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,
   8  * and including many others, as listed in the AUTHORS file in the
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  37
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43 #include <string.h>
  44
  45 #include "sysstuff.h"
  46 #include "typedefs.h"
  47 #include "macros.h"
  48 #include "force.h"
  49 #include "nrnb.h"
  50 #include "vec.h"
  51
  52 #include "gromacs/fileio/filenm.h"
  53 #include "gromacs/math/utilities.h"
  54 #include "gromacs/utility/cstringutil.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 void make_wall_tables(FILE *fplog, const output_env_t oenv,
  58                       const t_inputrec *ir, const char *tabfn,
  59                       const gmx_groups_t *groups,
  60                       t_forcerec *fr)
  61 {
  62     int           w, negp_pp, egp, i, j;
  63     int          *nm_ind;
  64     char          buf[STRLEN];
  65     t_forcetable *tab;
  66
  67     negp_pp = ir->opts.ngener - ir->nwall;
  68     nm_ind  = groups->grps[egcENER].nm_ind;
  69
  70     if (fplog)
  71     {
  72         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  73                 negp_pp, ir->nwall);
  74     }
  75
  76     snew(fr->wall_tab, ir->nwall);
  77     for (w = 0; w < ir->nwall; w++)
  78     {
  79         snew(fr->wall_tab[w], negp_pp);
  80         for (egp = 0; egp < negp_pp; egp++)
  81         {
  82             /* If the energy group pair is excluded, we don't need a table */
  83             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  84             {
  85                 tab = &fr->wall_tab[w][egp];
  86                 sprintf(buf, "%s", tabfn);
  87                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  88                         *groups->grpname[nm_ind[egp]],
  89                         *groups->grpname[nm_ind[negp_pp+w]],
  90                         ftp2ext(efXVG));
  91                 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
  92                 /* Since wall have no charge, we can compress the table */
  93                 for (i = 0; i <= tab->n; i++)
  94                 {
  95                     for (j = 0; j < 8; j++)
  96                     {
  97                         tab->data[8*i+j] = tab->data[12*i+4+j];
  98                     }
  99                 }
 100             }
 101         }
 102     }
 103 }
 104
 105 static void wall_error(int a, rvec *x, real r)
 106 {
 107     gmx_fatal(FARGS,
 108               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 109               "You might want to use the mdp option wall_r_linpot",
 110               x[a][XX], x[a][YY], x[a][ZZ], r);
 111 }
 112
 113 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 114               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 115 {
 116     int             nwall, w, lam, i;
 117     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 118     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
 119     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 120     dvec            xf_z;
 121     int             n0, nnn;
 122     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
 123     unsigned short *gid = md->cENER;
 124     t_forcetable   *tab;
 125
 126     nwall     = ir->nwall;
 127     ngid      = ir->opts.ngener;
 128     ntype     = fr->ntype;
 129     nbfp      = fr->nbfp;
 130     egp_flags = fr->egp_flags;
 131
 132     for (w = 0; w < nwall; w++)
 133     {
 134         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 135         switch (ir->wall_type)
 136         {
 137             case ewt93:
 138                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 139                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 140                 break;
 141             case ewt104:
 142                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 143                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 144                 break;
 145             default:
 146                 break;
 147         }
 148         Fwall[w] = 0;
 149     }
 150     wall_z[0] = 0;
 151     wall_z[1] = box[ZZ][ZZ];
 152
 153     Vtot      = 0;
 154     dvdlambda = 0;
 155     clear_dvec(xf_z);
 156     for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 157     {
 158         if (md->nPerturbed)
 159         {
 160             if (lam == 0)
 161             {
 162                 lamfac = 1 - lambda;
 163                 type   = md->typeA;
 164             }
 165             else
 166             {
 167                 lamfac = 0;
 168                 type   = md->typeB;
 169             }
 170         }
 171         else
 172         {
 173             lamfac = 1;
 174             type   = md->typeA;
 175         }
 176         for (i = 0; i < md->homenr; i++)
 177         {
 178             for (w = 0; w < nwall; w++)
 179             {
 180                 /* The wall energy groups are always at the end of the list */
 181                 ggid = gid[i]*ngid + ngid - nwall + w;
 182                 at   = type[i];
 183                 /* nbfp now includes the 6.0/12.0 derivative prefactors */
 184                 Cd = nbfp[ntw[w]+2*at]/6.0;
 185                 Cr = nbfp[ntw[w]+2*at+1]/12.0;
 186                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 187                 {
 188                     if (w == 0)
 189                     {
 190                         r = x[i][ZZ];
 191                     }
 192                     else
 193                     {
 194                         r = wall_z[1] - x[i][ZZ];
 195                     }
 196                     if (r < ir->wall_r_linpot)
 197                     {
 198                         mr = ir->wall_r_linpot - r;
 199                         r  = ir->wall_r_linpot;
 200                     }
 201                     else
 202                     {
 203                         mr = 0;
 204                     }
 205                     switch (ir->wall_type)
