+0];
 148                 iy               = shY + x[i3+1];
 149                 iz               = shZ + x[i3+2];
 150                 iq               = facel*charge[ai];
 151                 nti              = nvdwparam*ntype*type[ai];
 152
 153                 /* Note that this code currently calculates
 154                  * all LJ and Coulomb interactions,
 155                  * even if the LJ parameters or charges are zero.
 156                  * If required, this can be optimized.
 157                  */
 158
 159                 for (aj = aj0; (aj < aj1); aj++)
 160                 {
 161                     /* Check if this interaction is excluded */
 162                     if (excl[aj-aj0] & (1<<(ai-ai0)))
 163                     {
 164                         continue;
 165                     }
 166
 167                     j3               = aj*3;
 168                     jx               = x[j3+0];
 169                     jy               = x[j3+1];
 170                     jz               = x[j3+2];
 171                     dx               = ix - jx;
 172                     dy               = iy - jy;
 173                     dz               = iz - jz;
 174                     rsq              = dx*dx+dy*dy+dz*dz;
 175                     rinv             = gmx_invsqrt(rsq);
 176                     rinvsq           = rinv*rinv;
 177                     fscal            = 0;
 178
 179                     if (ielec == 3 || ivdw == 3)
 180                     {
 181                         r                = rsq*rinv;
 182                         rt               = r*tabscale;
 183                         n0               = rt;
 184                         eps              = rt-n0;
 185                         eps2             = eps*eps;
 186                         nnn              = table_nelements*n0;
 187                     }
 188
 189                     /* Coulomb interaction. ielec==0 means no interaction */
 190                     if (ielec > 0)
 191                     {
 192                         qq               = iq*charge[aj];
 193
 194                         switch (ielec)
 195                         {
 196                             case 1:
 197                                 /* Vanilla cutoff coulomb */
 198                                 vcoul            = qq*rinv;
 199                                 fscal            = vcoul*rinvsq;
 200                                 break;
 201
 202                             case 2:
 203                                 /* Reaction-field */
 204                                 krsq             = fr->k_rf*rsq;
 205                                 vcoul            = qq*(rinv+krsq-fr->c_rf);
 206                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 207                                 break;
 208
 209                             case 3:
 210                                 /* Tabulated coulomb */
 211                                 Y                = VFtab[nnn];
 212                                 F                = VFtab[nnn+1];
 213                                 Geps             = eps*VFtab[nnn+2];
 214                                 Heps2            = eps2*VFtab[nnn+3];
 215                                 nnn             += 4;
 216                                 Fp               = F+Geps+Heps2;
 217                                 VV               = Y+eps*Fp;
 218                                 FF               = Fp+Geps+2.0*Heps2;
 219                                 vcoul            = qq*VV;
 220                                 fscal            = -qq*FF*tabscale*rinv;
 221                                 break;
 222
 223                             case 4:
 224                                 /* GB */
 225                                 gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 226                                 break;
 227
 228                             default:
 229                                 gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 230                                 break;
 231                         }
 232                         vctot            = vctot+vcoul;
 233                     }  /* End of coulomb interactions */
 234
 235
 236                     /* VdW interaction. ivdw==0 means no interaction */
 237                     if (ivdw > 0)
 238                     {
 239                         tj               = nti+nvdwparam*type[aj];
 240
 241                         switch (ivdw)
 242                         {
 243                             case 1:
 244                                 /* Vanilla Lennard-Jones cutoff */
 245                                 c6               = vdwparam[tj];
 246                                 c12              = vdwparam[tj+1];
 247
 248                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 249                                 Vvdw_disp        = c6*rinvsix;
 250                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 251                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 252                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 253                                 break;
 254
 255                             case 2:
 256                                 /* Buckingham */
 257                                 c6               = vdwparam[tj];
 258                                 cexp1            = vdwparam[tj+1];
 259                                 cexp2            = vdwparam[tj+2];
 260
 261                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 262                                 Vvdw_disp        = c6*rinvsix;
 263                                 br               = cexp2*rsq*rinv;
 264                                 Vvdw_rep         = cexp1*exp(-br);
 265                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 266                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 267                                 break;
 268
 269                             case 3:
 270                                 /* Tabulated VdW */
 271                                 c6               = vdwparam[tj];
 272                                 c12              = vdwparam[tj+1];
 273
 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                                 Vvdw_disp        = c6*VV;
 282                                 fijD             = c6*FF;
 283                                 nnn             += 4;
 284                                 Y                = VFtab[nnn];
 285                                 F                = VFtab[nnn+1];
 286                                 Geps             = eps*VFtab[nnn+2];
 287                                 Heps2            = eps2*VFtab[nnn+3];
 288                                 Fp               = F+Geps+Heps2;
 289                                 VV               = Y+eps*Fp;
 290                                 FF               = Fp+Geps+2.0*Heps2;
 291                                 Vvdw_rep         = c12*VV;
 292                                 fijR             = c12*FF;
 293                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 294                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 295                                 break;
 296
 297                             default:
 298                                 gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 299                                 break;
 300                         }
 301                     }  /* end VdW interactions */
 302
 303
 304                     tx               = fscal*dx;
 305                     ty               = fscal*dy;
 306                     tz               = fscal*dz;
 307                     f[i3+0]         += tx;
 308                     f[i3+1]         += ty;
 309                     f[i3+2]         += tz;
 310                     f[j3+0]         -= tx;
 311                     f[j3+1]         -= ty;
 312                     f[j3+2]         -= tz;
 313                     fix             += tx;
 314                     fiy             += ty;
 315                     fiz             += tz;
 316                 }
 317             }
 318         }
 319
 320         fshift[is3]     += fix;
 321         fshift[is3+1]   += fiy;
 322         fshift[is3+2]   += fiz;
 323         ggid             = nlist->gid[n];
 324         Vc[ggid]        += vctot;
 325         Vvdw[ggid]      += Vvdwtot;
 326     }
 327     /* Estimate flops, average for generic cg kernel:
 328      * 12  flops per outer iteration
 329      * 100 flops per inner iteration
 330      */
 331     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_CG, nlist->nri*12 + nlist->jindex[n]*100);
 332 }