src/gmxlib/nonbonded/nb_generic_cg.c

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   7  * Copyright (c) 2012,2013, by the GROMACS development team, led by
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  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43
  44 #include "types/simple.h"
  45 #include "vec.h"
  46 #include "typedefs.h"
  47 #include "nb_generic_cg.h"
  48 #include "nonbonded.h"
  49 #include "nb_kernel.h"
  50 #include "nrnb.h"
  51
  52  void
  53 gmx_nb_generic_cg_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,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      real *        fshift;
  87      real *        Vc;
  88      real *        Vvdw;
  89      real          tabscale;
  90      real *        VFtab;
  91      real *        x;
  92      real *        f;
  93
  94      x                   = xx[0];
  95      f                   = ff[0];
  96      ielec               = nlist->ielec;
  97      ivdw                = nlist->ivdw;
  98
  99      fshift              = fr->fshift[0];
 100      Vc                  = kernel_data->energygrp_elec;
 101      Vvdw                = kernel_data->energygrp_vdw;
 102      tabscale            = kernel_data->table_elec_vdw->scale;
 103      VFtab               = kernel_data->table_elec_vdw->data;
 104
 105      /* avoid compiler warnings for cases that cannot happen */
 106      nnn                 = 0;
 107      vcoul               = 0.0;
 108      eps                 = 0.0;
 109      eps2                = 0.0;
 110
 111      /* 3 VdW parameters for buckingham, otherwise 2 */
 112      nvdwparam           = (nlist->ivdw==2) ? 3 : 2;
 113      table_nelements     = (ielec==3) ? 4 : 0;
 114      table_nelements    += (ivdw==3) ? 8 : 0;
 115
 116      charge              = mdatoms->chargeA;
 117      type                = mdatoms->typeA;
 118      facel               = fr->epsfac;
 119      shiftvec            = fr->shift_vec[0];
 120      vdwparam            = fr->nbfp;
 121      ntype               = fr->ntype;
 122
 123      for(n=0; (n<nlist->nri); n++)
 124      {
 125          is3              = 3*nlist->shift[n];
 126          shX              = shiftvec[is3];
 127          shY              = shiftvec[is3+1];
 128          shZ              = shiftvec[is3+2];
 129          nj0              = nlist->jindex[n];
 130          nj1              = nlist->jindex[n+1];
 131          ai0              = nlist->iinr[n];
 132          ai1              = nlist->iinr_end[n];
 133          vctot            = 0;
 134          Vvdwtot          = 0;
 135          fix              = 0;
 136          fiy              = 0;
 137          fiz              = 0;
 138
 139          for(k=nj0; (k<nj1); k++)
 140          {
 141              aj0              = nlist->jjnr[k];
 142              aj1              = nlist->jjnr_end[k];
 143              excl             = &nlist->excl[k*MAX_CGCGSIZE];
 144
 145              for(ai=ai0; (ai<ai1); ai++)
 146              {
 147                  i3               = ai*3;
 148                  ix               = shX + x[i3+0];
 149                  iy               = shY + x[i3+1];
 150                  iz               = shZ + x[i3+2];
 151                  iq               = facel*charge[ai];
 152                  nti              = nvdwparam*ntype*type[ai];
 153
 154                  /* Note that this code currently calculates
 155                   * all LJ and Coulomb interactions,
 156                   * even if the LJ parameters or charges are zero.
 157                   * If required, this can be optimized.
 158                   */
 159
 160                  for(aj=aj0; (aj<aj1); aj++)
 161                  {
 162                      /* Check if this interaction is excluded */
 163                      if (excl[aj-aj0] & (1<<(ai-ai0)))
 164                      {
 165                          continue;
 166                      }
 167
 168                      j3               = aj*3;
 169                      jx               = x[j3+0];
 170                      jy               = x[j3+1];
 171                      jz               = x[j3+2];
 172                      dx               = ix - jx;
 173                      dy               = iy - jy;
 174                      dz               = iz - jz;
 175                      rsq              = dx*dx+dy*dy+dz*dz;
 176                      rinv             = gmx_invsqrt(rsq);
 177                      rinvsq           = rinv*rinv;
 178                      fscal            = 0;
 179
 180                      if (ielec==3 || ivdw==3)
 181                      {
 182                          r                = rsq*rinv;
 183                          rt               = r*tabscale;
 184                          n0               = rt;
 185                          eps              = rt-n0;
 186                          eps2             = eps*eps;
 187                          nnn              = table_nelements*n0;
 188                      }
 189
 190                      /* Coulomb interaction. ielec==0 means no interaction */
 191                      if (ielec > 0)
 192                      {
 193                          qq               = iq*charge[aj];
 194
 195                          switch(ielec)
 196                          {
 197                          case 1:
 198                              /* Vanilla cutoff coulomb */
 199                              vcoul            = qq*rinv;
 200                              fscal            = vcoul*rinvsq;
 201                              break;
 202
 203                          case 2:
 204                              /* Reaction-field */
 205                              krsq             = fr->k_rf*rsq;
 206                              vcoul            = qq*(rinv+krsq-fr->c_rf);
 207                              fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 208                              break;
 209
 210                          case 3:
 211                              /* Tabulated coulomb */
 212                              Y                = VFtab[nnn];
