src/mdlib/wall.c

   1 /*
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   7  * Copyright (c) 2012,2013, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
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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     {
  70         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  71                 negp_pp, ir->nwall);
  72     }
  73
  74     snew(fr->wall_tab, ir->nwall);
  75     for (w = 0; w < ir->nwall; w++)
  76     {
  77         snew(fr->wall_tab[w], negp_pp);
  78         for (egp = 0; egp < negp_pp; egp++)
  79         {
  80             /* If the energy group pair is excluded, we don't need a table */
  81             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  82             {
  83                 tab = &fr->wall_tab[w][egp];
  84                 sprintf(buf, "%s", tabfn);
  85                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  86                         *groups->grpname[nm_ind[egp]],
  87                         *groups->grpname[nm_ind[negp_pp+w]],
  88                         ftp2ext(efXVG));
  89                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  90                 /* Since wall have no charge, we can compress the table */
  91                 for (i = 0; i <= tab->n; i++)
  92                 {
  93                     for (j = 0; j < 8; j++)
  94                     {
  95                         tab->data[8*i+j] = tab->data[12*i+4+j];
  96                     }
  97                 }
  98             }
  99         }
 100     }
 101 }
 102
 103 static void wall_error(int a, rvec *x, real r)
 104 {
 105     gmx_fatal(FARGS,
 106               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 107               "You might want to use the mdp option wall_r_linpot",
 108               x[a][XX], x[a][YY], x[a][ZZ], r);
 109 }
 110
 111 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 112               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 113 {
 114     int             nwall, w, lam, i;
 115     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 116     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 117     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 118     dvec            xf_z;
 119     int             n0, nnn;
 120     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 121     unsigned short *gid = md->cENER;
 122     t_forcetable   *tab;
 123
 124     nwall     = ir->nwall;
 125     ngid      = ir->opts.ngener;
 126     ntype     = fr->ntype;
 127     nbfp      = fr->nbfp;
 128     egp_flags = fr->egp_flags;
 129
 130     for (w = 0; w < nwall; w++)
 131     {
 132         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 133         switch (ir->wall_type)
 134         {
 135             case ewt93:
 136                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 137                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 138                 break;
 139             case ewt104:
 140                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 141                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 142                 break;
 143             default:
 144                 break;
 145         }
 146         Fwall[w] = 0;
 147     }
 148     wall_z[0] = 0;
 149     wall_z[1] = box[ZZ][ZZ];
 150
 151     Vtot      = 0;
 152     dvdlambda = 0;
 153     clear_dvec(xf_z);
 154     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 155     {
 156         if (md->nPerturbed)
 157         {
 158             if (lam == 0)
 159             {
 160                 lamfac = 1 - lambda;
 161                 type   = md->typeA;
 162             }
 163             else
 164             {
 165                 lamfac = lambda;
 166                 type   = md->typeB;
 167             }
 168         }
 169         else
 170         {
 171             lamfac = 1;
 172             type   = md->typeA;
 173         }
 174         for (i = md->start; i < md->start+md->homenr; i++)
 175         {
 176             for (w = 0; w < nwall; w++)
 177             {
 178                 /* The wall energy groups are always at the end of the list */
 179                 ggid = gid[i]*ngid + ngid - nwall + w;
 180                 at   = type[i];
 181                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 182                 Cd = nbfp[ntw[w]+2*at]/6.0;
 183                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 184                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 185                 {
 186                     if (w == 0)
 187                     {
 188                         r = x[i][ZZ];
 189                     }
 190                     else
 191                     {
 192                         r = wall_z[1] - x[i][ZZ];
 193                     }
 194                     if (r < ir->wall_r_linpot)
 195                     {
 196                         mr = ir->wall_r_linpot - r;
 197                         r  = ir->wall_r_linpot;
 198                     }
 199                     else
 200                     {
 201                         mr = 0;
 202                     }
 203                     switch (ir->wall_type)
 204                     {
 205                         case ewtTABLE:
 206                             if (r < 0)
 207                             {
 208                                 wall_error(i, x, r);
 209                             }
 210                             tab      = &(fr->wall_tab[w][gid[i]]);
 211                             tabscale = tab->scale;
 212                             VFtab    = tab->data;
