src/gromacs/mdlib/wall.c

   1 /*
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   5  * Copyright (c) 2001-2008, The GROMACS development team.
   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  37
  38 #include "gmxpre.h"
  39
  40 #include <math.h>
  41 #include <string.h>
  42
  43 #include "gromacs/legacyheaders/typedefs.h"
  44 #include "gromacs/legacyheaders/macros.h"
  45 #include "gromacs/legacyheaders/force.h"
  46 #include "gromacs/legacyheaders/nrnb.h"
  47 #include "gromacs/math/vec.h"
  48
  49 #include "gromacs/fileio/filenm.h"
  50 #include "gromacs/math/utilities.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 void make_wall_tables(FILE *fplog, const output_env_t oenv,
  55                       const t_inputrec *ir, const char *tabfn,
  56                       const gmx_groups_t *groups,
  57                       t_forcerec *fr)
  58 {
  59     int           w, negp_pp, egp, i, j;
  60     int          *nm_ind;
  61     char          buf[STRLEN];
  62     t_forcetable *tab;
  63
  64     negp_pp = ir->opts.ngener - ir->nwall;
  65     nm_ind  = groups->grps[egcENER].nm_ind;
  66
  67     if (fplog)
  68     {
  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     {
  76         snew(fr->wall_tab[w], negp_pp);
  77         for (egp = 0; egp < negp_pp; egp++)
  78         {
  79             /* If the energy group pair is excluded, we don't need a table */
  80             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  81             {
  82                 tab = &fr->wall_tab[w][egp];
  83                 sprintf(buf, "%s", tabfn);
  84                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  85                         *groups->grpname[nm_ind[egp]],
  86                         *groups->grpname[nm_ind[negp_pp+w]],
  87                         ftp2ext(efXVG));
  88                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  89                 /* Since wall have no charge, we can compress the table */
  90                 for (i = 0; i <= tab->n; i++)
  91                 {
  92                     for (j = 0; j < 8; j++)
  93                     {
  94                         tab->data[8*i+j] = tab->data[12*i+4+j];
  95                     }
  96                 }
  97             }
  98         }
  99     }
 100 }
 101
 102 static void wall_error(int a, rvec *x, real r)
 103 {
 104     gmx_fatal(FARGS,
 105               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 106               "You might want to use the mdp option wall_r_linpot",
 107               x[a][XX], x[a][YY], x[a][ZZ], r);
 108 }
 109
 110 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 111               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 112 {
 113     int             nwall, w, lam, i;
 114     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 115     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 116     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 117     dvec            xf_z;
 118     int             n0, nnn;
 119     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 120     unsigned short *gid = md->cENER;
 121     t_forcetable   *tab;
 122
 123     nwall     = ir->nwall;
 124     ngid      = ir->opts.ngener;
 125     ntype     = fr->ntype;
 126     nbfp      = fr->nbfp;
 127     egp_flags = fr->egp_flags;
 128
 129     for (w = 0; w < nwall; w++)
 130     {
 131         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 132         switch (ir->wall_type)
 133         {
 134             case ewt93:
 135                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 136                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 137                 break;
 138             case ewt104:
 139                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 140                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 141                 break;
 142             default:
 143                 break;
 144         }
 145         Fwall[w] = 0;
 146     }
 147     wall_z[0] = 0;
 148     wall_z[1] = box[ZZ][ZZ];
 149
 150     Vtot      = 0;
 151     dvdlambda = 0;
 152     clear_dvec(xf_z);
 153     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 154     {
 155         if (md->nPerturbed)
 156         {
 157             if (lam == 0)
 158             {
 159                 lamfac = 1 - lambda;
 160                 type   = md->typeA;
 161             }
 162             else
 163             {
 164                 lamfac = lambda;
 165                 type   = md->typeB;
 166             }
 167         }
 168         else
 169         {
 170             lamfac = 1;
 171             type   = md->typeA;
 172         }
 173         for (i = 0; i < md->homenr; i++)
 174         {
 175             for (w = 0; w < nwall; w++)
 176             {
 177                 /* The wall energy groups are always at the end of the list */
 178                 ggid = gid[i]*ngid + ngid - nwall + w;
 179                 at   = type[i];
 180                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 181                 Cd = nbfp[ntw[w]+2*at]/6.0;
 182                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 183                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 184                 {
 185                     if (w == 0)
 186                     {
 187                         r = x[i][ZZ];
 188                     }
 189                     else
 190                     {
 191                         r = wall_z[1] - x[i][ZZ];
 192                     }
 193                     if (r < ir->wall_r_linpot)
 194                     {
 195                         mr = ir->wall_r_linpot - r;
 196                         r  = ir->wall_r_linpot;
 197                     }
 198                     else
 199                     {
 200                         mr = 0;
 201                     }
 202                     switch (ir->wall_type)
 203                     {
