src/gromacs/gmxlib/nonbonded/nb_generic_cg.c

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  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
  47  void
  48  gmx_nb_generic_cg_kernel(t_nblist *           nlist,
  49                           t_forcerec *         fr,
  50                           t_mdatoms *          mdatoms,
  51                           real *               x,
  52                           real *               f,
  53                           real *               fshift,
  54                           real *               Vc,
  55                           real *               Vvdw,
  56                           real                 tabscale,
  57                           real *               VFtab,
  58                           int *                outeriter,
  59                           int *                inneriter)
  60 {
  61      int           nri,ntype,table_nelements,icoul,ivdw;
  62      real          facel,gbtabscale;
  63      int           n,is3,i3,k,nj0,nj1,j3,ggid,nnn,n0;
  64      int           ai0,ai1,ai,aj0,aj1,aj;
  65      real          shX,shY,shZ;
  66      real          fscal,tx,ty,tz;
  67      real          rinvsq;
  68      real          iq;
  69      real          qq,vcoul,krsq,vctot;
  70      int           nti,nvdwparam;
  71      int           tj;
  72      real          rt,r,eps,eps2,Y,F,Geps,Heps2,VV,FF,Fp,fijD,fijR;
  73      real          rinvsix;
  74      real          Vvdwtot;
  75      real          Vvdw_rep,Vvdw_disp;
  76      real          ix,iy,iz,fix,fiy,fiz;
  77      real          jx,jy,jz;
  78      real          dx,dy,dz,rsq,rinv;
  79      real          c6,c12,cexp1,cexp2,br;
  80      real *        charge;
  81      real *        shiftvec;
  82      real *        vdwparam;
  83      int *         shift;
  84      int *         type;
  85      t_excl *      excl;
  86
  87      icoul               = nlist->icoul;
  88      ivdw                = nlist->ivdw;
  89
  90      /* avoid compiler warnings for cases that cannot happen */
  91      nnn                 = 0;
  92      vcoul               = 0.0;
  93      eps                 = 0.0;
  94      eps2                = 0.0;
  95
  96      /* 3 VdW parameters for buckingham, otherwise 2 */
  97      nvdwparam           = (nlist->ivdw==2) ? 3 : 2;
  98      table_nelements     = (icoul==3) ? 4 : 0;
  99      table_nelements    += (ivdw==3) ? 8 : 0;
 100
 101      charge              = mdatoms->chargeA;
 102      type                = mdatoms->typeA;
 103      facel               = fr->epsfac;
 104      shiftvec            = fr->shift_vec[0];
 105      vdwparam            = fr->nbfp;
 106      ntype               = fr->ntype;
 107
 108      for(n=0; (n<nlist->nri); n++)
 109      {
 110          is3              = 3*nlist->shift[n];
 111          shX              = shiftvec[is3];
 112          shY              = shiftvec[is3+1];
 113          shZ              = shiftvec[is3+2];
 114          nj0              = nlist->jindex[n];
 115          nj1              = nlist->jindex[n+1];
 116          ai0              = nlist->iinr[n];
 117          ai1              = nlist->iinr_end[n];
 118          vctot            = 0;
 119          Vvdwtot          = 0;
 120          fix              = 0;
 121          fiy              = 0;
 122          fiz              = 0;
 123
 124          for(k=nj0; (k<nj1); k++)
 125          {
 126              aj0              = nlist->jjnr[k];
 127              aj1              = nlist->jjnr_end[k];
 128              excl             = &nlist->excl[k*MAX_CGCGSIZE];
 129
 130              for(ai=ai0; (ai<ai1); ai++)
 131              {
 132                  i3               = ai*3;
 133                  ix               = shX + x[i3+0];
 134                  iy               = shY + x[i3+1];
 135                  iz               = shZ + x[i3+2];
 136                  iq               = facel*charge[ai];
 137                  nti              = nvdwparam*ntype*type[ai];
 138
 139                  /* Note that this code currently calculates
 140                   * all LJ and Coulomb interactions,
 141                   * even if the LJ parameters or charges are zero.
 142                   * If required, this can be optimized.
