src/gromacs/gmxlib/nonbonded/nb_generic_adress.c

   1 /*
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   4  *
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   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
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  14
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  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
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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_adress.h"
  45
  46 #define ALMOST_ZERO 1e-30
  47 #define ALMOST_ONE 1-(1e-30)
  48 void
  49 gmx_nb_generic_adress_kernel(t_nblist *           nlist,
  50                                           t_forcerec *         fr,
  51                                           t_mdatoms *          mdatoms,
  52                                           real *               x,
  53                                           real *               f,
  54                                           real *               fshift,
  55                                           real *               Vc,
  56                                           real *               Vvdw,
  57                                           real                 tabscale,
  58                                           real *               VFtab,
  59                                           int *                outeriter,
  60                                           int *                inneriter,
  61                                           gmx_bool                bCG)
  62 {
  63     int           nri,ntype,table_nelements,icoul,ivdw;
  64     real          facel,gbtabscale;
  65     int           n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid,nnn,n0;
  66     real          shX,shY,shZ;
  67     real          fscal,tx,ty,tz;
  68     real          rinvsq;
  69     real          iq;
  70     real          qq,vcoul,krsq,vctot;
  71     int           nti,nvdwparam;
  72     int           tj;
  73     real          rt,r,eps,eps2,Y,F,Geps,Heps2,VV,FF,Fp,fijD,fijR;
  74     real          rinvsix;
  75     real          Vvdwtot;
  76     real          Vvdw_rep,Vvdw_disp;
  77     real          ix,iy,iz,fix,fiy,fiz;
  78     real          jx,jy,jz;
  79     real          dx,dy,dz,rsq,rinv;
  80     real          c6,c12,cexp1,cexp2,br;
  81     real *        charge;
  82     real *        shiftvec;
  83     real *        vdwparam;
  84     int *         shift;
  85     int *         type;
  86
  87     real *     wf;
  88     real       weight_cg1;
  89     real       weight_cg2;
  90     real       weight_product;
  91     real       hybscal; /* the multiplicator to the force for hybrid interactions*/
  92     gmx_bool   bHybrid; /*Are we in the hybrid zone ?*/
  93     real       force_cap;
  94
  95     wf                  = mdatoms->wf;
  96
  97     force_cap = fr->adress_ex_forcecap;
  98
  99     icoul               = nlist->icoul;
 100     ivdw                = nlist->ivdw;
 101
 102     /* avoid compiler warnings for cases that cannot happen */
 103     nnn                 = 0;
 104     vcoul               = 0.0;
 105     eps                 = 0.0;
 106     eps2                = 0.0;
 107
 108     /* 3 VdW parameters for buckingham, otherwise 2 */
 109     nvdwparam           = (nlist->ivdw==2) ? 3 : 2;
 110     table_nelements     = (icoul==3) ? 4 : 0;
 111     table_nelements    += (ivdw==3) ? 8 : 0;
 112
 113     charge              = mdatoms->chargeA;
 114     type                = mdatoms->typeA;
 115     facel               = fr->epsfac;
 116     shiftvec            = fr->shift_vec[0];
 117     vdwparam            = fr->nbfp;
 118     ntype               = fr->ntype;
 119
 120
 121
 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         ii               = nlist->iinr[n];
 132         ii3              = 3*ii;
 133         ix               = shX + x[ii3+0];
 134         iy               = shY + x[ii3+1];
 135         iz               = shZ + x[ii3+2];
 136         iq               = facel*charge[ii];
 137         nti              = nvdwparam*ntype*type[ii];
 138         vctot            = 0;
 139         Vvdwtot          = 0;
 140         fix              = 0;
 141         fiy              = 0;
 142         fiz              = 0;
 143
 144         weight_cg1       = wf[ii];
 145
 146         /* TODO: why does this line her not speed up things ?
