src/gromacs/mdlib/wall.cpp

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  37
  38 #include "gmxpre.h"
  39
  40 #include <string.h>
  41
  42 #include <algorithm>
  43
  44 #include "gromacs/fileio/filetypes.h"
  45 #include "gromacs/gmxlib/nrnb.h"
  46 #include "gromacs/math/utilities.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/mdlib/force.h"
  49 #include "gromacs/mdtypes/inputrec.h"
  50 #include "gromacs/mdtypes/md_enums.h"
  51 #include "gromacs/mdtypes/mdatom.h"
  52 #include "gromacs/mdtypes/nblist.h"
  53 #include "gromacs/tables/forcetable.h"
  54 #include "gromacs/topology/topology.h"
  55 #include "gromacs/utility/cstringutil.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 void make_wall_tables(FILE *fplog,
  60                       const t_inputrec *ir, const char *tabfn,
  61                       const gmx_groups_t *groups,
  62                       t_forcerec *fr)
  63 {
  64     int           negp_pp;
  65     int          *nm_ind;
  66     char          buf[STRLEN];
  67
  68     negp_pp = ir->opts.ngener - ir->nwall;
  69     nm_ind  = groups->grps[egcENER].nm_ind;
  70
  71     if (fplog)
  72     {
  73         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  74                 negp_pp, ir->nwall);
  75     }
  76
  77     snew(fr->wall_tab, ir->nwall);
  78     for (int w = 0; w < ir->nwall; w++)
  79     {
  80         snew(fr->wall_tab[w], negp_pp);
  81         for (int egp = 0; egp < negp_pp; egp++)
  82         {
  83             /* If the energy group pair is excluded, we don't need a table */
  84             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  85             {
  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                 fr->wall_tab[w][egp] = make_tables(fplog, fr->ic, buf, 0,
  92                                                    GMX_MAKETABLES_FORCEUSER);
  93
  94                 /* Since wall have no charge, we can compress the table */
  95                 for (int i = 0; i <= fr->wall_tab[w][egp]->n; i++)
  96                 {
  97                     for (int j = 0; j < 8; j++)
  98                     {
  99                         fr->wall_tab[w][egp]->data[8*i+j] =
 100                             fr->wall_tab[w][egp]->data[12*i+4+j];
 101                     }
 102                 }
 103             }
 104         }
 105     }
 106 }
 107
 108 static void wall_error(int a, const rvec *x, real r)
 109 {
 110     gmx_fatal(FARGS,
 111               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 112               "You might want to use the mdp option wall_r_linpot",
 113               x[a][XX], x[a][YY], x[a][ZZ], r);
 114 }
 115
 116 real do_walls(const t_inputrec *ir, t_forcerec *fr, matrix box, const t_mdatoms *md,
 117               const rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 118 {
 119     int             nwall;
 120     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 121     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr;
 122     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 123     dvec            xf_z;
 124     int             n0, nnn;
 125     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
 126     unsigned short *gid = md->cENER;
 127     t_forcetable   *tab;
 128
 129     nwall     = ir->nwall;
 130     ngid      = ir->opts.ngener;
 131     ntype     = fr->ntype;
 132     nbfp      = fr->nbfp;
 133     egp_flags = fr->egp_flags;
 134
 135     for (int w = 0; w < nwall; w++)
 136     {
 137         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 138         switch (ir->wall_type)
 139         {
 140             case ewt93:
 141                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 142                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 143                 break;
 144             case ewt104:
 145                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 146                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 147                 break;
 148             default:
 149                 break;
 150         }
 151     }
 152     wall_z[0] = 0;
 153     wall_z[1] = box[ZZ][ZZ];
 154
 155     dvdlambda = 0;
 156     clear_dvec(xf_z);
 157     for (int lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 158     {
 159         if (md->nPerturbed)
 160         {
 161             if (lam == 0)
 162             {
 163                 lamfac = 1 - lambda;
 164                 type   = md->typeA;
 165             }
 166             else
 167             {
 168                 lamfac = lambda;
 169                 type   = md->typeB;
 170             }
 171         }
 172         else
 173         {
 174             lamfac = 1;
 175             type   = md->typeA;
 176         }
 177
 178         real Vlambda = 0;
 179         for (int i = 0; i < md->homenr; i++)
 180         {
 181             for (int w = 0; w < std::min(nwall, 2); w++)
 182             {
 183                 /* The wall energy groups are always at the end of the list */
 184                 ggid = gid[i]*ngid + ngid - nwall + w;
 185                 at   = type[i];
 186                 /* nbfp now includes the 6/12 derivative prefactors */
 187                 Cd = nbfp[ntw[w]+2*at]/6;
 188                 Cr = nbfp[ntw[w]+2*at+1]/12;
 189                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 190                 {
 191                     if (w == 0)
 192                     {
 193                         r = x[i][ZZ];
 194                     }
 195                     else
 196                     {
 197                         r = wall_z[1] - x[i][ZZ];
 198                     }
 199                     if (r < ir->wall_r_linpot)
 200                     {
 201                         mr = ir->wall_r_linpot - r;
 202                         r  = ir->wall_r_linpot;
 203                     }
 204                     else
 205                     {
 206                         mr = 0;
 207                     }
 208                     switch (ir->wall_type)
