src/gromacs/mdlib/wall.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2008, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37
  38 #include "gmxpre.h"
  39
  40 #include "wall.h"
  41
  42 #include <cstring>
  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/forceoutput.h"
  51 #include "gromacs/mdtypes/inputrec.h"
  52 #include "gromacs/mdtypes/md_enums.h"
  53 #include "gromacs/mdtypes/mdatom.h"
  54 #include "gromacs/mdtypes/nblist.h"
  55 #include "gromacs/tables/forcetable.h"
  56 #include "gromacs/topology/topology.h"
  57 #include "gromacs/utility/cstringutil.h"
  58 #include "gromacs/utility/fatalerror.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 void make_wall_tables(FILE *fplog,
  62                       const t_inputrec *ir, const char *tabfn,
  63                       const SimulationGroups *groups,
  64                       t_forcerec *fr)
  65 {
  66     int           negp_pp;
  67     int          *nm_ind;
  68     char          buf[STRLEN];
  69
  70     negp_pp = ir->opts.ngener - ir->nwall;
  71     nm_ind  = groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind;
  72
  73     if (fplog)
  74     {
  75         fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
  76                 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]],
  91                         *groups->groupNames[nm_ind[negp_pp+w]],
  92                         ftp2ext(efXVG));
  93                 fr->wall_tab[w][egp] = make_tables(fplog, fr->ic, buf, 0,
  94                                                    GMX_MAKETABLES_FORCEUSER);
  95
  96                 /* Since wall have no charge, we can compress the table */
  97                 for (int i = 0; i <= fr->wall_tab[w][egp]->n; i++)
  98                 {
  99                     for (int j = 0; j < 8; j++)
 100                     {
 101                         fr->wall_tab[w][egp]->data[8*i+j] =
 102                             fr->wall_tab[w][egp]->data[12*i+4+j];
 103                     }
 104                 }
 105             }
 106         }
 107     }
 108 }
 109
 110 [[ noreturn ]] static void wall_error(int a, const rvec *x, real r)
 111 {
 112     gmx_fatal(FARGS,
 113               "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
 114               "You might want to use the mdp option wall_r_linpot",
 115               x[a][XX], x[a][YY], x[a][ZZ], r);
 116 }
 117
 118 static void tableForce(real                r,
 119                        const t_forcetable &tab,
 120                        real                Cd,
 121                        real                Cr,
 122                        real               *V,
 123                        real               *F)
 124 {
 125     const real  tabscale = tab.scale;
 126     const real *VFtab    = tab.data;
 127
 128     real        rt = r*tabscale;
 129     int         n0 = static_cast<int>(rt);
 130     if (n0 >= tab.n)
 131     {
 132         /* Beyond the table range, set V and F to zero */
 133         *V         = 0;
 134         *F         = 0;
 135     }
 136     else
 137     {
 138         real eps   = rt - n0;
 139         real eps2  = eps*eps;
 140         /* Dispersion */
 141         int  nnn   = 8*n0;
 142         real Yt    = VFtab[nnn];
 143         real Ft    = VFtab[nnn + 1];
 144         real Geps  = VFtab[nnn + 2]*eps;
 145         real Heps2 = VFtab[nnn + 3]*eps2;
 146         real Fp    = Ft + Geps + Heps2;
 147         real VV    = Yt + Fp*eps;
 148         real FF    = Fp + Geps + 2.0*Heps2;
 149         real Vd    = 6*Cd*VV;
 150         real Fd    = 6*Cd*FF;
 151         /* Repulsion */
 152         nnn        = nnn + 4;
 153         Yt         = VFtab[nnn];
 154         Ft         = VFtab[nnn+1];
 155         Geps       = VFtab[nnn+2]*eps;
 156         Heps2      = VFtab[nnn+3]*eps2;
 157         Fp         = Ft + Geps + Heps2;
 158         VV         = Yt + Fp*eps;
 159         FF         = Fp + Geps + 2.0*Heps2;
 160         real Vr    = 12*Cr*VV;
 161         real Fr    = 12*Cr*FF;
 162         *V         = Vd + Vr;
 163         *F         = -(Fd + Fr)*tabscale;
 164     }
 165 }
 166
 167 real do_walls(const t_inputrec &ir, const t_forcerec &fr,
 168               const matrix box, const t_mdatoms &md,
 169               const rvec *x, gmx::ForceWithVirial *forceWithVirial,
 170               real lambda, real Vlj[], t_nrnb *nrnb)
 171 {
 172     constexpr real        sixth   = 1.0/6.0;
 173     constexpr real        twelfth = 1.0/12.0;
 174
 175     int                   ntw[2];
 176     real                  fac_d[2], fac_r[2];
 177     const unsigned short *gid = md.cENER;
 178
 179     const int             nwall     = ir.nwall;
 180     const int             ngid      = ir.opts.ngener;
 181     const int             ntype     = fr.ntype;
 182     const real           *nbfp      = fr.nbfp;
 183     const int            *egp_flags = fr.egp_flags;
 184
 185     for (int w = 0; w < nwall; w++)
 186     {
 187         ntw[w] = 2*ntype*ir.wall_atomtype[w];
 188         switch (ir.wall_type)
 189         {
 190             case ewt93:
 191                 fac_d[w] = ir.wall_density[w]*M_PI/6;
 192                 fac_r[w] = ir.wall_density[w]*M_PI/45;
 193                 break;
 194             case ewt104:
