src/gromacs/mdlib/wall.c

   1 /*
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   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   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,
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  37
  38 #include "gmxpre.h"
  39
  40 #include <math.h>
  41 #include <string.h>
  42
  43 #include "gromacs/fileio/filenm.h"
  44 #include "gromacs/legacyheaders/force.h"
  45 #include "gromacs/legacyheaders/macros.h"
  46 #include "gromacs/legacyheaders/nrnb.h"
  47 #include "gromacs/legacyheaders/typedefs.h"
  48 #include "gromacs/math/utilities.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 void make_wall_tables(FILE *fplog, const output_env_t oenv,
  54                       const t_inputrec *ir, const char *tabfn,
  55                       const gmx_groups_t *groups,
  56                       t_forcerec *fr)
  57 {
  58     int           w, negp_pp, egp, i, j;
  59     int          *nm_ind;
  60     char          buf[STRLEN];
  61     t_forcetable *tab;
  62
  63     negp_pp = ir->opts.ngener - ir->nwall;
  64     nm_ind  = groups->grps[egcENER].nm_ind;
  65
  66     if (fplog)
  67     {
  68         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  69                 negp_pp, ir->nwall);
  70     }
  71
  72     snew(fr->wall_tab, ir->nwall);
  73     for (w = 0; w < ir->nwall; w++)
  74     {
  75         snew(fr->wall_tab[w], negp_pp);
  76         for (egp = 0; egp < negp_pp; egp++)
  77         {
  78             /* If the energy group pair is excluded, we don't need a table */
  79             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  80             {
  81                 tab = &fr->wall_tab[w][egp];
  82                 sprintf(buf, "%s", tabfn);
  83                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  84                         *groups->grpname[nm_ind[egp]],
  85                         *groups->grpname[nm_ind[negp_pp+w]],
  86                         ftp2ext(efXVG));
  87                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  88                 /* Since wall have no charge, we can compress the table */
  89                 for (i = 0; i <= tab->n; i++)
  90                 {
  91                     for (j = 0; j < 8; j++)
  92                     {
  93                         tab->data[8*i+j] = tab->data[12*i+4+j];
  94                     }
  95                 }
  96             }
  97         }
  98     }
  99 }
 100
 101 static void wall_error(int a, rvec *x, real r)
 102 {
 103     gmx_fatal(FARGS,
 104               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 105               "You might want to use the mdp option wall_r_linpot",
 106               x[a][XX], x[a][YY], x[a][ZZ], r);
 107 }
 108
 109 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 110               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 111 {
 112     int             nwall, w, lam, i;
 113     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 114     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 115     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 116     dvec            xf_z;
 117     int             n0, nnn;
 118     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 119     unsigned short *gid = md->cENER;
 120     t_forcetable   *tab;
 121
 122     nwall     = ir->nwall;
 123     ngid      = ir->opts.ngener;
 124     ntype     = fr->ntype;
 125     nbfp      = fr->nbfp;
 126     egp_flags = fr->egp_flags;
 127
 128     for (w = 0; w < nwall; w++)
 129     {
 130         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 131         switch (ir->wall_type)
 132         {
 133             case ewt93:
 134                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 135                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 136                 break;
 137             case ewt104:
 138                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 139                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 140                 break;
 141             default:
 142                 break;
 143         }
 144         Fwall[w] = 0;
 145     }
 146     wall_z[0] = 0;
 147     wall_z[1] = box[ZZ][ZZ];
 148
 149     Vtot      = 0;
 150     dvdlambda = 0;
 151     clear_dvec(xf_z);
 152     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 153     {
 154         if (md->nPerturbed)
 155         {
 156             if (lam == 0)
 157             {
 158                 lamfac = 1 - lambda;
 159                 type   = md->typeA;
 160             }
 161             else
 162             {
 163                 lamfac = lambda;
 164                 type   = md->typeB;
 165             }
 166         }
 167         else
 168         {
 169             lamfac = 1;
 170             type   = md->typeA;
 171         }
 172         for (i = 0; i < md->homenr; i++)
 173         {
 174             for (w = 0; w < nwall; w++)
 175             {
 176                 /* The wall energy groups are always at the end of the list */
 177                 ggid = gid[i]*ngid + ngid - nwall + w;
 178                 at   = type[i];
 179                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 180                 Cd = nbfp[ntw[w]+2*at]/6.0;
 181                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 182                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 183                 {
 184                     if (w == 0)
 185                     {
 186                         r = x[i][ZZ];
 187                     }
 188                     else
 189                     {
 190                         r = wall_z[1] - x[i][ZZ];
 191                     }
 192                     if (r < ir->wall_r_linpot)
 193                     {
 194                         mr = ir->wall_r_linpot - r;
 195                         r  = ir->wall_r_linpot;
 196                     }
 197                     else
 198                     {
 199                         mr = 0;
 200                     }
