src/gromacs/mdlib/wall.c

   1 /*  -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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   5  *
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  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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  14
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  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41 #include <string.h>
  42 #include "maths.h"
  43 #include "sysstuff.h"
  44 #include "typedefs.h"
  45 #include "macros.h"
  46 #include "smalloc.h"
  47 #include "force.h"
  48 #include "gromacs/fileio/filenm.h"
  49 #include "nrnb.h"
  50 #include "vec.h"
  51
  52 void make_wall_tables(FILE *fplog, const output_env_t oenv,
  53                       const t_inputrec *ir, const char *tabfn,
  54                       const gmx_groups_t *groups,
  55                       t_forcerec *fr)
  56 {
  57     int           w, negp_pp, egp, i, j;
  58     int          *nm_ind;
  59     char          buf[STRLEN];
  60     t_forcetable *tab;
  61
  62     negp_pp = ir->opts.ngener - ir->nwall;
  63     nm_ind  = groups->grps[egcENER].nm_ind;
  64
  65     if (fplog)
  66     {
  67         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  68                 negp_pp, ir->nwall);
  69     }
  70
  71     snew(fr->wall_tab, ir->nwall);
  72     for (w = 0; w < ir->nwall; w++)
  73     {
  74         snew(fr->wall_tab[w], negp_pp);
  75         for (egp = 0; egp < negp_pp; egp++)
  76         {
  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             {
  80                 tab = &fr->wall_tab[w][egp];
  81                 sprintf(buf, "%s", tabfn);
  82                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  83                         *groups->grpname[nm_ind[egp]],
  84                         *groups->grpname[nm_ind[negp_pp+w]],
  85                         ftp2ext(efXVG));
  86                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  87                 /* Since wall have no charge, we can compress the table */
  88                 for (i = 0; i <= tab->n; i++)
  89                 {
  90                     for (j = 0; j < 8; j++)
  91                     {
  92                         tab->data[8*i+j] = tab->data[12*i+4+j];
  93                     }
  94                 }
  95             }
  96         }
  97     }
  98 }
  99
 100 static void wall_error(int a, rvec *x, real r)
 101 {
 102     gmx_fatal(FARGS,
 103               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 104               "You might want to use the mdp option wall_r_linpot",
 105               x[a][XX], x[a][YY], x[a][ZZ], r);
 106 }
 107
 108 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 109               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 110 {
 111     int             nwall, w, lam, i;
 112     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 113     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 114     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 115     dvec            xf_z;
 116     int             n0, nnn;
 117     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 118     unsigned short *gid = md->cENER;
 119     t_forcetable   *tab;
 120
 121     nwall     = ir->nwall;
 122     ngid      = ir->opts.ngener;
 123     ntype     = fr->ntype;
 124     nbfp      = fr->nbfp;
 125     egp_flags = fr->egp_flags;
 126
 127     for (w = 0; w < nwall; w++)
 128     {
 129         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 130         switch (ir->wall_type)
 131         {
 132             case ewt93:
 133                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 134                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 135                 break;
 136             case ewt104:
 137                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 138                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 139                 break;
 140             default:
 141                 break;
 142         }
 143         Fwall[w] = 0;
 144     }
 145     wall_z[0] = 0;
 146     wall_z[1] = box[ZZ][ZZ];
 147
 148     Vtot      = 0;
 149     dvdlambda = 0;
 150     clear_dvec(xf_z);
 151     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 152     {
 153         if (md->nPerturbed)
 154         {
 155             if (lam == 0)
 156             {
 157                 lamfac = 1 - lambda;
 158                 type   = md->typeA;
 159             }
 160             else
 161             {
 162                 lamfac = 0;
 163                 type   = md->typeB;
 164             }
 165         }
 166         else
 167         {
 168             lamfac = 1;
 169             type   = md->typeA;
 170         }
 171         for (i = md->start; i < md->start+md->homenr; i++)
 172         {
 173             for (w = 0; w < nwall; w++)
 174             {
 175                 /* The wall energy groups are always at the end of the list */
 176                 ggid = gid[i]*ngid + ngid - nwall + w;
 177                 at   = type[i];
 178                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 179                 Cd = nbfp[ntw[w]+2*at]/6.0;
 180                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 181                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 182                 {
 183                     if (w == 0)
 184                     {
 185                         r = x[i][ZZ];
 186                     }
 187                     else
 188                     {
 189                         r = wall_z[1] - x[i][ZZ];
 190                     }
 191                     if (r < ir->wall_r_linpot)
 192                     {
 193                         mr = ir->wall_r_linpot - r;
 194                         r  = ir->wall_r_linpot;
 195                     }
 196                     else
 197                     {
 198                         mr = 0;
 199                     }
 200                     switch (ir->wall_type)
