src/gromacs/mdlib/wall.cpp

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   6  * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
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  37
  38 #include "gmxpre.h"
  39
  40 #include "wall.h"
  41
  42 #include <string.h>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/fileio/filetypes.h"
  47 #include "gromacs/gmxlib/nrnb.h"
  48 #include "gromacs/math/utilities.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/mdtypes/inputrec.h"
  51 #include "gromacs/mdtypes/md_enums.h"
  52 #include "gromacs/mdtypes/mdatom.h"
  53 #include "gromacs/mdtypes/nblist.h"
  54 #include "gromacs/tables/forcetable.h"
  55 #include "gromacs/topology/topology.h"
  56 #include "gromacs/utility/cstringutil.h"
  57 #include "gromacs/utility/fatalerror.h"
  58 #include "gromacs/utility/smalloc.h"
  59
  60 void make_wall_tables(FILE *fplog,
  61                       const t_inputrec *ir, const char *tabfn,
  62                       const gmx_groups_t *groups,
  63                       t_forcerec *fr)
  64 {
  65     int           negp_pp;
  66     int          *nm_ind;
  67     char          buf[STRLEN];
  68
  69     negp_pp = ir->opts.ngener - ir->nwall;
  70     nm_ind  = groups->grps[egcENER].nm_ind;
  71
  72     if (fplog)
  73     {
  74         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  75                 negp_pp, ir->nwall);
  76     }
  77
  78     snew(fr->wall_tab, ir->nwall);
  79     for (int w = 0; w < ir->nwall; w++)
  80     {
  81         snew(fr->wall_tab[w], negp_pp);
  82         for (int egp = 0; egp < negp_pp; egp++)
  83         {
  84             /* If the energy group pair is excluded, we don't need a table */
  85             if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
  86             {
  87                 sprintf(buf, "%s", tabfn);
  88                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  89                         *groups->grpname[nm_ind[egp]],
  90                         *groups->grpname[nm_ind[negp_pp+w]],
  91                         ftp2ext(efXVG));
  92                 fr->wall_tab[w][egp] = make_tables(fplog, fr->ic, buf, 0,
  93                                                    GMX_MAKETABLES_FORCEUSER);
  94
  95                 /* Since wall have no charge, we can compress the table */
  96                 for (int i = 0; i <= fr->wall_tab[w][egp]->n; i++)
  97                 {
  98                     for (int j = 0; j < 8; j++)
  99                     {
 100                         fr->wall_tab[w][egp]->data[8*i+j] =
 101                             fr->wall_tab[w][egp]->data[12*i+4+j];
 102                     }
 103                 }
 104             }
 105         }
 106     }
 107 }
 108
 109 [[ noreturn ]] static void wall_error(int a, const rvec *x, real r)
 110 {
 111     gmx_fatal(FARGS,
 112               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 113               "You might want to use the mdp option wall_r_linpot",
 114               x[a][XX], x[a][YY], x[a][ZZ], r);
 115 }
 116
 117 real do_walls(const t_inputrec *ir, t_forcerec *fr, matrix box, const t_mdatoms *md,
 118               const rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
 119 {
 120     int             nwall;
 121     int             ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
 122     real           *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr;
 123     real            wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
 124     dvec            xf_z;
 125     int             n0, nnn;
 126     real            tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
 127     unsigned short *gid = md->cENER;
 128     t_forcetable   *tab;
 129
 130     nwall     = ir->nwall;
 131     ngid      = ir->opts.ngener;
 132     ntype     = fr->ntype;
 133     nbfp      = fr->nbfp;
 134     egp_flags = fr->egp_flags;
 135
 136     for (int w = 0; w < nwall; w++)
 137     {
 138         ntw[w] = 2*ntype*ir->wall_atomtype[w];
 139         switch (ir->wall_type)
 140         {
 141             case ewt93:
 142                 fac_d[w] = ir->wall_density[w]*M_PI/6;
 143                 fac_r[w] = ir->wall_density[w]*M_PI/45;
 144                 break;
 145             case ewt104:
 146                 fac_d[w] = ir->wall_density[w]*M_PI/2;
 147                 fac_r[w] = ir->wall_density[w]*M_PI/5;
 148                 break;
 149             default:
 150                 break;
 151         }
 152     }
 153     wall_z[0] = 0;
 154     wall_z[1] = box[ZZ][ZZ];
 155
 156     dvdlambda = 0;
 157     clear_dvec(xf_z);
 158     for (int lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
 159     {
 160         if (md->nPerturbed)
 161         {
 162             if (lam == 0)
 163             {
 164                 lamfac = 1 - lambda;
 165                 type   = md->typeA;
 166             }
 167             else
 168             {
 169                 lamfac = lambda;
 170                 type   = md->typeB;
 171             }
 172         }
 173         else
 174         {
 175             lamfac = 1;
 176             type   = md->typeA;
 177         }
 178
 179         real Vlambda = 0;
 180         for (int i = 0; i < md->homenr; i++)
 181         {
 182             for (int w = 0; w < std::min(nwall, 2); w++)
 183             {
 184                 /* The wall energy groups are always at the end of the list */
 185                 ggid = gid[i]*ngid + ngid - nwall + w;
 186                 at   = type[i];
 187                 /* nbfp now includes the 6/12 derivative prefactors */
 188                 Cd = nbfp[ntw[w]+2*at]/6;
 189                 Cr = nbfp[ntw[w]+2*at+1]/12;
 190                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 191                 {
 192                     if (w == 0)
 193                     {
 194                         r = x[i][ZZ];
 195                     }
 196                     else
 197                     {
 198                         r = wall_z[1] - x[i][ZZ];
 199                     }
 200                     if (r < ir->wall_r_linpot)
 201                     {
 202                         mr = ir->wall_r_linpot - r;
 203                         r  = ir->wall_r_linpot;