 204                         case ewtTABLE:
 205                             if (r < 0)
 206                             {
 207                                 wall_error(i, x, r);
 208                             }
 209                             tab      = &(fr->wall_tab[w][gid[i]]);
 210                             tabscale = tab->scale;
 211                             VFtab    = tab->data;
 212
 213                             rt    = r*tabscale;
 214                             n0    = rt;
 215                             if (n0 >= tab->n)
 216                             {
 217                                 /* Beyond the table range, set V and F to zero */
 218                                 V     = 0;
 219                                 F     = 0;
 220                             }
 221                             else
 222                             {
 223                                 eps   = rt - n0;
 224                                 eps2  = eps*eps;
 225                                 /* Dispersion */
 226                                 nnn   = 8*n0;
 227                                 Yt    = VFtab[nnn];
 228                                 Ft    = VFtab[nnn+1];
 229                                 Geps  = VFtab[nnn+2]*eps;
 230                                 Heps2 = VFtab[nnn+3]*eps2;
 231                                 Fp    = Ft + Geps + Heps2;
 232                                 VV    = Yt + Fp*eps;
 233                                 FF    = Fp + Geps + 2.0*Heps2;
 234                                 Vd    = Cd*VV;
 235                                 Fd    = Cd*FF;
 236                                 /* Repulsion */
 237                                 nnn   = nnn + 4;
 238                                 Yt    = VFtab[nnn];
 239                                 Ft    = VFtab[nnn+1];
 240                                 Geps  = VFtab[nnn+2]*eps;
 241                                 Heps2 = VFtab[nnn+3]*eps2;
 242                                 Fp    = Ft + Geps + Heps2;
 243                                 VV    = Yt + Fp*eps;
 244                                 FF    = Fp + Geps + 2.0*Heps2;
 245                                 Vr    = Cr*VV;
 246                                 Fr    = Cr*FF;
 247                                 V     = Vd + Vr;
 248                                 F     = -lamfac*(Fd + Fr)*tabscale;
 249                             }
 250                             break;
 251                         case ewt93:
 252                             if (r <= 0)
 253                             {
 254                                 wall_error(i, x, r);
 255                             }
 256                             r1 = 1/r;
 257                             r2 = r1*r1;
 258                             r4 = r2*r2;
 259                             Vd = fac_d[w]*Cd*r2*r1;
 260                             Vr = fac_r[w]*Cr*r4*r4*r1;
 261                             V  = Vr - Vd;
 262                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 263                             break;
 264                         case ewt104:
 265                             if (r <= 0)
 266                             {
 267                                 wall_error(i, x, r);
 268                             }
 269                             r1 = 1/r;
 270                             r2 = r1*r1;
 271                             r4 = r2*r2;
 272                             Vd = fac_d[w]*Cd*r4;
 273                             Vr = fac_r[w]*Cr*r4*r4*r2;
 274                             V  = Vr - Vd;
 275                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 276                             break;
 277                         case ewt126:
 278                             if (r <= 0)
 279                             {
 280                                 wall_error(i, x, r);
 281                             }
 282                             r1 = 1/r;
 283                             r2 = r1*r1;
 284                             r4 = r2*r2;
 285                             Vd = Cd*r4*r2;
 286                             Vr = Cr*r4*r4*r4;
 287                             V  = Vr - Vd;
 288                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 289                             break;
 290                         default:
 291                             break;
 292                     }
 293                     if (mr > 0)
 294                     {
 295                         V += mr*F;
 296                     }
 297                     if (w == 1)
 298                     {
 299                         F = -F;
 300                     }
 301                     Vlj[ggid] += lamfac*V;
 302                     Vtot      += V;
 303                     f[i][ZZ]  += F;
 304                     /* Because of the single sum virial calculation we need
 305                      * to add  the full virial contribution of the walls.
 306                      * Since the force only has a z-component, there is only
 307                      * a contribution to the z component of the virial tensor.
 308                      * We could also determine the virial contribution directly,
 309                      * which would be cheaper here, but that would require extra
 310                      * communication for f_novirsum for with virtual sites
 311                      * in parallel.
 312                      */
 313                     xf_z[XX]  -= x[i][XX]*F;
 314                     xf_z[YY]  -= x[i][YY]*F;
 315                     xf_z[ZZ]  -= wall_z[w]*F;
 316                 }
 317             }
 318         }
 319         if (md->nPerturbed)
 320         {
 321             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 322         }
 323
 324         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 325     }
 326
 327     for (i = 0; i < DIM; i++)
 328     {
 329         fr->vir_wall_z[i] = -0.5*xf_z[i];
 330     }
 331
 332     return dvdlambda;
 333 }