src/mdlib/wall.c

   1 /*
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   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
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  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <math.h>
  44 #include <string.h>
  45 #include "maths.h"
  46 #include "sysstuff.h"
  47 #include "typedefs.h"
  48 #include "macros.h"
  49 #include "smalloc.h"
  50 #include "force.h"
  51 #include "filenm.h"
  52 #include "nrnb.h"
  53 #include "vec.h"
  54
  55 void make_wall_tables(FILE *fplog,const output_env_t oenv,
  56                       const t_inputrec *ir,const char *tabfn,
  57                       const gmx_groups_t *groups,
  58                       t_forcerec *fr)
  59 {
  60   int  w,negp_pp,egp,i,j;
  61   int  *nm_ind;
  62   char buf[STRLEN];
  63   t_forcetable *tab;
  64
  65   negp_pp = ir->opts.ngener - ir->nwall;
  66   nm_ind  = groups->grps[egcENER].nm_ind;
  67
  68   if (fplog) {
  69     fprintf(fplog,"Reading user tables for %d energy groups with %d walls\n",
  70             negp_pp,ir->nwall);
  71   }
  72
  73   snew(fr->wall_tab,ir->nwall);
  74   for(w=0; w<ir->nwall; w++) {
  75     snew(fr->wall_tab[w],negp_pp);
  76     for(egp=0; egp<negp_pp; egp++) {
  77       /* If the energy group pair is excluded, we don't need a table */
  78       if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL)) {
  79         tab = &fr->wall_tab[w][egp];
  80         sprintf(buf,"%s",tabfn);
  81         sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"_%s_%s.%s",
  82                 *groups->grpname[nm_ind[egp]],
  83                 *groups->grpname[nm_ind[negp_pp+w]],
  84                 ftp2ext(efXVG));
  85         *tab = make_tables(fplog,oenv,fr,FALSE,buf,0,GMX_MAKETABLES_FORCEUSER);
  86         /* Since wall have no charge, we can compress the table */
  87         for(i=0; i<=tab->n; i++)
  88           for(j=0; j<8; j++)
  89             tab->data[8*i+j] = tab->data[12*i+4+j];
  90       }
  91     }
  92   }
  93 }
  94
  95 static void wall_error(int a,rvec *x,real r)
  96 {
  97     gmx_fatal(FARGS,
  98               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
  99               "You might want to use the mdp option wall_r_linpot",
 100               x[a][XX],x[a][YY],x[a][ZZ],r);
 101 }
 102
 103 real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
 104               rvec x[],rvec f[],real lambda,real Vlj[],t_nrnb *nrnb)
 105 {
 106     int  nwall,w,lam,i;
 107     int  ntw[2],at,ntype,ngid,ggid,*egp_flags,*type;
 108     real *nbfp,lamfac,fac_d[2],fac_r[2],Cd,Cr,Vtot,Fwall[2];
 109     real wall_z[2],r,mr,r1,r2,r4,Vd,Vr,V=0,Fd,Fr,F=0,dvdlambda;
 110     dvec xf_z;
 111     int  n0,nnn;
 112     real tabscale,*VFtab,rt,eps,eps2,Yt,Ft,Geps,Heps,Heps2,Fp,VV,FF;
 113     unsigned short *gid=md->cENER;
 114     t_forcetable *tab;
 115
 116     nwall     = ir->nwall;
 117     ngid      = ir->opts.ngener;
 118     ntype     = fr->ntype;
 119     nbfp      = fr->nbfp;
 120     egp_flags = fr->egp_flags;
 121
 122     for(w=0; w<nwall; w++)
 123     {
 124         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 125         switch (ir->wall_type)
 126         {
 127         case ewt93:
 128             fac_d[w] = ir->wall_density[w]*M_PI/6;
 129             fac_r[w] = ir->wall_density[w]*M_PI/45;
 130             break;
 131         case ewt104:
 132             fac_d[w] = ir->wall_density[w]*M_PI/2;
 133             fac_r[w] = ir->wall_density[w]*M_PI/5;
 134             break;
 135         default:
 136             break;
 137         }
 138         Fwall[w] = 0;
 139     }
 140     wall_z[0] = 0;
 141     wall_z[1] = box[ZZ][ZZ];
 142
 143     Vtot = 0;
 144     dvdlambda = 0;
 145     clear_dvec(xf_z);
 146     for(lam=0; lam<(md->nPerturbed ? 2 : 1); lam++)
 147     {
 148         if (md->nPerturbed)
 149         {
 150             if (lam == 0)
 151             {
 152                 lamfac = 1 - lambda;
 153                 type = md->typeA;
 154             }
 155             else
 156             {
 157                 lamfac = 0;
 158                 type = md->typeB;
 159             }
 160         }
 161         else
 162         {
 163             lamfac = 1;
 164             type = md->typeA;
 165         }
 166         for(i=md->start; i<md->start+md->homenr; i++)
 167         {
 168             for(w=0; w<nwall; w++)
 169             {
 170                 /* The wall energy groups are always at the end of the list */
 171                 ggid = gid[i]*ngid + ngid - nwall + w;
 172                 at = type[i];
 173                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 174                 Cd = nbfp[ntw[w]+2*at]/6.0;
 175                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 176                 if (!((Cd==0 && Cr==0) || (egp_flags[ggid] & EGP_EXCL)))
 177                 {
 178                     if (w == 0)
 179                     {
 180                         r = x[i][ZZ];
 181                     }
 182                     else
 183                     {
 184                         r = wall_z[1] - x[i][ZZ];
 185                     }
 186                     if (r < ir->wall_r_linpot)
 187                     {
 188                         mr = ir->wall_r_linpot - r;
 189                         r  = ir->wall_r_linpot;
 190                     }
 191                     else
 192                     {
 193                         mr = 0;
 194                     }
 195                     switch (ir->wall_type)
 196                     {