 147          * if ((!bCG) && weight_cg1 < ALMOST_ZERO) continue;
 148          */
 149         for(k=nj0; (k<nj1); k++)
 150         {
 151             jnr              = nlist->jjnr[k];
 152             weight_cg2       = wf[jnr];
 153
 154             weight_product   = weight_cg1*weight_cg2;
 155
 156             if (weight_product < ALMOST_ZERO)
 157             {
 158                 /* if it's a explicit loop, skip this atom */
 159                 if (!bCG)
 160                 {
 161                     continue;
 162                 }
 163                 else /* if it's a coarse grained loop, include this atom */
 164                 {
 165                     bHybrid = FALSE;
 166                     hybscal = 1.0;
 167                 }
 168             }
 169             else if (weight_product >= ALMOST_ONE)
 170             {
 171
 172                 /* if it's a explicit loop, include this atom */
 173                 if(!bCG)
 174                 {
 175                     bHybrid = FALSE;
 176                     hybscal = 1.0;
 177                 }
 178                 else  /* if it's a coarse grained loop, skip this atom */
 179                 {
 180                     continue;
 181                 }
 182             }
 183             /* both have double identity, get hybrid scaling factor */
 184             else
 185             {
 186                 bHybrid = TRUE;
 187                 hybscal = weight_product;
 188
 189                 if(bCG)
 190                 {
 191                     hybscal = 1.0 - hybscal;
 192                 }
 193             }
 194
 195
 196             j3               = 3*jnr;
 197             jx               = x[j3+0];
 198             jy               = x[j3+1];
 199             jz               = x[j3+2];
 200             dx               = ix - jx;
 201             dy               = iy - jy;
 202             dz               = iz - jz;
 203             rsq              = dx*dx+dy*dy+dz*dz;
 204             rinv             = gmx_invsqrt(rsq);
 205             rinvsq           = rinv*rinv;
 206
 207
 208                         fscal            = 0;
 209
 210                         if(icoul==3 || ivdw==3)
 211                         {
 212                                 r                = rsq*rinv;
 213                                 rt               = r*tabscale;
 214                                 n0               = rt;
 215                                 eps              = rt-n0;
 216                                 eps2             = eps*eps;
 217                                 nnn              = table_nelements*n0;
 218                         }
 219
 220                         /* Coulomb interaction. icoul==0 means no interaction */
 221                         if(icoul>0)
 222                         {
 223                                 qq               = iq*charge[jnr];
 224
 225                                 switch(icoul)
 226                                 {
 227                                         case 1:
 228                                                 /* Vanilla cutoff coulomb */
 229                                                 vcoul            = qq*rinv;
 230                                                 fscal            = vcoul*rinvsq;
 231                                                 break;
 232
 233                                         case 2:
 234                                                 /* Reaction-field */
 235                                                 krsq             = fr->k_rf*rsq;
 236                                                 vcoul            = qq*(rinv+krsq-fr->c_rf);
 237                                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 238                                                 break;
 239
 240                                         case 3:
 241                                                 /* Tabulated coulomb */
 242                                                 Y                = VFtab[nnn];
 243                                                 F                = VFtab[nnn+1];
 244                                                 Geps             = eps*VFtab[nnn+2];
 245                                                 Heps2            = eps2*VFtab[nnn+3];
 246                                                 nnn             += 4;
 247                                                 Fp               = F+Geps+Heps2;
 248                                                 VV               = Y+eps*Fp;
 249                                                 FF               = Fp+Geps+2.0*Heps2;
 250                                                 vcoul            = qq*VV;
 251                                                 fscal            = -qq*FF*tabscale*rinv;
 252                                                 break;
 253
 254                                         case 4:
 255                                                 /* GB */
 256                                                 gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
 257                                                 break;
 258
 259                                         default:
 260                                                 gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
 261                                                 break;
 262                                 }
 263                                 vctot            = vctot+vcoul;
 264                         } /* End of coulomb interactions */
 265
 266
 267                         /* VdW interaction. ivdw==0 means no interaction */
 268                         if(ivdw>0)
 269                         {
 270                                 tj               = nti+nvdwparam*type[jnr];
 271
 272                                 switch(ivdw)
