src/gromacs/gmxlib/nonbonded/nb_generic.c

   1 /*
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   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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  14
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40
  41 #include "types/simple.h"
  42 #include "vec.h"
  43 #include "typedefs.h"
  44 #include "nb_generic.h"
  45
  46 void
  47 gmx_nb_generic_kernel(t_nblist *           nlist,
  48                                           t_forcerec *         fr,
  49                                           t_mdatoms *          mdatoms,
  50                                           real *               x,
  51                                           real *               f,
  52                                           real *               fshift,
  53                                           real *               Vc,
  54                                           real *               Vvdw,
  55                                           real                 tabscale,
  56                                           real *               VFtab,
  57                                           int *                outeriter,
  58                                           int *                inneriter)
  59 {
  60     int           nri,ntype,table_nelements,icoul,ivdw;
  61     real          facel,gbtabscale;
  62     int           n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid,nnn,n0;
  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
  84         icoul               = nlist->icoul;
  85         ivdw                = nlist->ivdw;
  86
  87         /* avoid compiler warnings for cases that cannot happen */
  88         nnn                 = 0;
  89         vcoul               = 0.0;
  90         eps                 = 0.0;
  91         eps2                = 0.0;
  92
  93         /* 3 VdW parameters for buckingham, otherwise 2 */
  94         nvdwparam           = (nlist->ivdw==2) ? 3 : 2;
  95         table_nelements     = (icoul==3) ? 4 : 0;
  96         table_nelements    += (ivdw==3) ? 8 : 0;
  97
  98     charge              = mdatoms->chargeA;
  99         type                = mdatoms->typeA;
 100         facel               = fr->epsfac;
 101         shiftvec            = fr->shift_vec[0];
 102         vdwparam            = fr->nbfp;
 103         ntype               = fr->ntype;
 104
 105         for(n=0; (n<nlist->nri); n++)
 106     {
 107         is3              = 3*nlist->shift[n];
 108         shX              = shiftvec[is3];
 109         shY              = shiftvec[is3+1];
 110         shZ              = shiftvec[is3+2];
 111         nj0              = nlist->jindex[n];
 112         nj1              = nlist->jindex[n+1];
 113         ii               = nlist->iinr[n];
 114         ii3              = 3*ii;
 115         ix               = shX + x[ii3+0];
 116         iy               = shY + x[ii3+1];
 117         iz               = shZ + x[ii3+2];
 118         iq               = facel*charge[ii];
 119         nti              = nvdwparam*ntype*type[ii];
 120         vctot            = 0;
 121         Vvdwtot          = 0;
 122         fix              = 0;
 123         fiy              = 0;
 124         fiz              = 0;
 125
 126         for(k=nj0; (k<nj1); k++)
 127         {
 128             jnr              = nlist->jjnr[k];
 129             j3               = 3*jnr;
 130             jx               = x[j3+0];
 131             jy               = x[j3+1];
 132             jz               = x[j3+2];
 133             dx               = ix - jx;
 134             dy               = iy - jy;
 135             dz               = iz - jz;
 136             rsq              = dx*dx+dy*dy+dz*dz;
 137             rinv             = gmx_invsqrt(rsq);
 138             rinvsq           = rinv*rinv;
 139                         fscal            = 0;
 140
 141                         if(icoul==3 || ivdw==3)
 142                         {
 143                                 r                = rsq*rinv;
 144                                 rt               = r*tabscale;
 145                                 n0               = rt;
 146                                 eps              = rt-n0;
 147                                 eps2             = eps*eps;
 148                                 nnn              = table_nelements*n0;
 149                         }
 150
 151                         /* Coulomb interaction. icoul==0 means no interaction */
 152                         if(icoul>0)
 153                         {
 154                                 qq               = iq*charge[jnr];
 155
 156                                 switch(icoul)
 157                                 {
 158                                         case 1:
 159                                                 /* Vanilla cutoff coulomb */
 160                                                 vcoul            = qq*rinv;
 161                                                 fscal            = vcoul*rinvsq;
 162                                                 break;
 163
 164                                         case 2:
 165                                                 /* Reaction-field */
 166                                                 krsq             = fr->k_rf*rsq;
 167                                                 vcoul            = qq*(rinv+krsq-fr->c_rf);
 168                                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 169                                                 break;
 170
 171                                         case 3:
 172                                                 /* Tabulated coulomb */
 173                                                 Y                = VFtab[nnn];
 174                                                 F                = VFtab[nnn+1];
 175                                                 Geps             = eps*VFtab[nnn+2];
 176                                                 Heps2            = eps2*VFtab[nnn+3];
 177                                                 nnn             += 4;
 178                                                 Fp               = F+Geps+Heps2;
 179                                                 VV               = Y+eps*Fp;
 180                                                 FF               = Fp+Geps+2.0*Heps2;
 181                                                 vcoul            = qq*VV;
