src/gromacs/mdlib/wall.c

   1 /*
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   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37
  38 #include "gmxpre.h"
  39
  40 #include "config.h"
  41
  42 #include <math.h>
  43 #include <string.h>
  44
  45 #include "gromacs/legacyheaders/typedefs.h"
  46 #include "gromacs/legacyheaders/macros.h"
  47 #include "gromacs/legacyheaders/force.h"
  48 #include "gromacs/legacyheaders/nrnb.h"
  49 #include "gromacs/math/vec.h"
  50
  51 #include "gromacs/fileio/filenm.h"
  52 #include "gromacs/math/utilities.h"
  53 #include "gromacs/utility/cstringutil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 void make_wall_tables(FILE *fplog, const output_env_t oenv,
  57                       const t_inputrec *ir, const char *tabfn,
  58                       const gmx_groups_t *groups,
  59                       t_forcerec *fr)
  60 {
  61     int           w, negp_pp, egp, i, j;
  62     int          *nm_ind;
  63     char          buf[STRLEN];
  64     t_forcetable *tab;
  65
  66     negp_pp = ir->opts.ngener - ir->nwall;
  67     nm_ind  = groups->grps[egcENER].nm_ind;
  68
  69     if (fplog)
  70     {
  71         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  72                 negp_pp, ir->nwall);
  73     }
  74
  75     snew(fr->wall_tab, ir->nwall);
  76     for (w = 0; w < ir->nwall; w++)
  77     {
  78         snew(fr->wall_tab[w], negp_pp);
  79         for (egp = 0; egp < negp_pp; egp++)
  80         {
  81             /* If the energy group pair is excluded, we don't need a table */
  82             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  83             {
  84                 tab = &fr->wall_tab[w][egp];
  85                 sprintf(buf, "%s", tabfn);
  86                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  87                         *groups->grpname[nm_ind[egp]],
  88                         *groups->grpname[nm_ind[negp_pp+w]],
  89                         ftp2ext(efXVG));
  90                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  91                 /* Since wall have no charge, we can compress the table */
  92                 for (i = 0; i <= tab->n; i++)
  93                 {
  94                     for (j = 0; j < 8; j++)
  95                     {
  96                         tab->data[8*i+j] = tab->data[12*i+4+j];
  97                     }
  98                 }
  99             }
 100         }
 101     }
 102 }
 103
 104 static void wall_error(int a, rvec *x, real r)
 105 {
 106     gmx_fatal(FARGS,
 107               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 108               "You might want to use the mdp option wall_r_linpot",
 109               x[a][XX], x[a][YY], x[a][ZZ], r);
 110 }
 111
 112 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 113               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 114 {
 115     int             nwall, w, lam, i;
 116     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 117     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 118     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 119     dvec            xf_z;
 120     int             n0, nnn;
 121     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 122     unsigned short *gid = md->cENER;
 123     t_forcetable   *tab;
 124
 125     nwall     = ir->nwall;
 126     ngid      = ir->opts.ngener;
 127     ntype     = fr->ntype;
 128     nbfp      = fr->nbfp;
 129     egp_flags = fr->egp_flags;
 130
 131     for (w = 0; w < nwall; w++)
 132     {
 133         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 134         switch (ir->wall_type)
 135         {
 136             case ewt93:
 137                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 138                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 139                 break;
 140             case ewt104:
 141                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 142                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 143                 break;
 144             default:
 145                 break;
 146         }
 147         Fwall[w] = 0;
 148     }
 149     wall_z[0] = 0;
 150     wall_z[1] = box[ZZ][ZZ];
 151
 152     Vtot      = 0;
 153     dvdlambda = 0;
 154     clear_dvec(xf_z);
 155     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 156     {
 157         if (md->nPerturbed)
 158         {
 159             if (lam == 0)
 160             {
 161                 lamfac = 1 - lambda;
 162                 type   = md->typeA;
 163             }
 164             else
 165             {
 166                 lamfac = lambda;
 167                 type   = md->typeB;
 168             }
 169         }
 170         else
 171         {
 172             lamfac = 1;
 173             type   = md->typeA;
 174         }
 175         for (i = 0; i < md->homenr; i++)
 176         {
 177             for (w = 0; w < nwall; w++)
 178             {
 179                 /* The wall energy groups are always at the end of the list */
 180                 ggid = gid[i]*ngid + ngid - nwall + w;
 181                 at   = type[i];
 182                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 183                 Cd = nbfp[ntw[w]+2*at]/6.0;
 184                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 185                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 186                 {
 187                     if (w == 0)
 188                     {
 189                         r = x[i][ZZ];
 190                     }
 191                     else
 192                     {
 193                         r = wall_z[1] - x[i][ZZ];
 194                     }
 195                     if (r < ir->wall_r_linpot)
 196                     {
 197                         mr = ir->wall_r_linpot - r;
 198                         r  = ir->wall_r_linpot;
 199                     }
 200                     else
 201                     {
 202                         mr = 0;
 203                     }
