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_FREE_ENERGY,nlist->nri*12 + nlist->jindex[n]*100);
 331 }
 332