 273                                 {
 274                                         case 1:
 275                                                 /* Vanilla Lennard-Jones cutoff */
 276                                                 c6               = vdwparam[tj];
 277                                                 c12              = vdwparam[tj+1];
 278
 279                                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 280                                                 Vvdw_disp        = c6*rinvsix;
 281                                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 282                                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 283                                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 284                                                 break;
 285
 286                                         case 2:
 287                                                 /* Buckingham */
 288                                                 c6               = vdwparam[tj];
 289                                                 cexp1            = vdwparam[tj+1];
 290                                                 cexp2            = vdwparam[tj+2];
 291
 292                                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 293                                                 Vvdw_disp        = c6*rinvsix;
 294                                                 br               = cexp2*rsq*rinv;
 295                                                 Vvdw_rep         = cexp1*exp(-br);
 296                                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 297                                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 298                                                 break;
 299
 300                                         case 3:
 301                                                 /* Tabulated VdW */
 302                                                 c6               = vdwparam[tj];
 303                                                 c12              = vdwparam[tj+1];
 304
 305                                                 Y                = VFtab[nnn];
 306                                                 F                = VFtab[nnn+1];
 307                                                 Geps             = eps*VFtab[nnn+2];
 308                                                 Heps2            = eps2*VFtab[nnn+3];
 309                                                 Fp               = F+Geps+Heps2;
 310                                                 VV               = Y+eps*Fp;
 311                                                 FF               = Fp+Geps+2.0*Heps2;
 312                                                 Vvdw_disp        = c6*VV;
 313                                                 fijD             = c6*FF;
 314                                                 nnn             += 4;
 315                                                 Y                = VFtab[nnn];
 316                                                 F                = VFtab[nnn+1];
 317                                                 Geps             = eps*VFtab[nnn+2];
 318                                                 Heps2            = eps2*VFtab[nnn+3];
 319                                                 Fp               = F+Geps+Heps2;
 320                                                 VV               = Y+eps*Fp;
 321                                                 FF               = Fp+Geps+2.0*Heps2;
 322                                                 Vvdw_rep         = c12*VV;
 323                                                 fijR             = c12*FF;
 324                                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 325                                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 326                                                 if(!bCG && force_cap>0 && (fabs(fscal)> force_cap))
 327                                                 {
 328                                                      fscal=force_cap*fscal/fabs(fscal);
 329                                                 }
 330                                                 break;
 331
 332                                         default:
 333                                                 gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
 334                                                 break;
 335                                 }
 336                         } /* end VdW interactions */
 337
 338              /* force weight is one anyway */
 339                     if (bHybrid)
 340                     {
 341                         fscal *= hybscal;
 342                     }
 343
 344             tx               = fscal*dx;
 345             ty               = fscal*dy;
 346             tz               = fscal*dz;
 347             fix              = fix + tx;
 348             fiy              = fiy + ty;
 349             fiz              = fiz + tz;
 350             f[j3+0]          = f[j3+0] - tx;
 351             f[j3+1]          = f[j3+1] - ty;
 352             f[j3+2]          = f[j3+2] - tz;
 353         }
 354
 355         f[ii3+0]         = f[ii3+0] + fix;
 356         f[ii3+1]         = f[ii3+1] + fiy;
 357         f[ii3+2]         = f[ii3+2] + fiz;
 358         fshift[is3]      = fshift[is3]+fix;
 359         fshift[is3+1]    = fshift[is3+1]+fiy;
 360         fshift[is3+2]    = fshift[is3+2]+fiz;
 361         ggid             = nlist->gid[n];
 362         Vc[ggid]         = Vc[ggid] + vctot;
 363         Vvdw[ggid]       = Vvdw[ggid] + Vvdwtot;
 364     }
 365
 366     *outeriter       = nlist->nri;
 367     *inneriter       = nlist->jindex[n];
 368 }
 369