 209                     {
 210                         case ewtTABLE:
 211                             if (r < 0)
 212                             {
 213                                 wall_error(i, x, r);
 214                             }
 215                             tab      = fr->wall_tab[w][gid[i]];
 216                             tabscale = tab->scale;
 217                             VFtab    = tab->data;
 218
 219                             rt    = r*tabscale;
 220                             n0    = static_cast<int>(rt);
 221                             if (n0 >= tab->n)
 222                             {
 223                                 /* Beyond the table range, set V and F to zero */
 224                                 V     = 0;
 225                                 F     = 0;
 226                             }
 227                             else
 228                             {
 229                                 eps   = rt - n0;
 230                                 eps2  = eps*eps;
 231                                 /* Dispersion */
 232                                 nnn   = 8*n0;
 233                                 Yt    = VFtab[nnn];
 234                                 Ft    = VFtab[nnn+1];
 235                                 Geps  = VFtab[nnn+2]*eps;
 236                                 Heps2 = VFtab[nnn+3]*eps2;
 237                                 Fp    = Ft + Geps + Heps2;
 238                                 VV    = Yt + Fp*eps;
 239                                 FF    = Fp + Geps + 2.0*Heps2;
 240                                 Vd    = 6*Cd*VV;
 241                                 Fd    = 6*Cd*FF;
 242                                 /* Repulsion */
 243                                 nnn   = nnn + 4;
 244                                 Yt    = VFtab[nnn];
 245                                 Ft    = VFtab[nnn+1];
 246                                 Geps  = VFtab[nnn+2]*eps;
 247                                 Heps2 = VFtab[nnn+3]*eps2;
 248                                 Fp    = Ft + Geps + Heps2;
 249                                 VV    = Yt + Fp*eps;
 250                                 FF    = Fp + Geps + 2.0*Heps2;
 251                                 Vr    = 12*Cr*VV;
 252                                 Fr    = 12*Cr*FF;
 253                                 V     = Vd + Vr;
 254                                 F     = -lamfac*(Fd + Fr)*tabscale;
 255                             }
 256                             break;
 257                         case ewt93:
 258                             if (r <= 0)
 259                             {
 260                                 wall_error(i, x, r);
 261                             }
 262                             r1 = 1/r;
 263                             r2 = r1*r1;
 264                             r4 = r2*r2;
 265                             Vd = fac_d[w]*Cd*r2*r1;
 266                             Vr = fac_r[w]*Cr*r4*r4*r1;
 267                             V  = Vr - Vd;
 268                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 269                             break;
 270                         case ewt104:
 271                             if (r <= 0)
 272                             {
 273                                 wall_error(i, x, r);
 274                             }
 275                             r1 = 1/r;
 276                             r2 = r1*r1;
 277                             r4 = r2*r2;
 278                             Vd = fac_d[w]*Cd*r4;
 279                             Vr = fac_r[w]*Cr*r4*r4*r2;
 280                             V  = Vr - Vd;
 281                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 282                             break;
 283                         case ewt126:
 284                             if (r <= 0)
 285                             {
 286                                 wall_error(i, x, r);
 287                             }
 288                             r1 = 1/r;
 289                             r2 = r1*r1;
 290                             r4 = r2*r2;
 291                             Vd = Cd*r4*r2;
 292                             Vr = Cr*r4*r4*r4;
 293                             V  = Vr - Vd;
 294                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 295                             break;
 296                         default:
 297                             break;
 298                     }
 299                     if (mr > 0)
 300                     {
 301                         V += mr*F;
 302                     }
 303                     if (w == 1)
 304                     {
 305                         F = -F;
 306                     }
 307                     Vlj[ggid] += lamfac*V;
 308                     Vlambda   += V;
 309                     f[i][ZZ]  += F;
 310                     /* Because of the single sum virial calculation we need
 311                      * to add  the full virial contribution of the walls.
 312                      * Since the force only has a z-component, there is only
 313                      * a contribution to the z component of the virial tensor.
 314                      * We could also determine the virial contribution directly,
 315                      * which would be cheaper here, but that would require extra
 316                      * communication for f_novirsum for with virtual sites
 317                      * in parallel.
 318                      */
 319                     xf_z[XX]  -= x[i][XX]*F;
 320                     xf_z[YY]  -= x[i][YY]*F;
 321                     xf_z[ZZ]  -= wall_z[w]*F;
 322                 }
 323             }
 324         }
 325         if (md->nPerturbed)
 326         {
 327             dvdlambda += (lam == 0 ? -1 : 1)*Vlambda;
 328         }
 329
 330         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 331     }
 332
 333     for (int i = 0; i < DIM; i++)
 334     {
 335         fr->vir_wall_z[i] = -0.5*xf_z[i];
 336     }
 337
 338     return dvdlambda;
 339 }