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44 #include "gromacs/math/utilities.h"
48 #include "gromacs/utility/smalloc.h"
50 #include "gromacs/fileio/filenm.h"
54 void make_wall_tables(FILE *fplog, const output_env_t oenv,
55 const t_inputrec *ir, const char *tabfn,
56 const gmx_groups_t *groups,
59 int w, negp_pp, egp, i, j;
64 negp_pp = ir->opts.ngener - ir->nwall;
65 nm_ind = groups->grps[egcENER].nm_ind;
69 fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n",
73 snew(fr->wall_tab, ir->nwall);
74 for (w = 0; w < ir->nwall; w++)
76 snew(fr->wall_tab[w], negp_pp);
77 for (egp = 0; egp < negp_pp; egp++)
79 /* If the energy group pair is excluded, we don't need a table */
80 if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL))
82 tab = &fr->wall_tab[w][egp];
83 sprintf(buf, "%s", tabfn);
84 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
85 *groups->grpname[nm_ind[egp]],
86 *groups->grpname[nm_ind[negp_pp+w]],
88 *tab = make_tables(fplog, oenv, fr, FALSE, buf, 0, GMX_MAKETABLES_FORCEUSER);
89 /* Since wall have no charge, we can compress the table */
90 for (i = 0; i <= tab->n; i++)
92 for (j = 0; j < 8; j++)
94 tab->data[8*i+j] = tab->data[12*i+4+j];
102 static void wall_error(int a, rvec *x, real r)
105 "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
106 "You might want to use the mdp option wall_r_linpot",
107 x[a][XX], x[a][YY], x[a][ZZ], r);
110 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
111 rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb)
113 int nwall, w, lam, i;
114 int ntw[2], at, ntype, ngid, ggid, *egp_flags, *type;
115 real *nbfp, lamfac, fac_d[2], fac_r[2], Cd, Cr, Vtot, Fwall[2];
116 real wall_z[2], r, mr, r1, r2, r4, Vd, Vr, V = 0, Fd, Fr, F = 0, dvdlambda;
119 real tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps, Heps2, Fp, VV, FF;
120 unsigned short *gid = md->cENER;
124 ngid = ir->opts.ngener;
127 egp_flags = fr->egp_flags;
129 for (w = 0; w < nwall; w++)
131 ntw[w] = 2*ntype*ir->wall_atomtype[w];
132 switch (ir->wall_type)
135 fac_d[w] = ir->wall_density[w]*M_PI/6;
136 fac_r[w] = ir->wall_density[w]*M_PI/45;
139 fac_d[w] = ir->wall_density[w]*M_PI/2;
140 fac_r[w] = ir->wall_density[w]*M_PI/5;
148 wall_z[1] = box[ZZ][ZZ];
153 for (lam = 0; lam < (md->nPerturbed ? 2 : 1); lam++)
173 for (i = 0; i < md->homenr; i++)
175 for (w = 0; w < nwall; w++)
177 /* The wall energy groups are always at the end of the list */
178 ggid = gid[i]*ngid + ngid - nwall + w;
180 /* nbfp now includes the 6.0/12.0 derivative prefactors */
181 Cd = nbfp[ntw[w]+2*at]/6.0;
182 Cr = nbfp[ntw[w]+2*at+1]/12.0;
183 if (!((Cd == 0 && Cr == 0) || (egp_flags[ggid] & EGP_EXCL)))
191 r = wall_z[1] - x[i][ZZ];
193 if (r < ir->wall_r_linpot)
195 mr = ir->wall_r_linpot - r;
196 r = ir->wall_r_linpot;
202 switch (ir->wall_type)
209 tab = &(fr->wall_tab[w][gid[i]]);
210 tabscale = tab->scale;
217 /* Beyond the table range, set V and F to zero */
229 Geps = VFtab[nnn+2]*eps;
230 Heps2 = VFtab[nnn+3]*eps2;
231 Fp = Ft + Geps + Heps2;
233 FF = Fp + Geps + 2.0*Heps2;
240 Geps = VFtab[nnn+2]*eps;
241 Heps2 = VFtab[nnn+3]*eps2;
242 Fp = Ft + Geps + Heps2;
244 FF = Fp + Geps + 2.0*Heps2;
248 F = -lamfac*(Fd + Fr)*tabscale;
259 Vd = fac_d[w]*Cd*r2*r1;
260 Vr = fac_r[w]*Cr*r4*r4*r1;
262 F = lamfac*(9*Vr - 3*Vd)*r1;
273 Vr = fac_r[w]*Cr*r4*r4*r2;
275 F = lamfac*(10*Vr - 4*Vd)*r1;
288 F = lamfac*(12*Vr - 6*Vd)*r1;
301 Vlj[ggid] += lamfac*V;
304 /* Because of the single sum virial calculation we need
305 * to add the full virial contribution of the walls.
306 * Since the force only has a z-component, there is only
307 * a contribution to the z component of the virial tensor.
308 * We could also determine the virial contribution directly,
309 * which would be cheaper here, but that would require extra
310 * communication for f_novirsum for with virtual sites
313 xf_z[XX] -= x[i][XX]*F;
314 xf_z[YY] -= x[i][YY]*F;
315 xf_z[ZZ] -= wall_z[w]*F;
321 dvdlambda += (lam == 0 ? -1 : 1)*Vtot;
324 inc_nrnb(nrnb, eNR_WALLS, md->homenr);
327 for (i = 0; i < DIM; i++)
329 fr->vir_wall_z[i] = -0.5*xf_z[i];