src/gromacs/mdlib/wall.cpp

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  38
  39 #include "gmxpre.h"
  40
  41 #include "wall.h"
  42
  43 #include <cstring>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/fileio/filetypes.h"
  48 #include "gromacs/gmxlib/nrnb.h"
  49 #include "gromacs/math/utilities.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/mdtypes/forceoutput.h"
  52 #include "gromacs/mdtypes/inputrec.h"
  53 #include "gromacs/mdtypes/md_enums.h"
  54 #include "gromacs/mdtypes/mdatom.h"
  55 #include "gromacs/mdtypes/nblist.h"
  56 #include "gromacs/tables/forcetable.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/cstringutil.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 void make_wall_tables(FILE*                   fplog,
  63                       const t_inputrec*       ir,
  64                       const char*             tabfn,
  65                       const SimulationGroups* groups,
  66                       t_forcerec*             fr)
  67 {
  68     int  negp_pp;
  69     char buf[STRLEN];
  70
  71     negp_pp                         = ir->opts.ngener - ir->nwall;
  72     gmx::ArrayRef<const int> nm_ind = groups->groups[SimulationAtomGroupType::EnergyOutput];
  73
  74     if (fplog)
  75     {
  76         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n", negp_pp, ir->nwall);
  77     }
  78
  79     snew(fr->wall_tab, ir->nwall);
  80     for (int w = 0; w < ir->nwall; w++)
  81     {
  82         snew(fr->wall_tab[w], negp_pp);
  83         for (int egp = 0; egp < negp_pp; egp++)
  84         {
  85             /* If the energy group pair is excluded, we don't need a table */
  86             if (!(fr->egp_flags[egp * ir->opts.ngener + negp_pp + w] & EGP_EXCL))
  87             {
  88                 sprintf(buf, "%s", tabfn);
  89                 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
  90                         *groups->groupNames[nm_ind[egp]], *groups->groupNames[nm_ind[negp_pp + w]],
  91                         ftp2ext(efXVG));
  92                 fr->wall_tab[w][egp] = make_tables(fplog, fr->ic, buf, 0, 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 [[noreturn]] 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 static void tableForce(real r, const t_forcetable& tab, real Cd, real Cr, real* V, real* F)
 117 {
 118     const real  tabscale = tab.scale;
 119     const real* VFtab    = tab.data;
 120
 121     real rt = r * tabscale;
 122     int  n0 = static_cast<int>(rt);
 123     if (n0 >= tab.n)
 124     {
 125         /* Beyond the table range, set V and F to zero */
 126         *V = 0;
 127         *F = 0;
 128     }
 129     else
 130     {
 131         real eps  = rt - n0;
 132         real eps2 = eps * eps;
 133         /* Dispersion */
 134         int  nnn   = 8 * n0;
 135         real Yt    = VFtab[nnn];
 136         real Ft    = VFtab[nnn + 1];
 137         real Geps  = VFtab[nnn + 2] * eps;
 138         real Heps2 = VFtab[nnn + 3] * eps2;
 139         real Fp    = Ft + Geps + Heps2;
 140         real VV    = Yt + Fp * eps;
 141         real FF    = Fp + Geps + 2.0 * Heps2;
 142         real Vd    = 6 * Cd * VV;
 143         real Fd    = 6 * Cd * FF;
 144         /* Repulsion */
 145         nnn     = nnn + 4;
 146         Yt      = VFtab[nnn];
 147         Ft      = VFtab[nnn + 1];
 148         Geps    = VFtab[nnn + 2] * eps;
 149         Heps2   = VFtab[nnn + 3] * eps2;
 150         Fp      = Ft + Geps + Heps2;
 151         VV      = Yt + Fp * eps;
 152         FF      = Fp + Geps + 2.0 * Heps2;
 153         real Vr = 12 * Cr * VV;
 154         real Fr = 12 * Cr * FF;
 155         *V      = Vd + Vr;
 156         *F      = -(Fd + Fr) * tabscale;
 157     }
 158 }
 159
 160 real do_walls(const t_inputrec&     ir,
 161               const t_forcerec&     fr,
 162               const matrix          box,
 163               const t_mdatoms&      md,
 164               const rvec*           x,
 165               gmx::ForceWithVirial* forceWithVirial,
 166               real                  lambda,
 167               real                  Vlj[],
 168               t_nrnb*               nrnb)
 169 {
 170     constexpr real sixth   = 1.0 / 6.0;
 171     constexpr real twelfth = 1.0 / 12.0;
 172
 173     int                   ntw[2];
 174     real                  fac_d[2], fac_r[2];
 175     const unsigned short* gid = md.cENER;
 176
 177     const int   nwall     = ir.nwall;
 178     const int   ngid      = ir.opts.ngener;
 179     const int   ntype     = fr.ntype;
 180     const real* nbfp      = fr.nbfp.data();
 181     const int*  egp_flags = fr.egp_flags;
 182
 183     for (int w = 0; w < nwall; w++)
 184     {
 185         ntw[w] = 2 * ntype * ir.wall_atomtype[w];
 186         switch (ir.wall_type)
 187         {
 188             case ewt93:
 189                 fac_d[w] = ir.wall_density[w] * M_PI / 6;
 190                 fac_r[w] = ir.wall_density[w] * M_PI / 45;
 191                 break;
 192             case ewt104:
 193                 fac_d[w] = ir.wall_density[w] * M_PI / 2;
 194                 fac_r[w] = ir.wall_density[w] * M_PI / 5;
 195                 break;
 196             default: break;