 201                     switch (ir->wall_type)
 202                     {
 203                         case ewtTABLE:
 204                             if (r < 0)
 205                             {
 206                                 wall_error(i, x, r);
 207                             }
 208                             tab      = &(fr->wall_tab[w][gid[i]]);
 209                             tabscale = tab->scale;
 210                             VFtab    = tab->data;
 211
 212                             rt    = r*tabscale;
 213                             n0    = rt;
 214                             if (n0 >= tab->n)
 215                             {
 216                                 /* Beyond the table range, set V and F to zero */
 217                                 V     = 0;
 218                                 F     = 0;
 219                             }
 220                             else
 221                             {
 222                                 eps   = rt - n0;
 223                                 eps2  = eps*eps;
 224                                 /* Dispersion */
 225                                 nnn   = 8*n0;
 226                                 Yt    = VFtab[nnn];
 227                                 Ft    = VFtab[nnn+1];
 228                                 Geps  = VFtab[nnn+2]*eps;
 229                                 Heps2 = VFtab[nnn+3]*eps2;
 230                                 Fp    = Ft + Geps + Heps2;
 231                                 VV    = Yt + Fp*eps;
 232                                 FF    = Fp + Geps + 2.0*Heps2;
 233                                 Vd    = Cd*VV;
 234                                 Fd    = Cd*FF;
 235                                 /* Repulsion */
 236                                 nnn   = nnn + 4;
 237                                 Yt    = VFtab[nnn];
 238                                 Ft    = VFtab[nnn+1];
 239                                 Geps  = VFtab[nnn+2]*eps;
 240                                 Heps2 = VFtab[nnn+3]*eps2;
 241                                 Fp    = Ft + Geps + Heps2;
 242                                 VV    = Yt + Fp*eps;
 243                                 FF    = Fp + Geps + 2.0*Heps2;
 244                                 Vr    = Cr*VV;
 245                                 Fr    = Cr*FF;
 246                                 V     = Vd + Vr;
 247                                 F     = -lamfac*(Fd + Fr)*tabscale;
 248                             }
 249                             break;
 250                         case ewt93:
 251                             if (r <= 0)
 252                             {
 253                                 wall_error(i, x, r);
 254                             }
 255                             r1 = 1/r;
 256                             r2 = r1*r1;
 257                             r4 = r2*r2;
 258                             Vd = fac_d[w]*Cd*r2*r1;
 259                             Vr = fac_r[w]*Cr*r4*r4*r1;
 260                             V  = Vr - Vd;
 261                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 262                             break;
 263                         case ewt104:
 264                             if (r <= 0)
 265                             {
 266                                 wall_error(i, x, r);
 267                             }
 268                             r1 = 1/r;
 269                             r2 = r1*r1;
 270                             r4 = r2*r2;
 271                             Vd = fac_d[w]*Cd*r4;
 272                             Vr = fac_r[w]*Cr*r4*r4*r2;
 273                             V  = Vr - Vd;
 274                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 275                             break;
 276                         case ewt126:
 277                             if (r <= 0)
 278                             {
 279                                 wall_error(i, x, r);
 280                             }
 281                             r1 = 1/r;
 282                             r2 = r1*r1;
 283                             r4 = r2*r2;
 284                             Vd = Cd*r4*r2;
 285                             Vr = Cr*r4*r4*r4;
 286                             V  = Vr - Vd;
 287                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 288                             break;
 289                         default:
 290                             break;
 291                     }
 292                     if (mr > 0)
 293                     {
 294                         V += mr*F;
 295                     }
 296                     if (w == 1)
 297                     {
 298                         F = -F;
 299                     }
 300                     Vlj[ggid] += lamfac*V;
 301                     Vtot      += V;
 302                     f[i][ZZ]  += F;
 303                     /* Because of the single sum virial calculation we need
 304                      * to add  the full virial contribution of the walls.
 305                      * Since the force only has a z-component, there is only
 306                      * a contribution to the z component of the virial tensor.
 307                      * We could also determine the virial contribution directly,
 308                      * which would be cheaper here, but that would require extra
 309                      * communication for f_novirsum for with virtual sites
 310                      * in parallel.
 311                      */
 312                     xf_z[XX]  -= x[i][XX]*F;
 313                     xf_z[YY]  -= x[i][YY]*F;
 314                     xf_z[ZZ]  -= wall_z[w]*F;
 315                 }
 316             }
 317         }
 318         if (md->nPerturbed)
 319         {
 320             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 321         }
 322
 323         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 324     }
 325
 326     for (i = 0; i < DIM; i++)
 327     {
 328         fr->vir_wall_z[i] = -0.5*xf_z[i];
 329     }
 330
 331     return dvdlambda;
 332 }