src/gromacs/gmxlib/nonbonded/nb_generic_cg.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41
  42 #include "types/simple.h"
  43 #include "vec.h"
  44 #include "typedefs.h"
  45 #include "nb_generic_cg.h"
  46 #include "nonbonded.h"
  47 #include "nb_kernel.h"
  48 #include "nrnb.h"
  49
  50 void
  51 gmx_nb_generic_cg_kernel(t_nblist *                nlist,
  52                          rvec *                    xx,
  53                          rvec *                    ff,
  54                          t_forcerec *              fr,
  55                          t_mdatoms *               mdatoms,
  56                          nb_kernel_data_t *        kernel_data,
  57                          t_nrnb *                  nrnb)
  58 {
  59     int           nri, ntype, table_nelements, ielec, ivdw;
  60     real          facel, gbtabscale;
  61     int           n, is3, i3, k, nj0, nj1, j3, ggid, nnn, n0;
  62     int           ai0, ai1, ai, aj0, aj1, aj;
  63     real          shX, shY, shZ;
  64     real          fscal, tx, ty, tz;
  65     real          rinvsq;
  66     real          iq;
  67     real          qq, vcoul, krsq, 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     t_excl *      excl;
  84     real *        fshift;
  85     real *        Vc;
  86     real *        Vvdw;
  87     real          tabscale;
  88     real *        VFtab;
  89     real *        x;
  90     real *        f;
  91
  92     x                   = xx[0];
  93     f                   = ff[0];
  94     ielec               = nlist->ielec;
  95     ivdw                = nlist->ivdw;
  96
  97     fshift              = fr->fshift[0];
  98     Vc                  = kernel_data->energygrp_elec;
  99     Vvdw                = kernel_data->energygrp_vdw;
 100     tabscale            = kernel_data->table_elec_vdw->scale;
 101     VFtab               = kernel_data->table_elec_vdw->data;
 102
 103     /* avoid compiler warnings for cases that cannot happen */
 104     nnn                 = 0;
 105     vcoul               = 0.0;
 106     eps                 = 0.0;
 107     eps2                = 0.0;
 108
 109     /* 3 VdW parameters for buckingham, otherwise 2 */
 110     nvdwparam           = (nlist->ivdw == 2) ? 3 : 2;
 111     table_nelements     = (ielec == 3) ? 4 : 0;
 112     table_nelements    += (ivdw == 3) ? 8 : 0;
 113
 114     charge              = mdatoms->chargeA;
 115     type                = mdatoms->typeA;
 116     facel               = fr->epsfac;
 117     shiftvec            = fr->shift_vec[0];
 118     vdwparam            = fr->nbfp;
 119     ntype               = fr->ntype;
 120
 121     for (n = 0; (n < nlist->nri); n++)
 122     {
 123         is3              = 3*nlist->shift[n];
 124         shX              = shiftvec[is3];
 125         shY              = shiftvec[is3+1];
 126         shZ              = shiftvec[is3+2];
 127         nj0              = nlist->jindex[n];
 128         nj1              = nlist->jindex[n+1];
 129         ai0              = nlist->iinr[n];
 130         ai1              = nlist->iinr_end[n];
 131         vctot            = 0;
 132         Vvdwtot          = 0;
 133         fix              = 0;
 134         fiy              = 0;
 135         fiz              = 0;
 136
 137         for (k = nj0; (k < nj1); k++)
 138         {
 139             aj0              = nlist->jjnr[k];
 140             aj1              = nlist->jjnr_end[k];
 141             excl             = &nlist->excl[k*MAX_CGCGSIZE];
 142
 143             for (ai = ai0; (ai < ai1); ai++)
 144             {
 145                 i3               = ai*3;
 146                 ix               = shX + x[i3+0];
 147                 iy               = shY + x[i3+1];
 148                 iz               = shZ + x[i3+2];
 149                 iq               = facel*charge[ai];
 150                 nti              = nvdwparam*ntype*type[ai];
 151
 152                 /* Note that this code currently calculates
 153                  * all LJ and Coulomb interactions,
 154                  * even if the LJ parameters or charges are zero.
 155                  * If required, this can be optimized.