 197         }
 198     }
 199     const real wall_z[2] = { 0, box[ZZ][ZZ] };
 200
 201     rvec* gmx_restrict f = as_rvec_array(forceWithVirial->force_.data());
 202
 203     real   dvdlambda = 0;
 204     double sumRF     = 0;
 205     for (int lam = 0; lam < (md.nPerturbed ? 2 : 1); lam++)
 206     {
 207         real       lamfac;
 208         const int* type;
 209         if (md.nPerturbed)
 210         {
 211             if (lam == 0)
 212             {
 213                 lamfac = 1 - lambda;
 214                 type   = md.typeA;
 215             }
 216             else
 217             {
 218                 lamfac = lambda;
 219                 type   = md.typeB;
 220             }
 221         }
 222         else
 223         {
 224             lamfac = 1;
 225             type   = md.typeA;
 226         }
 227
 228         real Vlambda = 0;
 229         for (int i = 0; i < md.homenr; i++)
 230         {
 231             for (int w = 0; w < std::min(nwall, 2); w++)
 232             {
 233                 /* The wall energy groups are always at the end of the list */
 234                 const int ggid = gid[i] * ngid + ngid - nwall + w;
 235                 const int at   = type[i];
 236                 /* nbfp now includes the 6/12 derivative prefactors */
 237                 const real Cd = nbfp[ntw[w] + 2 * at] * sixth;
 238                 const real Cr = nbfp[ntw[w] + 2 * at + 1] * twelfth;
 239                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 240                 {
 241                     real r, mr;
 242                     if (w == 0)
 243                     {
 244                         r = x[i][ZZ];
 245                     }
 246                     else
 247                     {
 248                         r = wall_z[1] - x[i][ZZ];
 249                     }
 250                     if (r < ir.wall_r_linpot)
 251                     {
 252                         mr = ir.wall_r_linpot - r;
 253                         r  = ir.wall_r_linpot;
 254                     }
 255                     else
 256                     {
 257                         mr = 0;
 258                     }
 259                     if (r <= 0)
 260                     {
 261                         wall_error(i, x, r);
 262                     }
 263
 264                     real V, F;
 265                     real r1, r2, r4, Vd, Vr;
 266                     switch (ir.wall_type)
 267                     {
 268                         case ewtTABLE:
 269                             tableForce(r, *fr.wall_tab[w][gid[i]], Cd, Cr, &V, &F);
 270                             F *= lamfac;
 271                             break;
 272                         case ewt93:
 273                             r1 = 1 / r;
 274                             r2 = r1 * r1;
 275                             r4 = r2 * r2;
 276                             Vd = fac_d[w] * Cd * r2 * r1;
 277                             Vr = fac_r[w] * Cr * r4 * r4 * r1;
 278                             V  = Vr - Vd;
 279                             F  = lamfac * (9 * Vr - 3 * Vd) * r1;
 280                             break;
 281                         case ewt104:
 282                             r1 = 1 / r;
 283                             r2 = r1 * r1;
 284                             r4 = r2 * r2;
 285                             Vd = fac_d[w] * Cd * r4;
 286                             Vr = fac_r[w] * Cr * r4 * r4 * r2;
 287                             V  = Vr - Vd;
 288                             F  = lamfac * (10 * Vr - 4 * Vd) * r1;
 289                             break;
 290                         case ewt126:
 291                             r1 = 1 / r;
 292                             r2 = r1 * r1;
 293                             r4 = r2 * r2;
 294                             Vd = Cd * r4 * r2;
 295                             Vr = Cr * r4 * r4 * r4;
 296                             V  = Vr - Vd;
 297                             F  = lamfac * (12 * Vr - 6 * Vd) * r1;
 298                             break;
 299                         default:
 300                             V = 0;
 301                             F = 0;
 302                             break;
 303                     }
 304                     if (mr > 0)
 305                     {
 306                         V += mr * F;
 307                     }
 308                     sumRF += r * F;
 309                     if (w == 1)
 310                     {
 311                         F = -F;
 312                     }
 313                     Vlj[ggid] += lamfac * V;
 314                     Vlambda += V;
 315                     f[i][ZZ] += F;
 316                 }
 317             }
 318         }
 319         if (md.nPerturbed)
 320         {
 321             dvdlambda += (lam == 0 ? -1 : 1) * Vlambda;
 322         }
 323
 324         inc_nrnb(nrnb, eNR_WALLS, md.homenr);
 325     }
 326
 327     if (forceWithVirial->computeVirial_)
 328     {
 329         rvec virial = { 0, 0, static_cast<real>(-0.5 * sumRF) };
 330         forceWithVirial->addVirialContribution(virial);
 331     }
 332
 333     return dvdlambda;
 334 }