 197                     case ewtTABLE:
 198                         if (r < 0)
 199                         {
 200                             wall_error(i,x,r);
 201                         }
 202                         tab = &(fr->wall_tab[w][gid[i]]);
 203                         tabscale = tab->scale;
 204                         VFtab    = tab->data;
 205
 206                         rt    = r*tabscale;
 207                         n0    = rt;
 208                         if (n0 >= tab->n)
 209                         {
 210                             /* Beyond the table range, set V and F to zero */
 211                             V     = 0;
 212                             F     = 0;
 213                         }
 214                         else
 215                         {
 216                             eps   = rt - n0;
 217                             eps2  = eps*eps;
 218                             /* Dispersion */
 219                             nnn   = 8*n0;
 220                             Yt    = VFtab[nnn];
 221                             Ft    = VFtab[nnn+1];
 222                             Geps  = VFtab[nnn+2]*eps;
 223                             Heps2 = VFtab[nnn+3]*eps2;
 224                             Fp    = Ft + Geps + Heps2;
 225                             VV    = Yt + Fp*eps;
 226                             FF    = Fp + Geps + 2.0*Heps2;
 227                             Vd    = Cd*VV;
 228                             Fd    = Cd*FF;
 229                             /* Repulsion */
 230                             nnn   = nnn + 4;
 231                             Yt    = VFtab[nnn];
 232                             Ft    = VFtab[nnn+1];
 233                             Geps  = VFtab[nnn+2]*eps;
 234                             Heps2 = VFtab[nnn+3]*eps2;
 235                             Fp    = Ft + Geps + Heps2;
 236                             VV    = Yt + Fp*eps;
 237                             FF    = Fp + Geps + 2.0*Heps2;
 238                             Vr    = Cr*VV;
 239                             Fr    = Cr*FF;
 240                             V     = Vd + Vr;
 241                             F     = -lamfac*(Fd + Fr)*tabscale;
 242                         }
 243                         break;
 244                     case ewt93:
 245                         if (r <= 0)
 246                         {
 247                             wall_error(i,x,r);
 248                         }
 249                         r1 = 1/r;
 250                         r2 = r1*r1;
 251                         r4 = r2*r2;
 252                         Vd = fac_d[w]*Cd*r2*r1;
 253                         Vr = fac_r[w]*Cr*r4*r4*r1;
 254                         V  = Vr - Vd;
 255                         F  = lamfac*(9*Vr - 3*Vd)*r1;
 256                         break;
 257                     case ewt104:
 258                         if (r <= 0)
 259                         {
 260                             wall_error(i,x,r);
 261                         }
 262                         r1 = 1/r;
 263                         r2 = r1*r1;
 264                         r4 = r2*r2;
 265                         Vd = fac_d[w]*Cd*r4;
 266                         Vr = fac_r[w]*Cr*r4*r4*r2;
 267                         V  = Vr - Vd;
 268                         F  = lamfac*(10*Vr - 4*Vd)*r1;
 269                         break;
 270                     case ewt126:
 271                         if (r <= 0)
 272                         {
 273                             wall_error(i,x,r);
 274                         }
 275                         r1 = 1/r;
 276                         r2 = r1*r1;
 277                         r4 = r2*r2;
 278                         Vd = Cd*r4*r2;
 279                         Vr = Cr*r4*r4*r4;
 280                         V  = Vr - Vd;
 281                         F  = lamfac*(12*Vr - 6*Vd)*r1;
 282                         break;
 283                     default:
 284                         break;
 285                     }
 286                     if (mr > 0)
 287                     {
 288                         V += mr*F;
 289                     }
 290                     if (w == 1)
 291                     {
 292                         F = -F;
 293                     }
 294                     Vlj[ggid] += lamfac*V;
 295                     Vtot      += V;
 296                     f[i][ZZ]  += F;
 297                     /* Because of the single sum virial calculation we need
 298                      * to add  the full virial contribution of the walls.
 299                      * Since the force only has a z-component, there is only
 300                      * a contribution to the z component of the virial tensor.
 301                      * We could also determine the virial contribution directly,
 302                      * which would be cheaper here, but that would require extra
 303                      * communication for f_novirsum for with virtual sites
 304                      * in parallel.
 305                      */
 306                     xf_z[XX]  -= x[i][XX]*F;
 307                     xf_z[YY]  -= x[i][YY]*F;
 308                     xf_z[ZZ]  -= wall_z[w]*F;
 309                 }
 310             }
 311         }
 312         if (md->nPerturbed)
 313         {
 314             dvdlambda += (lam==0 ? -1 : 1)*Vtot;
 315         }
 316
 317         inc_nrnb(nrnb,eNR_WALLS,md->homenr);
 318     }
 319
 320     for(i=0; i<DIM; i++)
 321     {
 322         fr->vir_wall_z[i] = -0.5*xf_z[i];
 323     }
 324
 325     return dvdlambda;
 326 }