 182                                                 fscal            = -qq*FF*tabscale*rinv;
 183                                                 break;
 184
 185                                         case 4:
 186                                                 /* GB */
 187                                                 gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
 188                                                 break;
 189
 190                                         default:
 191                                                 gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
 192                                                 break;
 193                                 }
 194                                 vctot            = vctot+vcoul;
 195                         } /* End of coulomb interactions */
 196
 197
 198                         /* VdW interaction. ivdw==0 means no interaction */
 199                         if(ivdw>0)
 200                         {
 201                                 tj               = nti+nvdwparam*type[jnr];
 202
 203                                 switch(ivdw)
 204                                 {
 205                                         case 1:
 206                                                 /* Vanilla Lennard-Jones cutoff */
 207                                                 c6               = vdwparam[tj];
 208                                                 c12              = vdwparam[tj+1];
 209
 210                                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 211                                                 Vvdw_disp        = c6*rinvsix;
 212                                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 213                                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 214                                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 215                                                 break;
 216
 217                                         case 2:
 218                                                 /* Buckingham */
 219                                                 c6               = vdwparam[tj];
 220                                                 cexp1            = vdwparam[tj+1];
 221                                                 cexp2            = vdwparam[tj+2];
 222
 223                                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 224                                                 Vvdw_disp        = c6*rinvsix;
 225                                                 br               = cexp2*rsq*rinv;
 226                                                 Vvdw_rep         = cexp1*exp(-br);
 227                                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 228                                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 229                                                 break;
 230
 231                                         case 3:
 232                                                 /* Tabulated VdW */
 233                                                 c6               = vdwparam[tj];
 234                                                 c12              = vdwparam[tj+1];
 235
 236                                                 Y                = VFtab[nnn];
 237                                                 F                = VFtab[nnn+1];
 238                                                 Geps             = eps*VFtab[nnn+2];
 239                                                 Heps2            = eps2*VFtab[nnn+3];
 240                                                 Fp               = F+Geps+Heps2;
 241                                                 VV               = Y+eps*Fp;
 242                                                 FF               = Fp+Geps+2.0*Heps2;
 243                                                 Vvdw_disp        = c6*VV;
 244                                                 fijD             = c6*FF;
 245                                                 nnn             += 4;
 246                                                 Y                = VFtab[nnn];
 247                                                 F                = VFtab[nnn+1];
 248                                                 Geps             = eps*VFtab[nnn+2];
 249                                                 Heps2            = eps2*VFtab[nnn+3];
 250                                                 Fp               = F+Geps+Heps2;
 251                                                 VV               = Y+eps*Fp;
 252                                                 FF               = Fp+Geps+2.0*Heps2;
 253                                                 Vvdw_rep         = c12*VV;
 254                                                 fijR             = c12*FF;
 255                                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 256                                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 257                                                 break;
 258
 259                                         default:
 260                                                 gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
 261                                                 break;
 262                                 }
 263                         } /* end VdW interactions */
 264
 265
 266             tx               = fscal*dx;
 267             ty               = fscal*dy;
 268             tz               = fscal*dz;
 269             fix              = fix + tx;
 270             fiy              = fiy + ty;
 271             fiz              = fiz + tz;
 272             f[j3+0]          = f[j3+0] - tx;
 273             f[j3+1]          = f[j3+1] - ty;
 274             f[j3+2]          = f[j3+2] - tz;
 275         }
 276
 277         f[ii3+0]         = f[ii3+0] + fix;
 278         f[ii3+1]         = f[ii3+1] + fiy;
 279         f[ii3+2]         = f[ii3+2] + fiz;
 280         fshift[is3]      = fshift[is3]+fix;
 281         fshift[is3+1]    = fshift[is3+1]+fiy;
 282         fshift[is3+2]    = fshift[is3+2]+fiz;
 283         ggid             = nlist->gid[n];
 284         Vc[ggid]         = Vc[ggid] + vctot;
 285         Vvdw[ggid]       = Vvdw[ggid] + Vvdwtot;
 286     }
 287
 288     *outeriter       = nlist->nri;
 289     *inneriter       = nlist->jindex[n];
 290 }
 291