 204                     }
 205                     else
 206                     {
 207                         mr = 0;
 208                     }
 209                     switch (ir->wall_type)
 210                     {
 211                         case ewtTABLE:
 212                             if (r < 0)
 213                             {
 214                                 wall_error(i, x, r);
 215                             }
 216                             tab      = fr->wall_tab[w][gid[i]];
 217                             tabscale = tab->scale;
 218                             VFtab    = tab->data;
 219
 220                             rt    = r*tabscale;
 221                             n0    = static_cast<int>(rt);
 222                             if (n0 >= tab->n)
 223                             {
 224                                 /* Beyond the table range, set V and F to zero */
 225                                 V     = 0;
 226                                 F     = 0;
 227                             }
 228                             else
 229                             {
 230                                 eps   = rt - n0;
 231                                 eps2  = eps*eps;
 232                                 /* Dispersion */
 233                                 nnn   = 8*n0;
 234                                 Yt    = VFtab[nnn];
 235                                 Ft    = VFtab[nnn+1];
 236                                 Geps  = VFtab[nnn+2]*eps;
 237                                 Heps2 = VFtab[nnn+3]*eps2;
 238                                 Fp    = Ft + Geps + Heps2;
 239                                 VV    = Yt + Fp*eps;
 240                                 FF    = Fp + Geps + 2.0*Heps2;
 241                                 Vd    = 6*Cd*VV;
 242                                 Fd    = 6*Cd*FF;
 243                                 /* Repulsion */
 244                                 nnn   = nnn + 4;
 245                                 Yt    = VFtab[nnn];
 246                                 Ft    = VFtab[nnn+1];
 247                                 Geps  = VFtab[nnn+2]*eps;
 248                                 Heps2 = VFtab[nnn+3]*eps2;
 249                                 Fp    = Ft + Geps + Heps2;
 250                                 VV    = Yt + Fp*eps;
 251                                 FF    = Fp + Geps + 2.0*Heps2;
 252                                 Vr    = 12*Cr*VV;
 253                                 Fr    = 12*Cr*FF;
 254                                 V     = Vd + Vr;
 255                                 F     = -lamfac*(Fd + Fr)*tabscale;
 256                             }
 257                             break;
 258                         case ewt93:
 259                             if (r <= 0)
 260                             {
 261                                 wall_error(i, x, r);
 262                             }
 263                             r1 = 1/r;
 264                             r2 = r1*r1;
 265                             r4 = r2*r2;
 266                             Vd = fac_d[w]*Cd*r2*r1;
 267                             Vr = fac_r[w]*Cr*r4*r4*r1;
 268                             V  = Vr - Vd;
 269                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 270                             break;
 271                         case ewt104:
 272                             if (r <= 0)
 273                             {
 274                                 wall_error(i, x, r);
 275                             }
 276                             r1 = 1/r;
 277                             r2 = r1*r1;
 278                             r4 = r2*r2;
 279                             Vd = fac_d[w]*Cd*r4;
 280                             Vr = fac_r[w]*Cr*r4*r4*r2;
 281                             V  = Vr - Vd;
 282                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 283                             break;
 284                         case ewt126:
 285                             if (r <= 0)
 286                             {
 287                                 wall_error(i, x, r);
 288                             }
 289                             r1 = 1/r;
 290                             r2 = r1*r1;
 291                             r4 = r2*r2;
 292                             Vd = Cd*r4*r2;
 293                             Vr = Cr*r4*r4*r4;
 294                             V  = Vr - Vd;
 295                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 296                             break;
 297                         default:
 298                             break;
 299                     }
 300                     if (mr > 0)
 301                     {
 302                         V += mr*F;
 303                     }
 304                     if (w == 1)
 305                     {
 306                         F = -F;
 307                     }
 308                     Vlj[ggid] += lamfac*V;
 309                     Vlambda   += V;
 310                     f[i][ZZ]  += F;
 311                     /* Because of the single sum virial calculation we need
 312                      * to add  the full virial contribution of the walls.
 313                      * Since the force only has a z-component, there is only
 314                      * a contribution to the z component of the virial tensor.
 315                      * We could also determine the virial contribution directly,
 316                      * which would be cheaper here, but that would require extra
 317                      * communication for f_novirsum for with virtual sites
 318                      * in parallel.
 319                      */
 320                     xf_z[XX]  -= x[i][XX]*F;
 321                     xf_z[YY]  -= x[i][YY]*F;
 322                     xf_z[ZZ]  -= wall_z[w]*F;
 323                 }
 324             }
 325         }
 326         if (md->nPerturbed)
 327         {
 328             dvdlambda += (lam == 0 ? -1 : 1)*Vlambda;
 329         }
 330
 331         inc_nrnb(nrnb, eNR_WALLS, md->homenr);
 332     }
 333
 334     for (int i = 0; i < DIM; i++)
 335     {
 336         fr->vir_wall_z[i] = -0.5*xf_z[i];
 337     }
 338
 339     return dvdlambda;
 340 }