 213                              F                = VFtab[nnn+1];
 214                              Geps             = eps*VFtab[nnn+2];
 215                              Heps2            = eps2*VFtab[nnn+3];
 216                              nnn             += 4;
 217                              Fp               = F+Geps+Heps2;
 218                              VV               = Y+eps*Fp;
 219                              FF               = Fp+Geps+2.0*Heps2;
 220                              vcoul            = qq*VV;
 221                              fscal            = -qq*FF*tabscale*rinv;
 222                              break;
 223
 224                          case 4:
 225                              /* GB */
 226                            gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
 227                            break;
 228
 229                          default:
 230                              gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for ielec=%d.\n",ielec);
 231                              break;
 232                          }
 233                          vctot            = vctot+vcoul;
 234                      } /* End of coulomb interactions */
 235
 236
 237                      /* VdW interaction. ivdw==0 means no interaction */
 238                      if (ivdw > 0)
 239                      {
 240                          tj               = nti+nvdwparam*type[aj];
 241
 242                          switch(ivdw)
 243                          {
 244                          case 1:
 245                              /* Vanilla Lennard-Jones cutoff */
 246                              c6               = vdwparam[tj];
 247                              c12              = vdwparam[tj+1];
 248
 249                              rinvsix          = rinvsq*rinvsq*rinvsq;
 250                              Vvdw_disp        = c6*rinvsix;
 251                              Vvdw_rep         = c12*rinvsix*rinvsix;
 252                              fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 253                              Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 254                              break;
 255
 256                          case 2:
 257                              /* Buckingham */
 258                              c6               = vdwparam[tj];
 259                              cexp1            = vdwparam[tj+1];
 260                              cexp2            = vdwparam[tj+2];
 261
 262                              rinvsix          = rinvsq*rinvsq*rinvsq;
 263                              Vvdw_disp        = c6*rinvsix;
 264                              br               = cexp2*rsq*rinv;
 265                              Vvdw_rep         = cexp1*exp(-br);
 266                              fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 267                              Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 268                              break;
 269
 270                          case 3:
 271                              /* Tabulated VdW */
 272                              c6               = vdwparam[tj];
 273                              c12              = vdwparam[tj+1];
 274
 275                              Y                = VFtab[nnn];
 276                              F                = VFtab[nnn+1];
 277                              Geps             = eps*VFtab[nnn+2];
 278                              Heps2            = eps2*VFtab[nnn+3];
 279                              Fp               = F+Geps+Heps2;
 280                              VV               = Y+eps*Fp;
 281                              FF               = Fp+Geps+2.0*Heps2;
 282                              Vvdw_disp        = c6*VV;
 283                              fijD             = c6*FF;
 284                              nnn             += 4;
 285                              Y                = VFtab[nnn];
 286                              F                = VFtab[nnn+1];
 287                              Geps             = eps*VFtab[nnn+2];
 288                              Heps2            = eps2*VFtab[nnn+3];
 289                              Fp               = F+Geps+Heps2;
 290                              VV               = Y+eps*Fp;
 291                              FF               = Fp+Geps+2.0*Heps2;
 292                              Vvdw_rep         = c12*VV;
 293                              fijR             = c12*FF;
 294                              fscal           += -(fijD+fijR)*tabscale*rinv;
 295                              Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 296                              break;
 297
 298                          default:
 299                              gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
 300                              break;
 301                          }
 302                      } /* end VdW interactions */
 303
 304
 305                      tx               = fscal*dx;
 306                      ty               = fscal*dy;
 307                      tz               = fscal*dz;
 308                      f[i3+0]         += tx;
 309                      f[i3+1]         += ty;
 310                      f[i3+2]         += tz;
 311                      f[j3+0]         -= tx;
 312                      f[j3+1]         -= ty;
 313                      f[j3+2]         -= tz;
 314                      fix             += tx;
 315                      fiy             += ty;
 316                      fiz             += tz;
 317                  }
 318              }
 319          }
 320
 321          fshift[is3]     += fix;
 322          fshift[is3+1]   += fiy;
 323          fshift[is3+2]   += fiz;
 324          ggid             = nlist->gid[n];
 325          Vc[ggid]        += vctot;
 326          Vvdw[ggid]      += Vvdwtot;
 327      }
 328     /* Estimate flops, average for generic cg kernel:
 329      * 12  flops per outer iteration
 330      * 100 flops per inner iteration
 331      */
 332     inc_nrnb(nrnb,eNR_NBKERNEL_FREE_ENERGY,nlist->nri*12 + nlist->jindex[n]*100);
 333 }
 334