 195                 fac_d[w] = ir.wall_density[w]*M_PI/2;
 196                 fac_r[w] = ir.wall_density[w]*M_PI/5;
 197                 break;
 198             default:
 199                 break;
 200         }
 201     }
 202     const real          wall_z[2] = { 0, box[ZZ][ZZ] };
 203
 204     rvec * gmx_restrict f = as_rvec_array(forceWithVirial->force_.data());
 205
 206     real                dvdlambda = 0;
 207     double              sumRF     = 0;
 208     for (int lam = 0; lam < (md.nPerturbed ? 2 : 1); lam++)
 209     {
 210         real       lamfac;
 211         const int *type;
 212         if (md.nPerturbed)
 213         {
 214             if (lam == 0)
 215             {
 216                 lamfac = 1 - lambda;
 217                 type   = md.typeA;
 218             }
 219             else
 220             {
 221                 lamfac = lambda;
 222                 type   = md.typeB;
 223             }
 224         }
 225         else
 226         {
 227             lamfac = 1;
 228             type   = md.typeA;
 229         }
 230
 231         real Vlambda = 0;
 232         for (int i = 0; i < md.homenr; i++)
 233         {
 234             for (int w = 0; w < std::min(nwall, 2); w++)
 235             {
 236                 /* The wall energy groups are always at the end of the list */
 237                 const int  ggid = gid[i]*ngid + ngid - nwall + w;
 238                 const int  at   = type[i];
 239                 /* nbfp now includes the 6/12 derivative prefactors */
 240                 const real Cd = nbfp[ntw[w] + 2*at]*sixth;
 241                 const real Cr = nbfp[ntw[w] + 2*at + 1]*twelfth;
 242                 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
 243                 {
 244                     real r, mr;
 245                     if (w == 0)
 246                     {
 247                         r = x[i][ZZ];
 248                     }
 249                     else
 250                     {
 251                         r = wall_z[1] - x[i][ZZ];
 252                     }
 253                     if (r < ir.wall_r_linpot)
 254                     {
 255                         mr = ir.wall_r_linpot - r;
 256                         r  = ir.wall_r_linpot;
 257                     }
 258                     else
 259                     {
 260                         mr = 0;
 261                     }
 262                     if (r <= 0)
 263                     {
 264                         wall_error(i, x, r);
 265                     }
 266
 267                     real V, F;
 268                     real r1, r2, r4, Vd, Vr;
 269                     switch (ir.wall_type)
 270                     {
 271                         case ewtTABLE:
 272                             tableForce(r, *fr.wall_tab[w][gid[i]], Cd, Cr, &V, &F);
 273                             F *= lamfac;
 274                             break;
 275                         case ewt93:
 276                             r1 = 1/r;
 277                             r2 = r1*r1;
 278                             r4 = r2*r2;
 279                             Vd = fac_d[w]*Cd*r2*r1;
 280                             Vr = fac_r[w]*Cr*r4*r4*r1;
 281                             V  = Vr - Vd;
 282                             F  = lamfac*(9*Vr - 3*Vd)*r1;
 283                             break;
 284                         case ewt104:
 285                             r1 = 1/r;
 286                             r2 = r1*r1;
 287                             r4 = r2*r2;
 288                             Vd = fac_d[w]*Cd*r4;
 289                             Vr = fac_r[w]*Cr*r4*r4*r2;
 290                             V  = Vr - Vd;
 291                             F  = lamfac*(10*Vr - 4*Vd)*r1;
 292                             break;
 293                         case ewt126:
 294                             r1 = 1/r;
 295                             r2 = r1*r1;
 296                             r4 = r2*r2;
 297                             Vd = Cd*r4*r2;
 298                             Vr = Cr*r4*r4*r4;
 299                             V  = Vr - Vd;
 300                             F  = lamfac*(12*Vr - 6*Vd)*r1;
 301                             break;
 302                         default:
 303                             V  = 0;
 304                             F  = 0;
 305                             break;
 306                     }
 307                     if (mr > 0)
 308                     {
 309                         V     += mr*F;
 310                     }
 311                     sumRF     += r*F;
 312                     if (w == 1)
 313                     {
 314                         F      = -F;
 315                     }
 316                     Vlj[ggid] += lamfac*V;
 317                     Vlambda   += V;
 318                     f[i][ZZ]  += F;
 319                 }
 320             }
 321         }
 322         if (md.nPerturbed)
 323         {
 324             dvdlambda += (lam == 0 ? -1 : 1)*Vlambda;
 325         }
 326
 327         inc_nrnb(nrnb, eNR_WALLS, md.homenr);
 328     }
 329
 330     if (forceWithVirial->computeVirial_)
 331     {
 332         rvec virial = { 0, 0, static_cast<real>(-0.5*sumRF) };
 333         forceWithVirial->addVirialContribution(virial);
 334     }
 335
 336     return dvdlambda;
 337 }