 156                  */
 157
 158                 for (aj = aj0; (aj < aj1); aj++)
 159                 {
 160                     /* Check if this interaction is excluded */
 161                     if (excl[aj-aj0] & (1<<(ai-ai0)))
 162                     {
 163                         continue;
 164                     }
 165
 166                     j3               = aj*3;
 167                     jx               = x[j3+0];
 168                     jy               = x[j3+1];
 169                     jz               = x[j3+2];
 170                     dx               = ix - jx;
 171                     dy               = iy - jy;
 172                     dz               = iz - jz;
 173                     rsq              = dx*dx+dy*dy+dz*dz;
 174                     rinv             = gmx_invsqrt(rsq);
 175                     rinvsq           = rinv*rinv;
 176                     fscal            = 0;
 177
 178                     if (ielec == 3 || ivdw == 3)
 179                     {
 180                         r                = rsq*rinv;
 181                         rt               = r*tabscale;
 182                         n0               = rt;
 183                         eps              = rt-n0;
 184                         eps2             = eps*eps;
 185                         nnn              = table_nelements*n0;
 186                     }
 187
 188                     /* Coulomb interaction. ielec==0 means no interaction */
 189                     if (ielec > 0)
 190                     {
 191                         qq               = iq*charge[aj];
 192
 193                         switch (ielec)
 194                         {
 195                             case 1:
 196                                 /* Vanilla cutoff coulomb */
 197                                 vcoul            = qq*rinv;
 198                                 fscal            = vcoul*rinvsq;
 199                                 break;
 200
 201                             case 2:
 202                                 /* Reaction-field */
 203                                 krsq             = fr->k_rf*rsq;
 204                                 vcoul            = qq*(rinv+krsq-fr->c_rf);
 205                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 206                                 break;
 207
 208                             case 3:
 209                                 /* Tabulated coulomb */
 210                                 Y                = VFtab[nnn];
 211                                 F                = VFtab[nnn+1];
 212                                 Geps             = eps*VFtab[nnn+2];
 213                                 Heps2            = eps2*VFtab[nnn+3];
 214                                 nnn             += 4;
 215                                 Fp               = F+Geps+Heps2;
 216                                 VV               = Y+eps*Fp;
 217                                 FF               = Fp+Geps+2.0*Heps2;
 218                                 vcoul            = qq*VV;
 219                                 fscal            = -qq*FF*tabscale*rinv;
 220                                 break;
 221
 222                             case 4:
 223                                 /* GB */
 224                                 gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 225                                 break;
 226
 227                             default:
 228                                 gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 229                                 break;
 230                         }
 231                         vctot            = vctot+vcoul;
 232                     }  /* End of coulomb interactions */
 233
 234
 235                     /* VdW interaction. ivdw==0 means no interaction */
 236                     if (ivdw > 0)
 237                     {
 238                         tj               = nti+nvdwparam*type[aj];
 239
 240                         switch (ivdw)
 241                         {
 242                             case 1:
 243                                 /* Vanilla Lennard-Jones cutoff */
 244                                 c6               = vdwparam[tj];
 245                                 c12              = vdwparam[tj+1];
 246
 247                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 248                                 Vvdw_disp        = c6*rinvsix;
 249                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 250                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 251                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 252                                 break;
 253
 254                             case 2:
 255                                 /* Buckingham */
 256                                 c6               = vdwparam[tj];
 257                                 cexp1            = vdwparam[tj+1];
 258                                 cexp2            = vdwparam[tj+2];
 259
 260                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 261                                 Vvdw_disp        = c6*rinvsix;
 262                                 br               = cexp2*rsq*rinv;
 263                                 Vvdw_rep         = cexp1*exp(-br);
 264                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 265                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 266                                 break;
 267
 268                             case 3:
 269                                 /* Tabulated VdW */
 270                                 c6               = vdwparam[tj];
 271                                 c12              = vdwparam[tj+1];
 272
 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                                 Vvdw_disp        = c6*VV;
 281                                 fijD             = c6*FF;
 282                                 nnn             += 4;
 283                                 Y                = VFtab[nnn];
 284                                 F                = VFtab[nnn+1];
 285                                 Geps             = eps*VFtab[nnn+2];
 286                                 Heps2            = eps2*VFtab[nnn+3];
 287                                 Fp               = F+Geps+Heps2;
 288                                 VV               = Y+eps*Fp;
 289                                 FF               = Fp+Geps+2.0*Heps2;
 290                                 Vvdw_rep         = c12*VV;
 291                                 fijR             = c12*FF;
 292                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 293                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 294                                 break;
 295
 296                             default:
 297                                 gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 298                                 break;
 299                         }
 300                     }  /* end VdW interactions */
 301
 302
 303                     tx               = fscal*dx;
 304                     ty               = fscal*dy;
 305                     tz               = fscal*dz;
 306                     f[i3+0]         += tx;
 307                     f[i3+1]         += ty;
 308                     f[i3+2]         += tz;
 309                     f[j3+0]         -= tx;
 310                     f[j3+1]         -= ty;
 311                     f[j3+2]         -= tz;
 312                     fix             += tx;
 313                     fiy             += ty;
 314                     fiz             += tz;
 315                 }
 316             }
 317         }
 318
 319         fshift[is3]     += fix;
 320         fshift[is3+1]   += fiy;
 321         fshift[is3+2]   += fiz;
 322         ggid             = nlist->gid[n];
 323         Vc[ggid]        += vctot;
 324         Vvdw[ggid]      += Vvdwtot;
 325     }
 326     /* Estimate flops, average for generic cg kernel:
 327      * 12  flops per outer iteration
 328      * 100 flops per inner iteration
 329      */
 330     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_CG, nlist->nri*12 + nlist->jindex[n]*100);
 331 }