 204                     switch (ir->wall_type)
 205                     {
 206                         case ewtTABLE:
 207                             if (r < 0)
 208                             {
 209                                 wall_error(i, x, r);
 210                             }
 211                             tab      = &(fr->wall_tab[w][gid[i]]);
 212                             tabscale = tab->scale;
 213                             VFtab    = tab->data;
 214
 215                             rt    = r*tabscale;
 216                             n0    = rt;
 217                             if (n0 >= tab->n)
 218                             {
 219                                 /* Beyond the table range, set V and F to zero */
 220                                 V     = 0;
 221                                 F     = 0;
 222                             }
 223                             else
 224                             {
 225                                 eps   = rt - n0;
 226                                 eps2  = eps*eps;
 227                                 /* Dispersion */
 228                                 nnn   = 8*n0;
 229                                 Yt    = VFtab[nnn];
 230                                 Ft    = VFtab[nnn+1];
 231                                 Geps  = VFtab[nnn+2]*eps;
 232                                 Heps2 = VFtab[nnn+3]*eps2;
 233                                 Fp    = Ft + Geps + Heps2;
 234                                 VV    = Yt + Fp*eps;
 235                                 FF    = Fp + Geps + 2.0*Heps2;
 236                                 Vd    = Cd*VV;
 237                                 Fd    = Cd*FF;
 238                                 /* Repulsion */
 239                                 nnn   = nnn + 4;
 240                                 Yt    = VFtab[nnn];
 241                                 Ft    = VFtab[nnn+1];
 242                                 Geps  = VFtab[nnn+2]*eps;
 243                                 Heps2 = VFtab[nnn+3]*eps2;
 244                                 Fp    = Ft + Geps + Heps2;
 245                                 VV    = Yt + Fp*eps;
 246                                 FF    = Fp + Geps + 2.0*Heps2;
 247                                 Vr    = Cr*VV;
 248                                 Fr    = Cr*FF;
 249                                 V     = Vd + Vr;
 250                                 F     = -lamfac*(Fd + Fr)*tabscale;
 251                             }
 252                             break;
 253                         case ewt93:
 254                             if (r <= 0)
 255                             {
 256                                 wall_error(i, x, r);
 257                             }
 258                             r1 = 1/r;
 259                             r2 = r1*r1;
 260                             r4 = r2*r2;
 261                             Vd = fac_d[w]*Cd*r2*r1;
 262                             Vr = fac_r[w]*Cr*r4*r4*r1;
 263                             V  = Vr - Vd;
 264                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 265                             break;
 266                         case ewt104:
 267                             if (r <= 0)
 268                             {
 269                                 wall_error(i, x, r);
 270                             }
 271                             r1 = 1/r;
 272                             r2 = r1*r1;
 273                             r4 = r2*r2;
 274                             Vd = fac_d[w]*Cd*r4;
 275                             Vr = fac_r[w]*Cr*r4*r4*r2;
 276                             V  = Vr - Vd;
 277                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 278                             break;
 279                         case ewt126:
 280                             if (r <= 0)
 281                             {
 282                                 wall_error(i, x, r);
 283                             }
 284                             r1 = 1/r;
 285                             r2 = r1*r1;
 286                             r4 = r2*r2;
 287                             Vd = Cd*r4*r2;
 288                             Vr = Cr*r4*r4*r4;
 289                             V  = Vr - Vd;
 290                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 291                             break;
 292                         default:
 293                             break;
 294                     }
 295                     if (mr > 0)
 296                     {
 297                         V += mr*F;
 298                     }
 299                     if (w == 1)
 300                     {
 301                         F = -F;
 302                     }
 303                     Vlj[ggid] += lamfac*V;
 304                     Vtot      += V;
 305                     f[i][ZZ]  += F;
 306                     /* Because of the single sum virial calculation we need
 307                      * to add  the full virial contribution of the walls.
 308                      * Since the force only has a z-component, there is only
 309                      * a contribution to the z component of the virial tensor.
 310                      * We could also determine the virial contribution directly,
 311                      * which would be cheaper here, but that would require extra
 312                      * communication for f_novirsum for with virtual sites
 313                      * in parallel.
 314                      */
 315                     xf_z[XX]  -= x[i][XX]*F;
 316                     xf_z[YY]  -= x[i][YY]*F;
 317                     xf_z[ZZ]  -= wall_z[w]*F;
 318                 }
 319             }
 320         }
 321         if (md->nPerturbed)
 322         {
 323             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 324         }
 325
 326         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 327     }
 328
 329     for (i = 0; i < DIM; i++)
 330     {
 331         fr->vir_wall_z[i] = -0.5*xf_z[i];
 332     }
 333
 334     return dvdlambda;
 335 }