 201                     {
 202                         case ewtTABLE:
 203                             if (r < 0)
 204                             {
 205                                 wall_error(i, x, r);
 206                             }
 207                             tab      = &(fr->wall_tab[w][gid[i]]);
 208                             tabscale = tab->scale;
 209                             VFtab    = tab->data;
 210
 211                             rt    = r*tabscale;
 212                             n0    = rt;
 213                             if (n0 >= tab->n)
 214                             {
 215                                 /* Beyond the table range, set V and F to zero */
 216                                 V     = 0;
 217                                 F     = 0;
 218                             }
 219                             else
 220                             {
 221                                 eps   = rt - n0;
 222                                 eps2  = eps*eps;
 223                                 /* Dispersion */
 224                                 nnn   = 8*n0;
 225                                 Yt    = VFtab[nnn];
 226                                 Ft    = VFtab[nnn+1];
 227                                 Geps  = VFtab[nnn+2]*eps;
 228                                 Heps2 = VFtab[nnn+3]*eps2;
 229                                 Fp    = Ft + Geps + Heps2;
 230                                 VV    = Yt + Fp*eps;
 231                                 FF    = Fp + Geps + 2.0*Heps2;
 232                                 Vd    = Cd*VV;
 233                                 Fd    = Cd*FF;
 234                                 /* Repulsion */
 235                                 nnn   = nnn + 4;
 236                                 Yt    = VFtab[nnn];
 237                                 Ft    = VFtab[nnn+1];
 238                                 Geps  = VFtab[nnn+2]*eps;
 239                                 Heps2 = VFtab[nnn+3]*eps2;
 240                                 Fp    = Ft + Geps + Heps2;
 241                                 VV    = Yt + Fp*eps;
 242                                 FF    = Fp + Geps + 2.0*Heps2;
 243                                 Vr    = Cr*VV;
 244                                 Fr    = Cr*FF;
 245                                 V     = Vd + Vr;
 246                                 F     = -lamfac*(Fd + Fr)*tabscale;
 247                             }
 248                             break;
 249                         case ewt93:
 250                             if (r <= 0)
 251                             {
 252                                 wall_error(i, x, r);
 253                             }
 254                             r1 = 1/r;
 255                             r2 = r1*r1;
 256                             r4 = r2*r2;
 257                             Vd = fac_d[w]*Cd*r2*r1;
 258                             Vr = fac_r[w]*Cr*r4*r4*r1;
 259                             V  = Vr - Vd;
 260                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 261                             break;
 262                         case ewt104:
 263                             if (r <= 0)
 264                             {
 265                                 wall_error(i, x, r);
 266                             }
 267                             r1 = 1/r;
 268                             r2 = r1*r1;
 269                             r4 = r2*r2;
 270                             Vd = fac_d[w]*Cd*r4;
 271                             Vr = fac_r[w]*Cr*r4*r4*r2;
 272                             V  = Vr - Vd;
 273                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 274                             break;
 275                         case ewt126:
 276                             if (r <= 0)
 277                             {
 278                                 wall_error(i, x, r);
 279                             }
 280                             r1 = 1/r;
 281                             r2 = r1*r1;
 282                             r4 = r2*r2;
 283                             Vd = Cd*r4*r2;
 284                             Vr = Cr*r4*r4*r4;
 285                             V  = Vr - Vd;
 286                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 287                             break;
 288                         default:
 289                             break;
 290                     }
 291                     if (mr > 0)
 292                     {
 293                         V += mr*F;
 294                     }
 295                     if (w == 1)
 296                     {
 297                         F = -F;
 298                     }
 299                     Vlj[ggid] += lamfac*V;
 300                     Vtot      += V;
 301                     f[i][ZZ]  += F;
 302                     /* Because of the single sum virial calculation we need
 303                      * to add  the full virial contribution of the walls.
 304                      * Since the force only has a z-component, there is only
 305                      * a contribution to the z component of the virial tensor.
 306                      * We could also determine the virial contribution directly,
 307                      * which would be cheaper here, but that would require extra
 308                      * communication for f_novirsum for with virtual sites
 309                      * in parallel.
 310                      */
 311                     xf_z[XX]  -= x[i][XX]*F;
 312                     xf_z[YY]  -= x[i][YY]*F;
 313                     xf_z[ZZ]  -= wall_z[w]*F;
 314                 }
 315             }
 316         }
 317         if (md->nPerturbed)
 318         {
 319             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 320         }
 321
 322         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 323     }
 324
 325     for (i = 0; i < DIM; i++)
 326     {
 327         fr->vir_wall_z[i] = -0.5*xf_z[i];
 328     }
 329
 330     return dvdlambda;
 331 }