 213
 214                             rt    = r*tabscale;
 215                             n0    = rt;
 216                             if (n0 >= tab->n)
 217                             {
 218                                 /* Beyond the table range, set V and F to zero */
 219                                 V     = 0;
 220                                 F     = 0;
 221                             }
 222                             else
 223                             {
 224                                 eps   = rt - n0;
 225                                 eps2  = eps*eps;
 226                                 /* Dispersion */
 227                                 nnn   = 8*n0;
 228                                 Yt    = VFtab[nnn];
 229                                 Ft    = VFtab[nnn+1];
 230                                 Geps  = VFtab[nnn+2]*eps;
 231                                 Heps2 = VFtab[nnn+3]*eps2;
 232                                 Fp    = Ft + Geps + Heps2;
 233                                 VV    = Yt + Fp*eps;
 234                                 FF    = Fp + Geps + 2.0*Heps2;
 235                                 Vd    = Cd*VV;
 236                                 Fd    = Cd*FF;
 237                                 /* Repulsion */
 238                                 nnn   = nnn + 4;
 239                                 Yt    = VFtab[nnn];
 240                                 Ft    = VFtab[nnn+1];
 241                                 Geps  = VFtab[nnn+2]*eps;
 242                                 Heps2 = VFtab[nnn+3]*eps2;
 243                                 Fp    = Ft + Geps + Heps2;
 244                                 VV    = Yt + Fp*eps;
 245                                 FF    = Fp + Geps + 2.0*Heps2;
 246                                 Vr    = Cr*VV;
 247                                 Fr    = Cr*FF;
 248                                 V     = Vd + Vr;
 249                                 F     = -lamfac*(Fd + Fr)*tabscale;
 250                             }
 251                             break;
 252                         case ewt93:
 253                             if (r <= 0)
 254                             {
 255                                 wall_error(i, x, r);
 256                             }
 257                             r1 = 1/r;
 258                             r2 = r1*r1;
 259                             r4 = r2*r2;
 260                             Vd = fac_d[w]*Cd*r2*r1;
 261                             Vr = fac_r[w]*Cr*r4*r4*r1;
 262                             V  = Vr - Vd;
 263                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 264                             break;
 265                         case ewt104:
 266                             if (r <= 0)
 267                             {
 268                                 wall_error(i, x, r);
 269                             }
 270                             r1 = 1/r;
 271                             r2 = r1*r1;
 272                             r4 = r2*r2;
 273                             Vd = fac_d[w]*Cd*r4;
 274                             Vr = fac_r[w]*Cr*r4*r4*r2;
 275                             V  = Vr - Vd;
 276                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 277                             break;
 278                         case ewt126:
 279                             if (r <= 0)
 280                             {
 281                                 wall_error(i, x, r);
 282                             }
 283                             r1 = 1/r;
 284                             r2 = r1*r1;
 285                             r4 = r2*r2;
 286                             Vd = Cd*r4*r2;
 287                             Vr = Cr*r4*r4*r4;
 288                             V  = Vr - Vd;
 289                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 290                             break;
 291                         default:
 292                             break;
 293                     }
 294                     if (mr > 0)
 295                     {
 296                         V += mr*F;
 297                     }
 298                     if (w == 1)
 299                     {
 300                         F = -F;
 301                     }
 302                     Vlj[ggid] += lamfac*V;
 303                     Vtot      += V;
 304                     f[i][ZZ]  += F;
 305                     /* Because of the single sum virial calculation we need
 306                      * to add  the full virial contribution of the walls.
 307                      * Since the force only has a z-component, there is only
 308                      * a contribution to the z component of the virial tensor.
 309                      * We could also determine the virial contribution directly,
 310                      * which would be cheaper here, but that would require extra
 311                      * communication for f_novirsum for with virtual sites
 312                      * in parallel.
 313                      */
 314                     xf_z[XX]  -= x[i][XX]*F;
 315                     xf_z[YY]  -= x[i][YY]*F;
 316                     xf_z[ZZ]  -= wall_z[w]*F;
 317                 }
 318             }
 319         }
 320         if (md->nPerturbed)
 321         {
 322             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 323         }
 324
 325         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 326     }
 327
 328     for (i = 0; i < DIM; i++)
 329     {
 330         fr->vir_wall_z[i] = -0.5*xf_z[i];
 331     }
 332
 333     return dvdlambda;
 334 }