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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"
59 void make_wall_tables(FILE *fplog,
60 const t_inputrec *ir, const char *tabfn,
61 const gmx_groups_t *groups,
68 negp_pp = ir->opts.ngener - ir->nwall;
69 nm_ind = groups->grps[egcENER].nm_ind;
73 fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
77 snew(fr->wall_tab, ir->nwall);
78 for (int w = 0; w < ir->nwall; w++)
80 snew(fr->wall_tab[w], negp_pp);
81 for (int egp = 0; egp < negp_pp; egp++)
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))
86 fr->wall_tab[w][egp] = make_tables(fplog, fr, buf, 0,
87 GMX_MAKETABLES_FORCEUSER);
88 sprintf(buf, "%s", tabfn);
89 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
90 *groups->grpname[nm_ind[egp]],
91 *groups->grpname[nm_ind[negp_pp+w]],
94 /* Since wall have no charge, we can compress the table */
95 for (int i = 0; i <= fr->wall_tab[w][egp]->n; i++)
97 for (int j = 0; j < 8; j++)
99 fr->wall_tab[w][egp]->data[8*i+j] =
100 fr->wall_tab[w][egp]->data[12*i+4+j];
108 static void wall_error(int a, rvec *x, real r)
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);
116 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
117 rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
120 int ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
121 real *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot;
122 real wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
125 real tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
126 unsigned short *gid = md->cENER;
130 ngid = ir->opts.ngener;
133 egp_flags = fr->egp_flags;
135 for (int w = 0; w < nwall; w++)
137 ntw[w] = 2*ntype*ir->wall_atomtype[w];
138 switch (ir->wall_type)
141 fac_d[w] = ir->wall_density[w]*M_PI/6;
142 fac_r[w] = ir->wall_density[w]*M_PI/45;
145 fac_d[w] = ir->wall_density[w]*M_PI/2;
146 fac_r[w] = ir->wall_density[w]*M_PI/5;
153 wall_z[1] = box[ZZ][ZZ];
158 for (int lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
178 for (int i = 0; i < md->homenr; i++)
180 for (int w = 0; w < std::min(nwall, 2); w++)
182 /* The wall energy groups are always at the end of the list */
183 ggid = gid[i]*ngid + ngid - nwall + w;
185 /* nbfp now includes the 6/12 derivative prefactors */
186 Cd = nbfp[ntw[w]+2*at]/6;
187 Cr = nbfp[ntw[w]+2*at+1]/12;
188 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
196 r = wall_z[1] - x[i][ZZ];
198 if (r < ir->wall_r_linpot)
200 mr = ir->wall_r_linpot - r;
201 r = ir->wall_r_linpot;
207 switch (ir->wall_type)
214 tab = fr->wall_tab[w][gid[i]];
215 tabscale = tab->scale;
219 n0 = static_cast<int>(rt);
222 /* Beyond the table range, set V and F to zero */
234 Geps = VFtab[nnn+2]*eps;
235 Heps2 = VFtab[nnn+3]*eps2;
236 Fp = Ft + Geps + Heps2;
238 FF = Fp + Geps + 2.0*Heps2;
245 Geps = VFtab[nnn+2]*eps;
246 Heps2 = VFtab[nnn+3]*eps2;
247 Fp = Ft + Geps + Heps2;
249 FF = Fp + Geps + 2.0*Heps2;
253 F = -lamfac*(Fd + Fr)*tabscale;
264 Vd = fac_d[w]*Cd*r2*r1;
265 Vr = fac_r[w]*Cr*r4*r4*r1;
267 F = lamfac*(9*Vr - 3*Vd)*r1;
278 Vr = fac_r[w]*Cr*r4*r4*r2;
280 F = lamfac*(10*Vr - 4*Vd)*r1;
293 F = lamfac*(12*Vr - 6*Vd)*r1;
306 Vlj[ggid] += lamfac*V;
309 /* Because of the single sum virial calculation we need
310 * to add the full virial contribution of the walls.
311 * Since the force only has a z-component, there is only
312 * a contribution to the z component of the virial tensor.
313 * We could also determine the virial contribution directly,
314 * which would be cheaper here, but that would require extra
315 * communication for f_novirsum for with virtual sites
318 xf_z[XX] -= x[i][XX]*F;
319 xf_z[YY] -= x[i][YY]*F;
320 xf_z[ZZ] -= wall_z[w]*F;
326 dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
329 inc_nrnb(nrnb, eNR_WALLS, md->homenr);
332 for (int i = 0; i < DIM; i++)
334 fr->vir_wall_z[i] = -0.5*xf_z[i];