 143                   */
 144
 145                  for(aj=aj0; (aj<aj1); aj++)
 146                  {
 147                      /* Check if this interaction is excluded */
 148                      if (excl[aj-aj0] & (1<<(ai-ai0)))
 149                      {
 150                          continue;
 151                      }
 152
 153                      j3               = aj*3;
 154                      jx               = x[j3+0];
 155                      jy               = x[j3+1];
 156                      jz               = x[j3+2];
 157                      dx               = ix - jx;
 158                      dy               = iy - jy;
 159                      dz               = iz - jz;
 160                      rsq              = dx*dx+dy*dy+dz*dz;
 161                      rinv             = gmx_invsqrt(rsq);
 162                      rinvsq           = rinv*rinv;
 163                      fscal            = 0;
 164
 165                      if (icoul==3 || ivdw==3)
 166                      {
 167                          r                = rsq*rinv;
 168                          rt               = r*tabscale;
 169                          n0               = rt;
 170                          eps              = rt-n0;
 171                          eps2             = eps*eps;
 172                          nnn              = table_nelements*n0;
 173                      }
 174
 175                      /* Coulomb interaction. icoul==0 means no interaction */
 176                      if (icoul > 0)
 177                      {
 178                          qq               = iq*charge[aj];
 179
 180                          switch(icoul)
 181                          {
 182                          case 1:
 183                              /* Vanilla cutoff coulomb */
 184                              vcoul            = qq*rinv;
 185                              fscal            = vcoul*rinvsq;
 186                              break;
 187
 188                          case 2:
 189                              /* Reaction-field */
 190                              krsq             = fr->k_rf*rsq;
 191                              vcoul            = qq*(rinv+krsq-fr->c_rf);
 192                              fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 193                              break;
 194
 195                          case 3:
 196                              /* Tabulated coulomb */
 197                              Y                = VFtab[nnn];
 198                              F                = VFtab[nnn+1];
 199                              Geps             = eps*VFtab[nnn+2];
 200                              Heps2            = eps2*VFtab[nnn+3];
 201                              nnn             += 4;
 202                              Fp               = F+Geps+Heps2;
 203                              VV               = Y+eps*Fp;
 204                              FF               = Fp+Geps+2.0*Heps2;
 205                              vcoul            = qq*VV;
 206                              fscal            = -qq*FF*tabscale*rinv;
 207                              break;
 208
 209                          case 4:
 210                              /* GB */
 211                            gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
 212                            break;
 213
 214                          default:
 215                              gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
 216                              break;
 217                          }
 218                          vctot            = vctot+vcoul;
 219                      } /* End of coulomb interactions */
 220
 221
 222                      /* VdW interaction. ivdw==0 means no interaction */
 223                      if (ivdw > 0)
 224                      {
 225                          tj               = nti+nvdwparam*type[aj];
 226
 227                          switch(ivdw)
 228                          {
 229                          case 1:
 230                              /* Vanilla Lennard-Jones cutoff */
 231                              c6               = vdwparam[tj];
 232                              c12              = vdwparam[tj+1];
 233
 234                              rinvsix          = rinvsq*rinvsq*rinvsq;
 235                              Vvdw_disp        = c6*rinvsix;
 236                              Vvdw_rep         = c12*rinvsix*rinvsix;
 237                              fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 238                              Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 239                              break;
 240
 241                          case 2:
 242                              /* Buckingham */
 243                              c6               = vdwparam[tj];
 244                              cexp1            = vdwparam[tj+1];
 245                              cexp2            = vdwparam[tj+2];
 246
 247                              rinvsix          = rinvsq*rinvsq*rinvsq;
 248                              Vvdw_disp        = c6*rinvsix;
 249                              br               = cexp2*rsq*rinv;
 250                              Vvdw_rep         = cexp1*exp(-br);
 251                              fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 252                              Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 253                              break;
 254
 255                          case 3:
 256                              /* Tabulated VdW */
 257                              c6               = vdwparam[tj];
 258                              c12              = vdwparam[tj+1];
 259
 260                              Y                = VFtab[nnn];
 261                              F                = VFtab[nnn+1];
 262                              Geps             = eps*VFtab[nnn+2];
 263                              Heps2            = eps2*VFtab[nnn+3];
 264                              Fp               = F+Geps+Heps2;
 265                              VV               = Y+eps*Fp;
 266                              FF               = Fp+Geps+2.0*Heps2;
 267                              Vvdw_disp        = c6*VV;
 268                              fijD             = c6*FF;
 269                              nnn             += 4;
 270                              Y                = VFtab[nnn];
 271                              F                = VFtab[nnn+1];
 272                              Geps             = eps*VFtab[nnn+2];
 273                              Heps2            = eps2*VFtab[nnn+3];
 274                              Fp               = F+Geps+Heps2;
 275                              VV               = Y+eps*Fp;
 276                              FF               = Fp+Geps+2.0*Heps2;
 277                              Vvdw_rep         = c12*VV;
 278                              fijR             = c12*FF;
 279                              fscal           += -(fijD+fijR)*tabscale*rinv;
 280                              Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 281                              break;
 282
 283                          default:
 284                              gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
 285                              break;
 286                          }
 287                      } /* end VdW interactions */
 288
 289
 290                      tx               = fscal*dx;
 291                      ty               = fscal*dy;
 292                      tz               = fscal*dz;
 293                      f[i3+0]         += tx;
 294                      f[i3+1]         += ty;
 295                      f[i3+2]         += tz;
 296                      f[j3+0]         -= tx;
 297                      f[j3+1]         -= ty;
 298                      f[j3+2]         -= tz;
 299                      fix             += tx;
 300                      fiy             += ty;
 301                      fiz             += tz;
 302                  }
 303              }
 304          }
 305
 306          fshift[is3]     += fix;
 307          fshift[is3+1]   += fiy;
 308          fshift[is3+2]   += fiz;
 309          ggid             = nlist->gid[n];
 310          Vc[ggid]        += vctot;
 311          Vvdw[ggid]      += Vvdwtot;
 312      }
 313
 314      *outeriter       = nlist->nri;
 315      *inneriter       = nlist->jindex[n];
 316 }
 317