 206                     {
 207                         case ewtTABLE:
 208                             if (r < 0)
 209                             {
 210                                 wall_error(i, x, r);
 211                             }
 212                             tab      = &(fr->wall_tab[w][gid[i]]);
 213                             tabscale = tab->scale;
 214                             VFtab    = tab->data;
 215
 216                             rt    = r*tabscale;
 217                             n0    = rt;
 218                             if (n0 >= tab->n)
 219                             {
 220                                 /* Beyond the table range, set V and F to zero */
 221                                 V     = 0;
 222                                 F     = 0;
 223                             }
 224                             else
 225                             {
 226                                 eps   = rt - n0;
 227                                 eps2  = eps*eps;
 228                                 /* Dispersion */
 229                                 nnn   = 8*n0;
 230                                 Yt    = VFtab[nnn];
 231                                 Ft    = VFtab[nnn+1];
 232                                 Geps  = VFtab[nnn+2]*eps;
 233                                 Heps2 = VFtab[nnn+3]*eps2;
 234                                 Fp    = Ft + Geps + Heps2;
 235                                 VV    = Yt + Fp*eps;
 236                                 FF    = Fp + Geps + 2.0*Heps2;
 237                                 Vd    = Cd*VV;
 238                                 Fd    = Cd*FF;
 239                                 /* Repulsion */
 240                                 nnn   = nnn + 4;
 241                                 Yt    = VFtab[nnn];
 242                                 Ft    = VFtab[nnn+1];
 243                                 Geps  = VFtab[nnn+2]*eps;
 244                                 Heps2 = VFtab[nnn+3]*eps2;
 245                                 Fp    = Ft + Geps + Heps2;
 246                                 VV    = Yt + Fp*eps;
 247                                 FF    = Fp + Geps + 2.0*Heps2;
 248                                 Vr    = Cr*VV;
 249                                 Fr    = Cr*FF;
 250                                 V     = Vd + Vr;
 251                                 F     = -lamfac*(Fd + Fr)*tabscale;
 252                             }
 253                             break;
 254                         case ewt93:
 255                             if (r <= 0)
 256                             {
 257                                 wall_error(i, x, r);
 258                             }
 259                             r1 = 1/r;
 260                             r2 = r1*r1;
 261                             r4 = r2*r2;
 262                             Vd = fac_d[w]*Cd*r2*r1;
 263                             Vr = fac_r[w]*Cr*r4*r4*r1;
 264                             V  = Vr - Vd;
 265                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 266                             break;
 267                         case ewt104:
 268                             if (r <= 0)
 269                             {
 270                                 wall_error(i, x, r);
 271                             }
 272                             r1 = 1/r;
 273                             r2 = r1*r1;
 274                             r4 = r2*r2;
 275                             Vd = fac_d[w]*Cd*r4;
 276                             Vr = fac_r[w]*Cr*r4*r4*r2;
 277                             V  = Vr - Vd;
 278                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 279                             break;
 280                         case ewt126:
 281                             if (r <= 0)
 282                             {
 283                                 wall_error(i, x, r);
 284                             }
 285                             r1 = 1/r;
 286                             r2 = r1*r1;
 287                             r4 = r2*r2;
 288                             Vd = Cd*r4*r2;
 289                             Vr = Cr*r4*r4*r4;
 290                             V  = Vr - Vd;
 291                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 292                             break;
 293                         default:
 294                             break;
 295                     }
 296                     if (mr > 0)
 297                     {
 298                         V += mr*F;
 299                     }
 300                     if (w == 1)
 301                     {
 302                         F = -F;
 303                     }
 304                     Vlj[ggid] += lamfac*V;
 305                     Vtot      += V;
 306                     f[i][ZZ]  += F;
 307                     /* Because of the single sum virial calculation we need
 308                      * to add  the full virial contribution of the walls.
 309                      * Since the force only has a z-component, there is only
 310                      * a contribution to the z component of the virial tensor.
 311                      * We could also determine the virial contribution directly,
 312                      * which would be cheaper here, but that would require extra
 313                      * communication for f_novirsum for with virtual sites
 314                      * in parallel.
 315                      */
 316                     xf_z[XX]  -= x[i][XX]*F;
 317                     xf_z[YY]  -= x[i][YY]*F;
 318                     xf_z[ZZ]  -= wall_z[w]*F;
 319                 }
 320             }
 321         }
 322         if (md->nPerturbed)
 323         {
 324             dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
 325         }
 326
 327         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 328     }
 329
 330     for (i = 0; i < DIM; i++)
 331     {
 332         fr->vir_wall_z[i] = -0.5*xf_z[i];
 333     }
 334
 335     return dvdlambda;
 336 }